JAX Handbook On Genetically Standardized Mice

The Jackson Laboratory
Handbook on
Genetically Standardized Mice
The Jackson Laboratory Handbook

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About The Jackson Laboratory

Founded in 1929, The Jackson Laboratory is a non-profit biomedical research
institution dedicated to leading the search for tomorrows cures.

Our mission: We discover precise genomic solutions for disease and empower the
global biomedical community in our shared quest to improve human health.

The Jackson Laboratory Handbook

on
Sixth Edition
Scientific Editor
Kevin Flurkey
Editor
Joanne M. Currer
Associate Editors
Edward H. Leiter
Barbara Witham
Bar Harbor, ME 04609 USA
Contributors
Bar Harbor, ME USA
Corrigan, Jennifer
Corrow, Dorcas
Currer, Joanne M.
Danneman, Peggy
Davisson, Muriel
Flurkey, Kevin
Harrison, David E.
Merriam, Jennifer
Strobel, Marge
Vonder Haar, Ray
Witham, Barbara
Linder, Carol
New Mexico Highlands
University,
Las Vegas, NM USA
Pritchett-Corning, Kathleen
Charles River Laboratories
Wilmington, MA USA
The Jackson Laboratory Handbook on Genetically Standardized Mice

Bar Harbor, ME 04609 USA
2009, The Jackson Laboratory. All rights reserved.
First Edition: first printing, March 1962
Second Edition: first printing, September 1968; second printing, February 1971
Third Edition: first printing, May 1980
Fourth Edition: first printing, April 1991
Fifth Edition: first printing, August 1997
Sixth Edition: first printing, October 2009
ISBN 978-0-578-04182-7
Registered trademarks of The Jackson Laboratory: JAX
www.jax.org
Acknowledgments
Many people at The Jackson Laboratory contributed to this edition of The Jackson Laboratory
Handbook on Genetically Standardized Mice.
We would like to thank the handbook steering committee, whose membership has included
Susie Airhart, Carol Bult, Greg Cox, Muriel Davisson, Edward Leiter, Cathy Lutz, John
Macauley, Janice Pendola, Brian Soper, Marge Strobel, Laura Trepanier, and Barbara Witham.
We also would like to acknowledge the assistance we received from the Technical Information
Services staff throughout the duration of this project: Karen Fancher, David Higgins, Peter
Kelmenson, Pat North-Hughes, Jennifer Merriam, Jay Palmer, Janice Pendola, James Yeadon,
Tanya Lansley, and Yan Yang. And, we want to thank Mike Astle for his pragmatic insight. We
especially want to thank Greg Cox, for his extra time and invaluable assistance. And, we want
to acknowledge the contribution of Karen Davis, in Multimedia Services, and Michael Greene,
in Marketing. Karen created the book cover and provided other invaluable graphical and design
help. Michael shaped and managed the production details of the book.
We also want to acknowledge the help we received from other reviewers. Specific contributions
are noted in individual chapters throughout the book.
And we want to recognize employees of The Jackson Laboratory not directly involved in the
Handbook. It is because of the contributions of each employee of The Jackson Laboratory that
JAX Mice are so widely usedand so well respectedthroughout the global research
community; that our animal care, technical support, and other services are so highly regarded;
and that our reputation as a research institution remains as exceptional as when the first
Handbook was published in 1962. It was a privilege to be involved in this project.
Thanks to all.
Kevin Flurkey
Joanne Currer
vii
Table of Contents
Preface ...................................................................................................................................... xiii
Section I: Introduction ...........................................................................

1: Why the mouse? ..........................................................................................................1
1.A. From inbred sweet peas to mice ......................................................................................1
1.B. From mice to inbred mice ...............................................................................................2
1.C. From inbred mice to JAX Mice ....................................................................................3
1.D. JAX Mice and The Jackson Laboratory ........................................................................3
1.E. It is still about the inbred mouse..................................................................................7
1.F. For more information ...................................................................................................7
1.G. References .........................................................................................................................8
2: Some Basic Genetics of the Mouse ..........................................................................9
2.A. Basic information about the laboratory mouse ............................................................10
2.B. The vocabulary of genetic architecture ........................................................................11
2.C. The basic inbred strain experimentstrain differences capture
genetic differences .........................................................................................................14
2.D. Linkage analysis..............................................................................................................15
2.E. Genotyping: what it is and how it is used ....................................................................16
2.F. Mapping: definition and tools .......................................................................................17
2.G. Coat color genetics..........................................................................................................20
2.H. For more information .................................................................................................23
2.I. Resources.........................................................................................................................23
Section II: Using Mice in Research

Chapter 3: Categories of Laboratory MiceDefinitions, Uses, Nomenclature ...25
3.A. A few words about nomenclature and terminology .....................................................26
3.A.1. Nomenclature ..................................................................................................26
3.A.2. Strain definition and breeding terminology ..................................................27
3.B. Inbred strains and crosses ..........................................................................................28
3.B.1. Inbred strains, substrains ................................................................................28
3.B.2. Wild-derived inbred strains ............................................................................36
3.B.3. F1 and F2 hybrids ...........................................................................................38
3.B.4. Multi-strain crosses .........................................................................................42
3.C. Strains with single-locus mutations ..............................................................................45
3.C.1. Spontaneous, induced, and genetically engineered mutant strains ..............46
3.C.2. Congenic and conplastic strains .....................................................................54
3.D. Recombinant strain panels .............................................................................................59
3.D.1. Overview .........................................................................................................59
3.D.2. Recombinant inbred (RI) strain panels ..........................................................62
3.D.3. Recombinant congenic (RC) strain panels ....................................................65
3.D.4. Chromosome substitution (CS) strains panels and genome-tagged mice ...67
3.E. Mice with chromosomal aberrations ................................................................................70
3.F. References ..........................................................................................................................73
viii Table of Contents
Chapter 4: Characteristics of Popular Strains of JAX Mice, Including

Reproductive Performance .......................................................................................... 77
4.A. Strain characteristics (in order of strain name) ............................................................78
4.B. Reproductive performance ......................................................................................138
4.C. References ....................................................................................................................140
Chapter 5: Choosing a Mouse Strain for ResearchConsiderations and
Resources ..................................................................................................................... 149
5.A. General sources of information about mouse strains .................................................150
5.A.1. Resources at The Jackson Laboratory website: www.jax.org ...................150
5.A.2. An example of a strain characteristic comparison from the
Mouse Phenome Database (MPD): www.jax.org/phenome ......................151
5.A.3. Other websites ...............................................................................................152
5.A.4. Books .............................................................................................................152
5.B. Seven considerations for selecting a mouse strain ....................................................153
5.C. Guidelines for selecting and planning for control mice ........................................156
5.D. Guidelines for selecting a supplier of mice ................................................................158
5.E. Guidelines for alternatives to maintaining live mice .................................................158
5.F. Sources of information related to specific research areas .........................................159
5.G. References ....................................................................................................................164
Section III: Bioinformatics

Chapter 6: Bioinformatics Resources at Mouse Genome Informatics (MGI) and
The Jackson Laboratory ............................................................................................. 165
6.A. What is bioinformatics? ...............................................................................................166
6.B. Introduction to bioinformatics resources at the Mouse Genome Informatics
(MGI) website ..............................................................................................................166
6.B.1. How to access MGI and get help .................................................................166
6.B.2. What you can do from the MGI website (www.informatics.jax.org) ........167
6.B.3. Examples: using MGI to find a mouse model associated with a
disease and to find phenotypic information for a gene ...............................170
6.C. Reference information: bioinformatics resources at MGI and
The Jackson Laboratory ..............................................................................................171
6.C.1. Databases that are part of MGI ....................................................................171
6.C.2. Other databases .............................................................................................173
6.C.3. Online books available from MGI ...............................................................174
6.C.4. Additional resources .....................................................................................174
6.D. Literature ......................................................................................................................174
Section IV: Colony Management

Overview ......................................................................................................................177
Chapter 7: Animal HealthPreventing, Identifying, and Eradicating Microbial
Contamination .............................................................................................................. 179
7.A. Developing an animal health plan ..............................................................................180
7.A.1. The exclusion listmicrobial agents that are unacceptable in
your colonies .................................................................................................180
7.A.2. Preventive measures to keep unacceptable agents out of your colonies ...181
Table of Contents ix
7.A.3.
7.A.4.
7.B.
7.C.
Monitoring procedures to identify the presence of unacceptable agents ..182

Containment and eradication procedures to prevent the spread of an
infection and to eliminate it from your colony ...........................................184
Our animal health plan at The Jackson Laboratory ...................................................184
7.B.1 Our exclusion list ..........................................................................................184
7.B.2. Our preventive measures ..............................................................................185
7.B.3. Our monitoring procedures ..........................................................................186
7.B.4. Our containment and eradication procedures ..............................................188
7.B.5. Routine health reports ...................................................................................189
References ....................................................................................................................189
Chapter 8: Genetic Quality ControlPreventing Genetic Contamination and

Minimizing Genetic Drift ............................................................................................. 191
8.A. Genetic contamination and genetic drift: what they are and how to manage them ..192
8.A.1. Genetic contamination ..................................................................................192
8.A.2. Genetic drift ...................................................................................................193
8.A.3. Identifying and managing events of genetic contamination and
genetic drift.....................................................................................................194
8.B. What we do at The Jackson Laboratory .....................................................................195
8.B.1. Our mouse colony structure: how it helps us maintain
genetic quality control ..................................................................................195
8.B.2. Our genetic integrity programs ....................................................................197
8.C. References ....................................................................................................................200
Chapter 9: Animal Husbandry ................................................................................... 201
9.A. Physical aspects of a mouse room ..............................................................................202
9.A.1. Caging ............................................................................................................202
9.A.2. Water delivery ...............................................................................................204
9.A.3. Room environment .......................................................................................205
9.A.4. Cage bedding .................................................................................................206
9.B. Day-to-day care ............................................................................................................207
9.B.1. Mouse room entry and exit procedures; traffic patterns within and
among mouse rooms .....................................................................................207
9.B.2. Changing cages .............................................................................................208
9.B.3. Providing food and water .............................................................................209
9.B.4. Keeping mouse rooms clean ........................................................................210
9.B.5. Minimizing genetic contamination ..............................................................210
9.C. Other issues related to animal husbandry ...................................................................211
9.C.1. Providing environmental enrichment to alleviate stress .............................211
9.C.2. Managing agression in a colony ..................................................................212
9.C.3. Caring for wild-derived inbred mice ...........................................................213
9.D. Sources of information regarding animal care ...........................................................214
9.E. References ....................................................................................................................215
x Table of Contents
Chapter 10: Food and WaterNutritional and Health Implications .................... 217
10.A. Choosing a diet and arranging for decontamination and storage of feed ..................218
10.A.1. Types of diet...................................................................................................218
10.A.2. Physical form of the feed .............................................................................219
10.A.3. Decontamination of feed ..............................................................................220
10.A.4. On-site storage of feed ..................................................................................222
10.A.5. Nutritional composition of feed and requirements for healthy mice .........222
10.A.6. Quality control ..............................................................................................225
10.A.7. What we do at The Jackson Laboratory ......................................................226
10.B. Treating water ..............................................................................................................226
10.B.1. Guidelines for safe water ..............................................................................226
10.B.2. What we do at The Jackson Laboratory ......................................................226
10.C. References ....................................................................................................................227
Chapter 11: Recordkeeping and Identification of Mice ......................................... 229
11.A. Identifying individual mice .........................................................................................230
11.A.1. Identification methods ...................................................................................230
11.B. Keeping day-to-day records ........................................................................................232
11.B.1. Recommendations and strategies .................................................................232
11.C. Choosing colony management software .....................................................................234
11.C.1. Advantages of a colony management system .............................................234
11.C.2. Considerations when choosing a colony management system ..................234
11.C.3. The Jackson Laboratorys Colony Management System (JAX-CMS)
for research mouse colonies .........................................................................235
11.D. References .....................................................................................................................235
Chapter 12: Introduction of New Mice into a Colony ............................................. 237
12.A. Precautions when introducing live mice ....................................................................238
12.A.1. Protecting against pathogens.........................................................................238
12.A.2. Protecting against genetic contamination ....................................................238
12.A.3. Identifying and recovering a loss of phenotypic expression
12.B. Handling newly arrived mice ......................................................................................238
12.B.1. Recognizing and managing the physiological effects of stress related
to transportation ............................................................................................238
12.B.2. Special handling for newly arrived, wild-derived inbred mice ..................239
12.B.3. What to do if you have an automatic watering system and your
newly arrived JAX Mice wont use it ........................................................240
12.C. What we do at The Jackson Laboratory .....................................................................240
Chapter 13: Breeding Strategies and Techniques ................................................. 241
13.A. Factors that affect the breeding of laboratory mice ...................................................242
13.A.1. Biological breeding data................................................................................242
13.A.2. Environmental factors that can affect breeding performance ....................243
13.A.3. Strategies for setting up and monitoring breeding to optimize
colony production .........................................................................................244
13.A.4. General guidelines for successful breeding .................................................244
Table of Contents xi
13.B.
13.C.
13.D.
13.E.
13.F.
13.G.
13.H.
13.I.
Breeding schemes ........................................................................................................246

Sizing a breeding colony for a research program ......................................................246
Strategies for maintaining a line or strain without expansion ...................................247
Using reproductive techniques ....................................................................................247
13.E.1. Standard reproductive techniques .................................................................247
13.E.2. Assisted reproductive techniques (ARTs) ...................................................250
Maintaining the genetic integrity of your colonies ....................................................250
13.F.1. Preventing genetic contamination and minimizing genetic drift ................250
13.F.2. Confirming phenotypes and genotypes .......................................................250
Troubleshooting breeding problems ...........................................................................252
Resources.......................................................................................................................253
References ....................................................................................................................253
Chapter 14: Emergency Planning ............................................................................. 255

14.A. Developing your plan ..................................................................................................256
14.A.1. Minimizing the initial effect of an emergency .............................................256
14.A.2. Keeping your animals safe ...........................................................................256
14.A.3. Minimizing the loss of data ...........................................................................257
14.A.4. Returning to normal operations ....................................................................257
14.A.5. Managing a loss of employees ......................................................................257
14.B. What we do at The Jackson Laboratory .....................................................................258
14.C. References ....................................................................................................................258
Chapter 15: Human Health ConcernsMouse Allergies, Bites,
Zoonotic Disease ......................................................................................................... 259
15.A. Mouse allergens ...........................................................................................................260
15.A.1. The most common offending allergen: Mus m1 ..........................................260
15.A.2. Protection from laboratory animal allergies (LAA)s ..................................260
15.B. Animal bites .................................................................................................................261
15.C. Zoonotic disease ...........................................................................................................261
15.D. What we do at The Jackson Laboratory .....................................................................262
15.D.1. Allergies .........................................................................................................262
15.D.2. Bites ...............................................................................................................262
15.D.3. Zoonotic disease ............................................................................................262
15.E. Resources ......................................................................................................................263
15.F. References ....................................................................................................................263
Chapter 16: Vivarium Staff Development and Contribution ................................ 265
16.A. Training and career development ................................................................................266
16.A.1. Considerations................................................................................................266
16.B. Effective communications ...........................................................................................269
16.B.1. Considerations ...............................................................................................269
xii Table of Contents
Section V: Ordering JAX Mice and JAX Services
Chapter 17: Ordering JAX Mice and JAX ServicesContact Information

for Customer Service and Technical Support; Frequently Asked Questions ... 271
Chapter 18: JAX Services .......................................................................................... 277

Chapter 19: The Jackson LaboratoryWest ........................................................... 283
Appendixes
Appendix A: Strain Nomenclature Quick Reference ............................................. 285
Appendix B: 129 StrainsNomenclature and Related ES Cell Lines ................ 291
Appendix C: Origins and Relationships among Common Strains and
Substrains of Laboratory Mice .................................................................................. 295
Appendix D: Commonly-Used Inbred Strains and Substrains of JAX Mice

Genes and Research Applications ........................................................................... 303
Appendix E: Coat Color Alleles for Popular Strains of JAX Mice ..................... 307
Appendix F: Histocompatibility Haplotypes and Loci ........................................... 313
Appendix G: Equivalencies of Human Age to Life Phases of Mice .................... 329
Appendix H: Transfer of a Mutant or Variant Allele to a New Genetic
Background by Phenotypic Selection ...................................................................... 333
Appendix I: Using a Balanced Stock to Carry a Recessive Mutation
That Is Sterile or Lethal, Including Embryonic Lethal ........................................... 335
Appendix J: Cryopreservation ................................................................................... 341
Appendix K: Donating or Submitting a Strain of Mice to
The Jackson Laboratory.............................................................................................. 347
Appendix L: Simplifying Power Analysis to Determine Sample Size.................. 349
Appendix M: Courses and Educational Programs.................................................. 355
Appendix N: Sources of Information about Laboratory Mice ............................... 359
Appendix O: General Biological Information about Laboratory Mice ................. 361
Index..................................................................................................363
xiii
Preface
This is the 6th edition of The Jackson Laboratory Handbook on Genetically Standardized Mice,
which at The Jackson Laboratory, we often refer to simply as the Handbook.
The first edition was published in 1962 as a small booklet. The editor was Earl Green, the
Director of The Jackson Laboratory. At that time The Jackson Laboratory employed
approximately 350 people; 68 were researchers. We offered over 60 strains of mice, half of
which were maintained by researchers. The objective of that edition of the Handbook was to
provide assistance in planning experiments, in choosing the best types of mice, and placing
orders for mice with our Production Department.
In the 46 years since then, The Jackson Laboratory has undergone tremendous changeas have
the ways by which we record and access information. We now employ about 1,400 people, with
a research staff close to 500. We offer more than 4,000 strains of mice, which are used by
approximately 16,000 investigators in 53 countries. Ninety-seven percent of these strains are
available only at The Jackson Laboratory. Our website provides access to information about
mice in a variety of databases, several of which are updated daily. But the objectives of the
Handbook remain consistent: to support our mission by enabling research and education for the
global biomedical community, and by providing information about laboratory mice and about
choosing and ordering mice.
With this edition of the Handbook, we were faced with two major challenges: how to balance
the benefits of paper-based vs. web-based documentation, and how to avoid unnecessary
redundancy both within the Handbook and with other sources of information about JAX Mice.
Our strategy is to include information that readers may want to browse or keep handy by their
desks. For information that is updated frequently, we refer the reader to the resource with the
most current information.
The organization of The Handbook

The Handbook is organized as follows:
Section I, Introduction (Chapters 1 and 2): background information about the history of
the laboratory mouse and its value as a mammalian genetics research tool; also, overview
information related to the genetics of laboratory mice.
Section II, Using Mice in Research (Chapters 35): reference information about
laboratory mice and JAX Mice and about selecting a strain and controls for research.
Section III, Bioinformatics (Chapter 6): information about bioinformatics resources
available through our and other websites.
Section IV, Colony Management (Chapters 716): information about managing a mouse
colony, including animal health, genetic quality control, breeding strategies, day-to-day care,
emergency planning, and vivarium staff development.
Section V, Ordering JAX Mice and JAX Services (Chapters 1719): information
about placing orders, getting technical help, and frequently asked questions; also, an overview
of JAX Services and The Jackson LaboratoryWest.
Back matter: Appendixes and an index.
Conventions used in the Handbook

Throughout the handbook, we include the JAX Mice stock number in parentheses after the full
strain name, as in B6.129P2-Apoetm1Unc/J (002052). We define abbreviations the first time they
are used within each chapter. If we think a good portion of readers might not understand a term,
we define it within the text.
Chapter 1: Why the Mouse?

Kevin Flurkey, Joanne M. Currer
It is a very exciting time for biomedical research. Over the past century, advances in science,
medicine, and public health have led to preventions and cures for many of the most devastating
infectious diseases. Polio has been virtually eliminated; smallpox has been completely
eliminated. Lifespan in developed countries has nearly doubled.
During the last half of the 20th century, research efforts also led to a greater understanding of a
different category of major killers generally unrelated to infectious diseasechronic diseases
such as cancer, diabetes, and heart diseasewhich are heavily influenced by genetic factors.
The discovery, in the late 1970s, of the means to rapidly sequence DNA led to powerful
techniques for the identification of the very genes that determine the risk factors for developing
these diseases. As researchers learn more about the genetic bases for such diseases, they develop
more options for intervention, such as drug therapies that alter the way specific genes work.
Ultimately, todays research sets the stage for the introduction of novel gene therapies that will
directly alter the functions of defective genes or even introduce entirely new genes.
From the beginning of mammalian genetics research, the mouse, especially the inbred mouse,
has been a critical tool in the endeavor to understand the genetics of human disease. Subsequent
developments in technology have led to a substantial increase in the versatility and value of the
inbred mouse. Today, the inbred mouse is universally accepted as the primary model for
inherited human disease (Davisson and Linder, 2006).
We anticipate that the great success of science and medicine over the past century will extend
into the current century to continue the remarkable progress in alleviating human suffering and
improving human health. Much of this progress will be a result of the revolution in genetic
technology and its application to research using models based on the inbred mouse.
1.A. From inbred sweet peas to mice

1.A.1. Mendels work with peas
For most of us, our first formal exposure to the genetics of inheritance was probably when we
learned about Gregor Mendels research on sweet peas, conducted in the 1860s in a monastery
in the Austrian Empire (now the Czech Republic). Ironically, Mendel had wanted to study mice,
but due to restrictions in the monastery, he instead worked with a species of peas that he bred
for generations so that characteristics that differed between plants were maintained constant
within a line. It is through Mendels work with these inbred peas that we learned about simple,
dominant vs. recessive, inherited traits: When he crossed purple-flowered plants with whiteflowered plants, he got more plants with purple flowers (dominant) than white flowers
(recessive). No flowers were pink. Even today, we call such simple traits, i.e., traits that are
determined primarily by a single gene, Mendelian traits.
1.A.2. Galtons work with peas

Later in the 19th century, Englishman Sir Francis Galton, who had a broad range of scientific
interests, studied inheritance in sweet peas from a different perspective: A pioneer in statistical
analysis, Galtons research indicated that inheritance of some traits, such as the size of the peas,
was not quite as straightforward as Mendels conclusions regarding flower color. These traits
were complex, and often additive, and they were just as heritable as the traits Mendel studied.
Today, we call these types of traits quantitative. They are determined by multiple genes rather
than a single gene.
2 Section I: Introduction
1.A.3. Application of Mendels and Galtons theories to mammals

Toward the end of the 19 th century and the beginning of the 20th century, scientists began to ask
if the rules of inheritance formulated by Mendel and Galton applied to other organisms.
Mammals were an obvious choice as models to test these ideas because of the potential for
applications to normal human biology and to human disease.
These researchers became interested in the fancy mice that
How do simple and quantitative traits relate
to human physiology and disease?
hobbyists had been breeding in China, Japan, Europe, and the
United States to create pets with specific coat styles and colors.
Inheritance of some human traits and disease is
simplebased on a single gene. One example
These fancy mice were appealing as research models because
related to normal anatomy is ear lobe structure.
they were already domesticated, readily available, and easy to
A single gene determines whether ear lobes are
breed and maintain. Importantly, variants of a simple phenotype,
attached or free. Another example relates to
coat color, were well known. In fact, the first paper describing
blood type. Combinations of the three versions of
the same gene result in one of four blood types,
the application of Mendelian genetics to mammals was on the
commonly known as A, B, AB, or O. Two
coat colors of mice (Cunot, 1902).
examples related to disease are cystic fibrosis
and Huntingtons disease, both of which are the
result of a mutation in just one gene.
However, most human traits and geneticallybased diseases are quantitativerelated to

multiple genes. Several examples of normal
traits under complex genetic regulation are eye
color, size and shape of the nose, and height.
Several examples related to disease are type 2
diabetes and most types of cancer, which involve
multiple genes that interact with each other to
establish an individuals risk of developing the
disease.
1.B. From mice to inbred mice

1.B.1. Littles early research and ideas on
inbreeding
Clarence Cook Little was one of the early researchers interested

in using fancy mice. His first two papers, published when he was
still an undergraduate in William Castles laboratory at Harvard
University, were on the coat colors of mice (Castle and Little,
1909, 1910), but his interests also included the possibility that
the new field of genetics might provide solutions to the
problem of cancer. The discovery, in the late 19th century, that
tumors could survive transplantation in mice was exciting for researchers because it gave them a
way to experimentally control the incidence of cancer. Disappointment followed, however, as
success rates proved to be highly variable (Strong, 1978). Little believed that one way to
eliminate some of that variability would be to study animals as genetically similar as possible
(Staats, 1966). The only known strategy to achieve this was genetic fixation by inbreeding
producing stocks that would breed true for any genetically determined characteristic. Little
recognized three distinct advantages with this strategy:
By removing genetic variance within a strain, researchers could more directly relate disease
expression to a specific genotype.
By developing multiple inbred strains, each with unique characteristics, researchers could
compare one inbred strain with another. Any difference between the strains could be defined
as genetically based, even though the genes involved were not known. By selectively
intercrossing inbred strains, researchers could begin to understand the heritability of disease .
By using the same inbred strains in multiple laboratories and from program to program,
researchers could expect experimental results to be reliable and replicable.
1.B.2. Littles and Strongs development of inbred mice

Castle, among many others, recognized the advantages of inbreeding, but he was dubious that
inbred lines of mice would survive the severe impairments in reproductive performance
resulting from inbreeding depression. For some young scientists such as Little and Leonell
Strong, however, the potential payoff was worth the considerable effort and years of work
required in attempts to inbreed mice. Thus, in 1909, at the newly founded Bussey Institute
(Harvard), Little began developing the first inbred mouse lines for his study of coat color
genetics. His work succeeded, and eventually led to the first inbred strainDBA. By 1918, at
the Cold Spring Harbor Laboratory (New York), Little and Strong were instrumental in
developing several of the most common inbred strains still in use today. One of these strains
was C57BL/6, the progenitor of the C57BL/6J (000664) strain of JAX Micethe first inbred
strain chosen (in fact, the first animal after humans) for complete DNA sequencing (Mouse
Genome Sequencing Consortium, 2002).
Chapter 1: Why the Mouse? 3
1.C. From inbred mice to JAX Mice

1.C.1. Littles founding of The Jackson Laboratory
Little continued his research using mice to explore the genetic basis of cancer. He further
developed his academic career as president of first, the University of Maine, and then the
University of Michigan. When he left the presidency of the University of Michigan in 1929 to
return to full-time research, it was funding by philanthropists that enabled him to found The
Jackson Laboratory.
1.C.2. Littles vision for The Jackson

Laboratory
Littles goal was to continue the development of inbred strains of
mice at The Jackson Laboratory and to use these strains to study
cancer and other genetically-based human diseases. With the
inclusion of Leonell Strong on the original Jackson Laboratory
staff, a number of inbred strainsincluding A, C3H, and CBA
were added to the unique and growing collection maintained at
The Jackson Laboratory. As recognition of the value of inbred
mice grew, it became difficult for The Jackson Laboratory staff to
keep pace with requests from other researchers for breeding stocks
(Strong, 1978).
The stock market crash of 1929 decimated research funding
opportunities, which were primarily from private sources at the
time. Little was determined to continue his research, however. To
defray some of the costs of rearing the inbred strains at The
Jackson Laboratory, in the early 1930s he began a formal program
to distribute mice to other researchers. And thus he solidified the
mission of The Jackson Laboratory that exists to this day: to
conduct critical mammalian genetic research and to supply highquality inbred miceJAX Miceto researchers throughout the
world (Rader, 2004).
1.D. JAX Mice and The Jackson

Laboratory
Why geneticists love mice

The numerous advantages of mice as mammalian
research models include size (among the smallest
mammals, they are inexpensive to maintain);
robustness (they thrive and breed under a wide
range of environmental conditions); and fecundity
(they have a short gestation, produce large litters,
and develop rapidly, which allows for rapid
expansion of a colony). And, most laboratory mice
are quite tame.
As research with mice has progressed, a
surprising, yet frequent, observation has been
how closely mice and humans are related
biologically, despite the size difference. Mice have
almost all the same organs as humans, and they
share a 95% DNA coding sequence identity with
humans. Because of their close metabolic and
anatomical similarities to humans, mice have
many syndromes that are similar to human
inherited diseases. In fact, mice are at least as
closely related biologically to humans as any of
the familiar agricultural and domestic mammalian
species. Only primates are closer evolutionarily.
This results in the comparable ordering of genes
for long stretches on mouse and human
chromosomes (synteny), which makes the mouse
extremely useful for comparative genetics.
Almost certainly, the single most valuable
characteristic of the mouse as a research tool,
however, is the ability of some lineages to survive
inbreeding depression, permitting the
development of inbred strains.
Many important scientific discoveries related to genetics have

involved research using inbred mice at The Jackson Laboratory.
Several examples are worth noting here because they advanced the field of mammalian genetics
and resulted in broad application to human health.
1.D.1. George Snell and congenic strain development

1.D.1.a. Snells research on tumor rejection among inbred strains
One of the most significant advances in the use of inbred mice as research tools was George
Snells development of congenic strains. In a congenic strain, a small segment of DNA
containing a genetic variant of interest is transferred from one strain into another through
directed breeding. In the 1940s, a few years after Snell joined The Jackson Laboratory, he began
looking for a research project that offered the prospect of yielding some really clear-cut and
basic information. (Snell, 1978.) Snell learned that Little had identified inbred mouse strains
that had genetic differences in tumor rejection and that these differences involved numerous
loci. Snell recognized that this work was relevant to the genetics of tissue rejection and that
understanding this issue had important biomedical implications. To progress, however, he
needed a way to isolate the loci that determined rejection (tumor resistance) so that he could
study each locus individually.
Snell began the laborious process of creating his congenic lines by crossing a strain that
accepted a specific transplanted tumor (a susceptible strain) with a strain that rejected the
transplanted tumor (a resistant strain). He then tested the hybrid offspring using tumor
transplantation. Resistant mice were then backcrossed again to the susceptible strain. With
repeated backcrossing, the alleles unrelated to resistance eventually became extinct in the line.
This isolated the allele of the gene (or genes) in the selected congenic segment responsible for
resistance on a defined, inbred, genetic background.
An interesting problem was that, because tumor resistance is usually recessive, every backcross
to the susceptible recipient strain (producing offspring heterozygous for the susceptibility
alleles) produced only susceptible offspring. How was Snell to identify carriers of the resistant
alleles? He solved this problem with a creative breeding strategy (for the solution see Appendix
H, Transfer of a Mutant or Variant Allele to a New Genetic Background by Phenotypic
Selection), and after years of work, produced a series of congenic resistance lines that
identified a number of histocompatibility loci. One locus, the H2 locus, appeared far more
frequently in Snells lines than any of the other loci because it had a more powerful effect on
resistance than the other loci. This led to the discovery of a comparable locus in humans, the
major histocompatibility locus (MHC), which governs immune self-recognition and thus,
rejection of transplanted tissue in humans, as the H2 locus does in mice.
1.D.1.b. Snells legacy: organ transplantation, the congenic mouseand

the Nobel Prize
Snells work is well known because it paved the way to successful organ transplantation in
humans. But this same research also resulted in two remarkable achievements specifically
related to the use of the inbred mouse in research. First, by creating a set of inbred lines that
differed at only at a defined genetic segment, he enabled future researchers to characterize the
molecular mechanisms of tissue rejection, as well as identify the mechanism of antigen
presentation, which helps determine the specificity of the acquired immune response. These
discoveries have implications for the treatment of virtually all infectious diseases, as well as all
autoimmune diseases such as lupus and type I diabetes. Second, Snells work demonstrated that
effects of a single gene could be isolated for study, even for a complex phenotype, by creating a
congenic straina living tool. Snell showed how a gene could be converted from one allele
type to another in a living animal, and thus, long before the development of modern genetics,
established a strategy that still is used extensively today, more than 50 years later. Indeed, the
use of congenic strains in conjunction with the tools of genetic engineering makes it possible for
researchers to isolate and archive, in living repositories, both natural and engineered genetic
variants that enable the study of virtually any gene in its vital setting. None of this could have
been accomplished without the inbred mouse.
Snells work, conducted in the 1940s and 1950s at The Jackson Laboratory, secured the value of
the congenic strain in biomedical research. Today, in fact, the congenic strain is the
predominant type of inbred strain populating The Jackson Laboratorys national repository for
mutant mice, the Induced Mutant Resource (IMR). For his work using inbred mice, which laid
the foundation for tissue and organ transplantation, Snell was awarded the Nobel Prize in
Physiology or Medicine in 1980.
1.D.2. Donald Bailey, the recombinant inbred strain panel, and the
Collaborative Cross
1.D.2.a. The concepts of linked traits and linkage groups
Shortly after the rediscovery of Mendels laws at the end of the 19th century, geneticists
recognized that Mendels law of independent assortment applied to groups of phenotypes, later
called linkage groups, rather than to all individual phenotypes. The assignment of phenotypes to
linkage groups was a major challenge to geneticists throughout the mid 20th century. The
results of this effort built the foundation for gene mapping and gene discovery in mice, which is
essential for todays application of the genetics revolution to human health.
Before 1985, mapping a genetic locus usually took years, and in many cases, was impossible.
Success depended on determining whether a phenotype of interest assorted independently of, or
was linked to, a previously mapped genetic marker (such as coat color) for each linkage group.
This was accomplished by testing for the co-expression of the phenotype and the marker in
progeny from crosses between a strain that expressed the phenotype and a strain that expressed
the marker. Such crosses are called mapping crosses. Mapping a locus for a new phenotype
required multiple mapping crosses and many hundreds of mice.
1.D.2.b. Baileys insight into preserving recombinations in a panel of

inbred strains
In the 1960s Don Bailey, explored ways to simplify mapping. Baileys insight (1971) was that
the unique, random recombinations of the genomes of two parental strains that are necessary for
mapping could actually be preserved for future research by creating inbred strains from the
progeny of a mapping cross. These inbred strains would make up a recombinant inbred (RI)
panel. Because, for each RI strain, the recombinant genotype would be stable across
generations, it would be necessary to genetically type the mice only once, no matter how many
mapping studies the RI panel was used for. To map a new phenotype, it would be necessary
only to evaluate that new phenotype in the RI strains of the panel.
Baileys work was pivotal in accelerating the pace of gene mapping in mice through the 1970s
and 1980s. The results provided the scaffolding necessary for later detailed mapping that
eventually led to the complete sequencing of the mouse genome in 2002 (Mouse Genome
Sequencing Consortium, 2002).
1.D.2.c. The reinvigoration of the recombinant inbred strain

Today, the powerful tools of molecular genetics have diminished the use of RI strains for
mapping fully penetrant phenotypes, i.e., phenotypes that are expressed in all individuals that
have the appropriate genotype. RI strains are still useful, however, for phenotypes with low
heritability or low penetrance because multiple individuals with the identical recombinant
genotype (i.e., individuals of the same RI strain) can be evaluated.
One of the drawbacks of the current RI strain panels is that they are primarily useful for
mapping monogenic traits, whereas the majority of disease traits are determined by complex
combinations of genes. This problem can be overcome by increasing the number of RI strains in
a panel and by increasing the diversity of founder strains. These tasks will soon be
accomplished through the efforts of the Complex Trait Consortium (Churchill et al., 2004;
Chesler et al., 2008), by creating a huge RI strain panel, called The Collaborative Cross, in
which hundreds of strains will be generated from a highly diverse 8-way cross. The genetic
diversity of the founder strains, which includes three subspecies, was devised to more accurately
simulate the genetic diversity of human populations, and specifically designed for complex trait
analysis. By providing a common set of genetically defined inbred mice in a very large RI
panel, the Collaborative Cross is intended to become a focal point for cumulative and integrated
data collection across institutions and time. These data will greatly expand the use the inbred
mouse by enabling a more effective analysis of the complex genetics of normal and pathological
functioning of the mammalian organism.
1.D.3. The inbred mouse and further seminal research at The

Jackson Laboratory
Throughout the history of The Jackson Laboratory, many investigators have been involved in
pioneering research. Their scientific contributions, made possible by the genetic consistency of
inbred mice and related models, have influenced the course of biomedical research to improve
human health. Several examples follow.
1.D.3.a. A few of the biomedical research breakthroughs at The Jackson

Laboratory
Leroy Stevens, in the 1950s, conducted research on pluripotency and differentiation. Stevens
had observed that mice of the 129 strain were more susceptible than mice of other strains to
teratocarcinoma, a rare form of cancer in which tumor cells of one tissue spontaneously
differentiate into cell types of other tissues (for example, a teratocarcinoma cell in ovarian tissue
might differentiate into neuronal cells). Using directed breeding strategies, he created a 129
substrain with enhanced expression of the cancer, and was thus able to isolate and study the
pluripontency of the teratocarcinoma cells. This work led to the demonstration that embryonic
stem cells could be similarly isolated and studied, which enabled two revolutionary technologies
in genetics: First, with embryonic stem (ES) cells in culture, researchers gained access to the
cellular substratum required to create living knock-out and knock-in mouse models from
genomes genetically engineered in vitro. Second, with the knowledge that ES cells could
produce various differentiated cells, researchers recognized the real prospect of human stem cell
therapy.
Other researchers at The Jackson Laboratory used inbred mice in their pioneering work in the
field of physiological genetics. Elizabeth Tibby Russells work on hematopoiesis, using a
number of inbred strains, helped define the field of red blood cell biology and led to the first
bone marrow transplant to cure a diseasein this case, anemia.
Douglas Coleman discovered a recessive mutation that causes obesity and diabetes on one
inbred strain background, but only obesity on another. He observed the same background effect
when another recessive, obesity-producing mutationoriginally discovered by Snellwas
studied on the same two strain backgrounds (the diabetes-susceptible background was
C57BLKS/J [000662]; the diabetes-resistant background was C57BL/6J [000664]). Both
mutations produced identical phenotypes when studied on the same inbred strain background,
but clearly were on different chromosomes. Coleman intuited that one might be a gene that
encodes a receptor in a satiety center, and the other its ligand. Indeed, the obesity-producing
mutation originally discovered by Snell was later found to encode leptin, the first hormone
shown to be secreted by fat tissue (and inform the brain as to nutrient homeostasis). The
mutation discovered by Coleman was in the leptin receptor gene. Colemans work not only
established the relationship between the two mutations, but also was the first demonstration of
the presence of modifier genes that differed in the various inbred strains of mice. This was a
seminal discovery in the field of biochemical genetics.
1.D.3.b. Bioinformatics
Groundbreaking work at The Jackson Laboratory also enhanced the way researchers collected,
organized, and disseminated information about inbred strains of mice. In 1958, Margaret Green
established an index card file of genetic data on inbred strains. In 1990, Muriel Davisson and
Thomas Roderick used these data as a foundation for one of the first computer-based mouse
databases (Gbase). And in 1992, Janan Eppig began the process of integrating the access to a
series of key databases related to mouse genetics. This work grew into the Mouse Genome
Informatics (MGI) database collaboration, which today provides integrated retrieval and
analysis of data on the genetics of the laboratory mouse to researchers throughout the world at
the click of a button. It is due to the genetic consistency of the inbred mouse that so much
reliable data has been collected throughout the years and that these data are still relevant today.
It is now possible for a researcher almost anywhere in the world to use the power of the
computer to expand the power of the inbred mouseto analyze data and even develop novel
hypotheseseven before setting foot in a mouse room.
1.D.3.c. JAX Mice

Many researchers at The Jackson Laboratory have developed new inbred strains and new mouse
models based on the inbred strain. The Jackson Laboratory also has continued to import new
strains from other investigators, while maintaining even the oldest of the original inbred strains,
such as the C57BL/6J (000664) strain, which has now been inbred for more than 226
generations. The number of available strains of JAX Mice is now around 4,000.
1.E. It is still about the inbred mouse

It is not clear why mice can be successfully inbred. Perhaps it is because they evolved living in
small, closely knit family groups (demes). Whatever the reason, we are fortunate that a mammal
that physically is so ideally suited for researchand genetically so similar to humansis also
so ideally suited for inbreeding.
Because mice could be inbred, a foundation of genetic information was established upon which
ever more sophisticated living research tools could be built. And because knowledge of the
mouse genome became more advanced than that of any other experimental mammal, the inbred
mouse became the ideal vehicle for translation of the recent genetics revolution to mammalian
biology. Today, we can add, subtract, or selectively alter virtually any gene in the mouse
genome, and we can even use the mouse as a host for genes from other species ranging from
algae to human. The present capability to manipulate the mouse genome was almost
unimaginable just 35 years ago, and the potential advancement of our understanding of
mammalian genetics, and its relationship to human disease, now seems virtually unlimited.
Littles legacythe inbred strains he developed and The Jackson Laboratory that he founded
remain at the forefront of biomedical research today. As we search for tomorrows cures in the
21st century, we still turn to the inbred mouseand models based on the inbred mousethat
Little pioneered almost 100 years ago.
1.F. For more information

To learn more about the history of the mouse in research or The Jackson Laboratory, see the
following resources:
Biology of the Laboratory Mouse, 2nd Edition. Staff of The Jackson Laboratory. Green EL, Ed.
1968. Dover Publications, NY.
The Jackson Laboratory website. www.jax.org
The Laboratory Mouse. Hedrich HJ, Ed. 2004. Elsevier, London.
Making Mice: Standardizing Animals for American Biomedical Research, 19001955. Rader
KA. 2004. Princeton University Press.
Mouse Genetics: Concepts and Applications. Oxford University Press. Silver LM. 1995.
Available online from Mouse Genome Informatics (MGI):
www.informatics.jax.org/resources.shtml
Origins of Inbred Mice. Morse, HE III, Ed. 1978. Academic Press, NY.
1.G. References
Bailey DW. 1971. Recombinant-inbred strains: an aid to finding identity, linkage, and function
of histocompatibility and other genes. Transplantation. 11:325327.
Castle WE, Little CC. 1909. The peculiar inheritance of pink eyes among colored mice. Science.
30:313314.
Castle WE, Little CC. 1910. On a modified Mendelian ratio among yellow mice. Science.
32:868870.
Chesler EJ, Miller DR, Branstetter LR, Galloway LD, Jackson BL, Philip VM, Voy BH, Culiat
CT, Threadgill DW, Williams RW, et al. 2008. The Collaborative Cross at Oak Ridge National
Laboratory: developing a powerful resource for system genetics. Mamm Genome. 19:382389.
Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK,
Bennett B, Berrettini W, et al. 2004. The Collaborative Cross, a community resource for the
genetic analysis of complex traits. Nature Genetics. 36:11331136.
Cunot L. 1902. La loi de Mendel et lhrdit de la pigmentation chez les souris. Arch. Zool.
Exp. Gen. 3:2730.
Linder CC, Davisson MT. 2004. Historical foundations, in The Laboratory Mouse. Hedrich
HJ (ed). Elsevier, London. pp. 1524.
Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of
the mouse genome. Nature. 420:520562.
Rader KA. 2004. Making Mice: Standardizing Animals for American Biomedical Research,
19001955. Princeton University Press.
Snell GD. 1978. Congenic Resistant Strains of Mice, in Origins of Inbred Mice. Morse HE III
(ed). Academic Press, NY.
Staats J. 1968. The Laboratory Mouse, in Biology of the Laboratory Mouse. Dover
Publications, Inc. NY. pp. 1.
Strong LC. 1978. Inbred Mice in Science, in Origins of Inbred Mice. Morse, HE III (ed).
Academic Press, NY.
Chapter 2: Some Basic Genetics of the Mouse

Throughout this handbook, we presume that readers have a familiarity with basic genetics. For
readers who might be unfamiliar with some of the concepts, especially as they apply to the
mouse, this chapter provides background and perspective.
The chapter is organized as follows:
2.A. Origins and basic genetic characteristics of the laboratory mouse .......10
2.B. The vocabulary of genetic architecture...................................................11
2.B.1. Terminology ..................................................................................11
2.B.2. Selected topics...........................................................................12
2.B.2.a. When is a gene not a gene?........................................12
2.B.2.b. How can an allele be dominant and recessive at
the same time?................................................................12
2.B.2.c. When is dominance not dominance?.........................13
2.B.2.d. Is a locus also a gene?....................................................13
2.B.2.e. What do geneticists mean by segregation? ...............13
2.B.2.f. Complex genetic regulation and the myth of the
Mendelian trait ...............................................................14
2.C. The basic inbred strain experimentstrain differences capture
genetic differences....................................................................................14
2.D. Linkage analysis .......................................................................................15
2.E. Genotyping: what it is and how it is used...............................................16
2.F. Mapping: definition and tools..................................................................16
2.F.1. What is mapping? What is a centimorgan (cM)?........................17
2.F.2. Why map a trait? ...........................................................................17
2.F.3. What strategies are used for mapping?........................................18
2.F.4. What tools are used for mapping?................................................18
2.F.5. How can bioinformatics be used to enhance mapping? .............18
2.F.6. Once a locus is established, how is the gene found? ..................20
2.G. Coat color genetics ...................................................................................20
2.G.1. The interactions of coat color genes ............................................21
2.G.2. Five genes responsible for the most common coat
color variations in laboratory mice ..............................................22
2.H. For more information...........................................................................23
2.I. Resources ..................................................................................................23
Acknowledgments: We would like to thank Janice Pendola and James Yeadon for their
valuable review of this chapter.
2.A. Origins and basic genetic characteristics of the

laboratory mouse
Most conventional strains of laboratory mice are genetic mixtures of Mus musculus domesticus
(about 8590%), M. m. musculus (about 515%) and M. m. castaneus (less than 1%) (Yang et
al., 2007). Most wild-derived lines are pure M. m. domesticus, M. m. musculus, or M. m.
castaneus; however, some are M. m. molossinus, which is an ancient mixture of M. m. musculus
and M. m. castaneus. Other M. musculus subspecies, such as M. m. bactrianus, M. m. praetextus
and M. m. wagneri, remain greatly underrepresented among inbred laboratory strains. Figure 2.1
provides an overview of the origins of mice used in research.
Figure 2.1. Origins of mice used in research.
Drawing adapted from Yoshiki and Moriwaki (2006).

Table 2.1. Basic genetic information about the laboratory mouse; comparisons with
humans.
Value for mice
Value for humans
Number of
chromosomes
Characteristic
Haploid number = 20
(19 autosomes; 1 sex chromosome)
Diploid number = 40
Haploid number = 23
(22 autosomes; 1 sex chromosome)
Diploid number = 46
Number of genes
23,000 identified;
potentially 25,000
20,00025,000 (Human Genome

Project Information, 2008)
Number of
centimorgans (cM)*
1,500
(average chromosome: 75 cM)
3,000
(average chromosome: 130 cM)
Number of base pairs
2,700,000,000
3,200,000,000
*The centimorgan (cM) refers to genetic distance based on recombination frequency.
Chapter 2: Some Basic Genetics about the Mouse 11
2.B. The vocabulary of genetic architecture

The genetic architecture of a phenotype refers to the specific genes and allelesand their
interactionsthat influence the expression of the phenotype. Much of biomedical genetics is
concerned with elucidating the genetic architecture of heritable traits. Following are definitions
and comparisons of terms used when defining the genetic architecture of a phenotype.
2.B.1. Terminology
Basic terms used throughout the book include the following:
genome
genotype
phenotype
The genetic makeup of an organism as a whole, represented by a full set of

chromosomes.
Depending on context, the allelic composition of
a single gene in an individual,
multiple genes that affect a single trait in an individual, or
all the genes of an organism.
A physical characteristic determined by a genotype and its interaction with the
environment. The term phenotype is often used interchangeably with trait and
character.
Genetic diversity within a species occasionally is due to deletion or duplication of genes, but
usually is due to genes that are polymorphic.
polymorphic
Refers to
a trait that occurs in multiple versions, or
a locus or gene with multiple alleles.
By convention, a trait or a locus is considered polymorphic when the most common
version or allele occurs at a frequency of less than 95%. This definition contrasts
with monomorphic, which refers to a trait or a locus with little or no variation
within a defined population.
Terms used to describe specific types of alleles include the following:

wild-type allele
The most common allele of a gene within a population.
mutant allele
An allele of a gene that appears at less than 1% frequency in the population.
variant allele
An allele of a gene that appears less frequently than the wild-type allele, but at
greater than 1% frequency in the population.
All alleles arise through mutation. If the frequency of a mutant allele increases in a
population, it may be called a variant. The distinction, 1% frequency in the
population, is only approximate.
The relationship between the alleles at a specific locus is described by the following:
heterozygous
Having two different alleles at a locus.
homozygous
Having two identical alleles at a locus.
hemizygous
Having only one allele at a locus, such as an allele on the unpaired Chr X of a male
or an unpaired transgene.
When, for a designated population, all alleles for a gene or a locus are identical, the
gene or locus is said to be fixed.
The terms used to describe the functional relationship of two different alleles at a specific locus
are the same terms used to describe the mode of inheritance of a phenotype:
Recessive
For the phenotype to be expressed, the alleles must be homozygous.
Dominant
For the phenotype to be expressed, the allele can be homozygous or heterozygous.
Semi-dominant or
additive
The expression level of the phenotype in heterozygotes is intermediate between the

expression level of the phenotype in homozygotes for one allele and homozygotes
for the alternate allele.
Most of the terms defined on the previous page refer to single genes or loci, or to traits
(phenotypes) that are determined primarily by a single gene. Many individual traits, however,
are influenced by multiple genes. The description of the additive and interactive effects of
polygenic regulation of a trait completes the description of the traits genetic architecture.
Simple trait
Complex trait
Quantitative trait
Epistasis
A trait for which the genetic variance is due primarily to allelic variation at a single
locus.
A trait for which the genetic variance can be apportioned among multiple loci.
A complex traitsuch as body weightthat is measured on a continuous scale.
Polygenic influences can be additive (the effect of the genotype at each locus is
independent of the genotypes at other loci) or interactive (the influence of the
genotype at one locus is altered by the genotype at another locus) or both.
The result of an interaction of two or more loci on the expression of a phenotype
(e.g., see 2.B.2.c).
2.B.2. Selected topics

2.B.2.a. When is a gene not a gene?
How many of you have the cystic fibrosis gene? Eric Lander would ask as he began his
lecture on basic genetics at The Jackson Laboratorys annual Short Course on Biomedical
Genetics. Typically, about half the class would raise their hands. Of course, everyone in the
class had the gene, as virtually all of us do. In fact, if you did not have the gene, you would have
the disease. The cystic fibrosis gene is a chloride ion channel gene formally named cystic
fibrosis transmembrane conductance regulator or CFTR. When both copies of the gene in a
person are null alleles (i.e., the alleles produce either nonfunctional CFTR proteins or no
protein), the person is completely missing the CFTR chloride ion channel. The disease, cystic
fibrosis, results. In other words, people with two cystic fibrosis alleles at their CFTR gene have
the disease; those with at least one wild-type allele at their CFTR gene are normal. But we all
have the cystic fibrosis gene, whether or not we have the disease.
A gene is a heritable unit that influences a phenotype. An allele is a version of a gene that
produces a specific phenotype. A given gene may have only one known allele, in which case the
terms are effectively interchangeable. Or, a given gene may be polymorphic, with two or more
known alleles, in which case the terms gene and allele refer to different thingsfor example,
the gene leptin (Lep); the alleles leptin; obese 2 Jackson (Lepob-2J), leptin; obese (Lepob),
and the wild-type allele leptin; wild-type (Lep+).
The widespread practice of informally naming a gene after the deviant phenotype produced by a
mutation of the gene leads to occasional misunderstandings, even among geneticists. To say that
an inbred strain does not have the gene for some disease phenotype because it does not
express the disease is almost always incorrect (except where deletions are involved). The
practice of calling a mutant allele a gene has become entrenched because of its convenience,
and to simplify public communication, but it should be avoided in all scientific
communications.
Scientific communication is also not well served when investigators continue to use purely
phenotypic descriptors (originally used to name mutations) after the gene itself is identified. For
example, once a missense mutation in the carboxypeptidase E (Cpe) gene was shown to be the
molecular basis for the fat mutation, the correct nomenclature for the mutation became Cpefat
rather than fat.
2.B.2.b. How can an allele be dominant and recessive at the same time?
Formally, dominance is a phenotypic, not a genotypic, relationship. Mendel was unaware of our
concept of genotypes when he introduced the terms dominant and recessive to describe the
relationship between the phenotypes of traits he studied. Yet, for the sake of convenience, we
commonly refer to a dominant or recessive allele as the allele that produces a dominant or
recessive phenotype. This shorthand is generally clear, except in cases where the gene is
pleiotropic, i.e., it influences multiple phenotypes.
The 2008 Wikipedia provides an example of how multiple modes of inheritance can apply to a
single allele. The allele that produces the sickle cell trait in red blood cells is caused by a base
pair substitution in the beta-globin gene that replaces a glutamine with a valine. When only one
of the two copies of the beta-globin gene is the mutant allele, resistance to malaria is conferred.
This indicates that the allele is dominant. But both copies of the same mutant allele are needed
to produce anemia. This indicates that the allele is recessive. Furthermore, the phenotype of
blood cell sickling is co-dominantit occurs when only one copy of the mutant allele is present,
but it is more severe when both copies are the mutant allele. Thus, the same allele can display
different modes of inheritance if the gene is pleiotropic (has multiple effects), even though each
of the associated phenotypes has only one mode of inheritance.
2.B.2.c. When is dominance not dominance?

Dominance refers to a relationship of two traits that are controlled by the same locus. Masking
epistasis refers to a relationship of two genes, in which a particular genotype at one gene
prevents the expression of the other gene. For many phenotypes that involve complex
inheritance, dominance often gets confused with masking epistatis.
Coat color in mice provides a classical example. Among laboratory strains, at least five genes
have common variants that alter coat color. One of these, Tyr (tyrosinase), governs the influence
of the other genes on coat color because its activity is required to produce melanin, the pigment
responsible for coat and skin color. When Tyr is inactive, melanin is not produced, and albinism
results, no matter which alleles are at the other coat color genes. The albino trait masks the
expression of the other coat color genes. The albino trait is sometimes, incorrectly, said to be
dominant over other coat color phenotypes. But because both copies of the Tyr gene must be
inactive for albinism to result, the albino trait is recessive. Thus, albinism is a recessive trait that
masks the expression of other coat color genes; it is not dominant over other coat color
phenotypes. (For more details about coat color genes, see 2.F., Coat color genetics.)
2.B.2.d. Is a locus also a gene?

Often the terms locus and gene are used interchangeably; however, they do have different
meanings. A locus is a segment of a chromosome that is demonstrated, by mapping, to contain
at least one genetic modification that influences a trait. That chromosomal segment may contain
hundreds of genes or only one gene. Although naming a locus for a specific trait (for example, a
hyperlipidemia locus) does not mean the gene is known, once a locus is named, often the
putative gene that influences the trait is referred to by the same name. Thus, as of 2008, a
hypertriglyceridemia locus (e.g., Tgl1) may be said to contain the Tgl gene, even though a
specific gene within that locus has not been unequivocally specified.
On the other hand, numerous genes that were historically identified as loci before the specific
gene was known may still be referred to as loci. The albino locus is one common example.
We now know that the albino phenotype results when the gene tyrosinase (Tyr) is inactivated.
There is no need to continue to use the less precise term albino locus to refer to the gene;
however, the practice continues due to traditional usage. Thus, although gene and locus
have precise, and different, definitions, common usage often mixes the terms.
2.B.2.e. What do geneticists mean by segregation?

Segregation refers to the separation, in the parent, of two heterozygous alleles into different
gametes (and therefore, into different offspring) during meiosis. When geneticists refer to
segregation of a phenotype in a cross, they mean that the phenotype appears in some, but not all,
offspring because the genotype is not fixed. When a population is said to be segregating, it
means that the line is not fully inbred and that one or more loci are not fixed. It is worth noting
that variable expression of a phenotype is not sufficient evidence to claim that the phenotype is
segregating. For example, all genes affecting the phenotype may be fixed, but the phenotype
may display incomplete penetrance; i.e., environmental or random factors may prevent
expression of the phenotype in some individuals.
2.B.2.f. Complex genetic regulation and the myth of the Mendelian trait
When Mendel started his studies of inheritance, he specifically chose to study only binary
traitstraits with only two alternatives, such as purple or white flowers. He also limited his
study population to plants that bred true, i.e., plants that did not express other flower colors,
seed coat varieties, or any alternate variations of the other binary traits. As a result, Mendel
studied traits that were each controlled by a single gene. Today, we use the term Mendelian
trait when referring to binary traits that appear to be controlled by a single locus.
However, there may be no true Mendelian traits. The idea that some phenotypes may be
determined by a single gene is an oversimplification. It is more likely that all phenotypes are
determined by networks of genes. But to simplify the study of a trait, researchers often create
experimental conditions so that a single locus accounts for almost all of the genetically
determined variance of a phenotype within their study population. (For example, researchers
will study genetic regulation of a trait using only two parental genotypes rather than genotypes
representing the entire population of mice.) Under such conditions, we still use the term
Mendelian as shorthand to indicate that much of the genetic variance can be explained by a
single locus.
An example of how this shorthand can create confusion is when a variant or mutant allele for a
Mendelian trait is transferred to a different genetic background, as when creating a congenic
strain. Often, the expression of the phenotype disappears or is altered by interactions of the gene
of interest with other genes that differ between the two backgrounds and act epistatically as
modifier genes. The altered phenotype can be surprising to those who considered the trait
truly Mendelian. Thus, it is wise to keep in mind that, although we may use the term Mendelian
as shorthand to describe the inheritance of a trait under limited conditions, the genetic regulation
of the trait is unlikely to be that simple.
2.C. The basic inbred strain experimentstrain

differences capture genetic differences
The basic inbred strain experiment compares the expression of a phenotype between two inbred
strains. Any strain difference indicates the existence a genetic difference that governs the
phenotype. This difference could be due to a variant allele, a mutation, or a deletion or addition
of a gene.
This experimental strategy is possible because of the nature of inbred strains. Mice were
originally inbred to make expression of a trait as consistent as possible by removing genetic
variance. Inbreeding achieves this by 1) fixing an allele that produces the trait, so that alternate
alleles are excluded from the lineage, and 2) removing variation in the background genotype, so
that epistatic interactions do not vary. The result is a strain of mice in which all members are
genetically uniform. A profound consequence of this genetic uniformity is that, when comparing
two inbred strains under controlled conditions, any phenotypic difference between the strains
must result from a genotypic difference. For example, if researchers discover that mice from one
inbred strain have a different level of high density lipoproteins than mice from another inbred
strain, they have demonstrated that a gene or genes regulating blood lipids differs between the
two strains.
An additional advantage of inbreeding is that, by preserving exact genotypes, it facilitates
replication and greatly simplifies further study of the genetic regulation. Initial characterization
involves three steps. The first question is to resolve the degree of penetrance of the phenotype.
If the phenotype is expressed in some, but not all, individuals of a homogenic population (a
population in which all individuals have the same genotype, such as an inbred strain or an F1
population), it is considered incompletely penetrant. Incomplete penetrance must be taken into
account in further analysis.
The next question concerns the mode of inheritance. Typically, this is determined by crossing
the strains that differentially express the trait, i.e., by making F1 hybrids. Additional information
about maternal and paternal effects can be obtained by analyzing reciprocal F1 hybrids
hybrids produced by reversing the strains of the mothers and fathers.
The final question to resolve in a preliminary genetic analysis is whether the phenotype is
monogenic or polygenic, i.e., whether the trait is determined by one locus or more than one. To
address this question, typically, F1 mice are crossed to produce a population of F2 mice. The
distribution of values for the trait among the F2 mice is used to determine whether the trait is
monogenic or polygenic. The F2 mice can also be used to map the trait using linkage analysis,
thus identifying the approximate location of the gene (or genes) that controls expression of the
phenotypic difference.
2.D. Linkage analysis

Before it was possible to map a gene to a chromosome, researchers knew that not all traits
assorted independently. Two traits were considered linked when they appeared together in the
same individuals more often than expected by chance. Groups of linked traits were called
linkage groups.
If two traits distributed independently of each
other within a population, they were defined
as being from different linkage groups. The
more frequently two linked traits appeared
together, the closer they were considered to
be. In fact, the genetic distance between the
linked loci (that determined the linked
traits) was defined by the degree of
association between the linked traits. Thus,
even before researchers could determine the
physical positions of loci on chromosomes,
they could calculate genetic distances.
How to get from a strain difference to a locus:

mapping a gene.
1. Cross 2 inbred strains that differ in a trait of
interest.
2. Phenotype the offspring in the first generation that
produces genetically unique individuals (usually
an F2 or N2 generation).
3. Genotype the offspring using about 610 DNA
markers (that distinguish the 2 strains) per
chromosome, as evenly spaced as possible.
4. Correlate the trait variation (phenotype) with the
allelic variation (genotype) at each DNA marker.
5. Where this correlation is very strong, express the
results as statistical scores and chromosomal
positions (loci) or confidence intervals that are
likely to contain a gene that regulates the trait.
6. Using statistical procedures on the mapping data,
test for epistatic interactions among the mapped
loci.
(Adapted from a presentation given by Ken Paigen
[2007].)
Once researchers assigned conveniently

scored genetic markers to each linkage group,
they could map a newly discovered
phenotype by evaluating the association of
the new phenotype with those established
genetic markers. Because researchers could
calculate the genetic distance of the new trait
from other traits in the linkage group, they could identify a locus for the trait.
In 1971 Eva Eicher reported the first assignment of a linkage group (linkage group XII) to a
chromosome (Chr 19). Within a few years, assignment of the other linkage groups was
completed. By the mid 1980s, technical advances enabled the use of the numerous DNA
polymorphisms as markers for mapping. This method, which soon replaced the classical
physical and biochemical markers, allowed much more rapid and precise mapping of loci.
(Mapping is discussed further in 2.F.) Before the mid 1980s, it took years to map a simple trait;
today, multiple loci for complex traits can be mapped within months. Typically, the slowest
steps are the generation of the mapping cross (typically an F2 or N2) and the development of the
phenotype. The genotyping for hundreds of DNA markers, and association of the genotypic
variation with phenotypic variation among individuals in the cross, takes only days. The steps
involved in mapping the genes that govern a phenotypic variant are summarized in the sidebar,
How to get from a strain difference to a locus: mapping a gene.
2.E. Genotyping: what it is and how it is used

As a noun, genotype refers to the genetic makeup of a locus, a genomic region, or an entire
organism. As a verb, genotype is a way to determine or identify a genetic composition.
Genotyping has multiple purposes, which include the following:
For single loci:
To select appropriate subjects for an experiment when the phenotype does not clearly
distinguish mice with differential genotypes, as occurs with many quantitative traits or when
the phenotype is not directly observable.
To identify carriers, for example, when selecting appropriate breeders.
For portions of genomes or for entire genomes involving multiple loci:
To map genes.
To test for genetic contamination due to inadvertent outcrossing.
To determine lineage relationships among heterogenic mice.
Sometimes we can genotype mice by sighta specific coat color or an observable phenotype
such as a kinky tail or a behavior. But sometimes, we need sophisticated techniques such as a
biological assay or a variation in DNA sequence such as a single nucleotide polymorphism
(SNP). Table 3.1 provides an overview of some of the most frequently used methods of
genotyping. For information on genotyping strains of JAX Mice, refer to the sidebar, If you
need to genotype your JAX Mice or have questions about genotyping, in 13.F.2,
Confirming phenotypes and genotypes.
Table 2.3. Commonly used methods of genotyping.
Markers
Comments
Single nucleotide polymorphisms (SNPs):

Allelic distinction based on a single nucleotide
difference in a very short DNA sequence. Typically,
any 2 strains differ by thousands of SNPs.
Uses polymerase chain reaction (PCR):

reliable, simple, quick, inexpensive;
amenable to high throughput.
Suitable for large- and small-scale
production.
Useful for typing mice before they are bred.
Simple sequence length polymorphisms (SSLPs),

sometimes called microsatellite markers or MIT
markers:
Allelic distinction based on DNA sequence
differences in base pair repeats (usually CA or CG).
Typically, any 2 strains differ by hundreds of
SSLPs.
Same comments as for SNPs (above).
Primers based on sequence variation of a vector or

engineered gene, for example, sequence variation of
a transgenic vector.
Uses polymerase chain reaction (PCR):

reliable, simple, quick, inexpensive;
amenable to high throughput.
Used frequently to genotype transgenics,
knockouts, and knockins.
Biochemical markers (isoenzymes) and

immunological markers:
Comparison of proteins that exhibit different
physical characteristics, such as electrophoretic
mobility or enzymatic activity. Typically, any 2
strains differ by from 350 biochemical and
immunological markers.
Quick, technically simple, readily

reproducible, inexpensive.
Determinations can often be made from
plasma or red blood cell lysates.
Coat color and other observable phenotypes such as

body size, skeletal structure, behavior, reproductive
performance, tumor susceptibility, transplanted
tissue rejection.
Readily observable indicators of possible

mutations or breeding errors.
Can include disease onset and necropsy.
2.F. Mapping: definition and tools

Genetic mapping locates a region of a specific chromosome that contains one or more genes that
influences a trait. Mapping is of particular interest for genes that control diseases and is usually
the first step in identifying the gene itself, which can lead to new approaches for treatment of the
disease.
2.F.1. What is mapping? What is a centimorgan (cM)?

The process of genetic mapping usually involves a mapping crossa cross between individuals
of two different inbred strains that differentially express the trait of interest and that possess
numerous differences in genetic markers. (Markers are useful only when they distinguish
maternal- vs. paternal-derived alleles in the offspring.) The first generation of the cross (F1) is
homogenic (i.e., all individuals are identical to each other), with each pair of chromosomes
comprising one from the mother and one from the father. Gametes from a single F1, however,
will differ from each other because chromosomes assort independently during meiosis; each
gamete will carry a unique a mix of parental chromosomes.
By scoring the offspring in the F2 generation (the first segregating generation) for the genetic
markers and the trait, the researcher can identify which marker the trait associates with, thus
designating the chromosomal location of a gene or genes controlling the trait.
An additional feature of genetic mapping that permits resolution to a sub-region of a
chromosome involves recombination. When homologous chromosomes recombine during
meiosis, a genetic marker on one chromosome will cross over to the other chromosome. The
further apart two different markers are on one chromosome, the more crossovers will occur
between them. Thus, the frequency of crossovers between markers provides a genetic distance
between the markers that is approximately related to the physical distance between them. This
genetic distance is quantified in centimorgans (cM), a unit of measure of recombination
frequency that is equal to a 1% chance that a marker at one locus will be separated from a
marker at a second locus due to crossing over in a single generation. For example if 20% of the
offspring are the result of a recombination between two markers, the markers are said to be 20
cM apart. Binary traits, which have only two values (Mendels pea plant flowers that were
either purple or white, for example) can be treated exactly the same as genetic markers, and so
the genetic distance between a known genetic marker and a gene that controls a binary trait can
be determined directly in a segregating cross. For quantitative traits such as body weight, which
are measured on a continuous scale, the analytical procedure is somewhat different, but the
principle to determine the genetic distance between a marker and a gene is the same.
In mammals, recombinations do not occur entirely at random across the chromosome, but tend
to cluster in recombinational hotspots. As a result, centimorgans do not correlate precisely
with physical distances. Hundreds of hotspots are distributed across each chromosome. The
specific locations of hotspots along each chromosome differ among inbred strains.
2.F.2. Why map a trait?

Why do geneticists go to all this trouble just to determine the approximate chromosomal
location and number of genes that regulate a trait? As stated above, it is the first step in
identifying the specific genes that regulate a trait. In mice, this is relatively straightforward
when studying a trait for which a single gene accounts for most of the variance in a
phenotypeas with a mutant mousebecause researchers can create a segregating population
in which the phenotypic signal-to-noise ratio is very high. As a result, a large number of genes
have been identified by analyzing mutants.
However, for quantitative trait loci (QTLs), each of which accounts for only a portion of the
phenotypic variance of a trait, mapping has resulted in identification of far fewer genes. Yet,
researchers devote considerable effort to map quantitative traits because knowledge of map
locations enables further study of the gene, even before its identity is known. In particular,
researchers may construct congenic strains to isolate and highlight effects of the variant allele
on a defined genetic background and to study genetic interactions with other (modifier) genes.
Also, researchers continue to develop more advanced mapping techniques that improve the
success rate of gene identification using QTLs (e.g., see 2.F.5, How does bioinformatics
enhance mapping?).
2.F.3. What strategies are used for mapping?

Generally, initial mapping is performed using an F2 (segregating) cross with four to ten
polymorphic markers per chromosome. An N2 population (a backcross to one of the parental
strains) may be used if the mode of inheritance is known. However, an N2 population will
reveal only recessive, not dominant, traits contributed by the parental strain to which the F1
generation is backcrossed, and only dominant, not recessive, traits of the other parental strain.
Additive traits can also be detected in backcrosses, but the power to do so is diminished because
the full range of the trait will not be expressed. In addition, because the background genotype in
a backcross is less diverse than in an F2 cross, the potential to discover epistatic interactions is
diminished. Thus, generally an F2 population is used for mapping an uncharacterized trait, and
an N2 population is used to test specific hypotheses about map locations.
Panels of inbred strains that were constructed specifically for mapping may also be used (see
3.D, Recombinant strain panels). Such panels freeze the recombinations of a cross by
creating inbred strains from the progeny of a cross. Because mice of these mapping panels are
inbred, the identical chromosomal recombination, represented in a given strain of the panel, can
be reproduced in any quantity (for example, see Figure 3.8, Creation of recombinant inbred
[RI] lines). Use of a strain panel provides an opportunity to study traits with low penetrance,
where it may be necessary to generate multiple individuals before the trait can be observed in a
few individuals, and to study traits with high environmental variance, because effects of this
variance can be minimized by testing multiple individuals with the same recombinations. An
additional advantage of mapping panels is that information on the strains is cumulative; once the
strains are genotyped, studies of new traits do not require additional genotyping.
Initial mapping studies typically identify a locus that is 1030 cM long, usually containing more
than 100 genes. Often, congenic strains are then created to study the mapped mutant or variant
allele on a standard genetic background or to investigate interactions with other genes. If the
locus is too large to identify a few good candidates for the specific gene that accounts for the
phenotype of interest, the next step in this process is to fine mapreduce the size of the locus,
usually to less than 1 cM, to a region containing just a few candidates. Fine mapping was
traditionally accomplished using crosses of up to 1,000 mice, often with F3 or F4 generations, to
produce a large number of crossovers and enhance the mapping precision. However, strategies
using the continually growing databases of phenotypic and genotypic information
bioinformatics databasesare increasingly supplanting the large, advanced cross for fine
mapping.
2.F.4. What tools are used for mapping?

Two of the common genotyping methods (Table 2.3) are well suited for mapping studies: single
nucleotide polymorphisms (SNPs) and simple sequence length polymorphisms (SSLPs),
sometimes called microsatellite (or MIT) markers. The chromosomal density of these markers
for any strain comparison is much higher than the density for morphologic and biochemical
markers. Typically, hundreds to thousands of markers are polymorphic for most pairs of strains,
which permits the detailed mapping of any differential locus between all but the most closely
related strains.
2.F.5. How can bioinformatics be used to enhance mapping?

Bioinformatics refers to the computer access, integration, and analysis of collections of
biological data. The high-density genotyping information now available through multiple
databases can be employed to enhance mapping strategies. Four strategies using comparative
genomics and bioinformatics approaches were described by DiPetrillo et al. (2005); their
application was illustrated by Burgess-Herbert et al., (2008):
1) Comparative genomics uses synteny among species to narrow a locus for a phenotype.
Synteny refers to the comparable linear organization, between two species, of genes on a
chromosomal segment. Because of evolutionary relationships, long segments of
chromosomes from different related species contain homologous genes in the same order.
Comparing mice to humans, about 340 syntenic segments are
conserved (Pennacchio, 2003).
Application of bioinformatics techniques: from
quantitative trait locus to candidate genes.
2) Combined cross analysis compares results from different
mapping crosses for the same phenotype. Most of the
Burgess-Herbert et al. (2008) illustrate the use of
combined bioinformatics strategies to
phenotypic differences among inbred strains result from the
systematically specify candidate genes for
different mixes of the ancestral substrain genotypes (primarily
quantitative trait loci (QTL) for plasma levels of
M. m. domesticus and M. m. musculus), rather than fixed
high-density lipoprotein (HDL). Using combined
mutations. Thus, when trait loci for the same phenotype are
cross analysis, the researchers first identified a
found at the same chromosomal location in multiple crosses
QTL for HDL on Chr 12 that they could limit to a
26.3 megabase (Mb) interval containing 135
using different inbred strains, all strains displaying the one
genes. Next, by comparison to human HDL
phenotype are assumed to share the same ancestral allele of
mapping data, using comparative genomics, they
the same gene. In contrast, strains displaying the alternate
further reduced the locus to 12.0 Mb, containing 49
phenotype are assumed to share the alternative ancestral allele.
genes.
This assumption justifies the application of statistical methods
The researchers then used haplotype block
to combine data from multiple crosses of different inbred
analysis, employing data from a combination of
SNP resources (Wellcome Trust, Broad Institute,
strains to increase the power to map a given trait.
and Perlegen) and the Mouse Phenome Database
3) Interval-specific haplotype analysis, also called haplotype
(MPD; www.jax.org/phenome) to further reduce the
block analysis, uses SNP-defined haplotypes as markers to
locus to 2.9 Mb and the number of genes in the
interval from 49 to 11.
identify a chromosomal interval that could contain a causal
polymorphism. A haplotype, which is usually defined by
Finally, using haplotype association mapping with
data from the MPD, from published studies, and
threefive SNPs, is a combination of alleles at loci that are so
from their own laboratory, the researchers further
closely linked that they rarely recombine. Thus, a given
reduced the QTL from 2.9 Mb to 0.6 Mb,
haplotype generally derives from an ancestral source and is
corresponding to a final reduction to 7 candidate
unlikely to contain a DNA sequence variation. Among
genes.
different strains, haplotype polymorphisms at the same locus
The researchers then searched publicly available
are inherited from different ancestral sources, and thus,
sequence databases and gene expression
potentially, contain a causal polymorphism. Compared to the
databases to specify, from among the 7 possible
genes, the 3 most likely candidates based on their
typical 10 cM trait locus identified by standard mapping
altered DNA sequences or altered expression
crosses, haplotypes are very small. Thus, when haplotypes
profiles that were consistent with altered plasma
within a QTL are compared between strains in a cross, it is
HDL levels in the appropriate strains. Using these
often possible to considerably narrow the region that is
criteria, the researchers designated the aryl
proposed to contain the causal polymorphism without
hydrocarbon receptor (Ahr) as the most likely
candidate.
additional genotyping of the hundreds of mice traditionally
required for fine mapping.
Using these bioinformatics strategies, BurgessHerbert et al. (2008) suggest specific hypothesis-
4) Genome-wide haplotype association, unlike interval-specific

driven studies that could confirm Ahr as the gene
haplotype analysis, predicts the location of trait loci without
responsible for the effect of the Chr 12 QTL on
prior mapping studies. This analysis compares phenotypic
circulating HDL levels.
expression among multiple strains (a strain panel) with
haplotype differences across the genome, using a sliding
window of analysis. As this window moves through the marker map, strains with shared
haplotypes are grouped, the mean phenotype values of the haplotype groups are computed,
and permutations are performed to establish thresholds of significance. The statistical power
of the analysis is influenced by the composition of the strain panel, the density and
distribution of SNPs used, and the sliding window size. Genetic loci where haplotype
differences correlate with phenotypic differences can then be identified. Because such loci
often overlap, but are not identical to, loci for the same trait that were identified by other
means, comparison of the results often can narrow a trait locus to less than 1 cM. Although
genome-wide haplotype association is controversial because of the potential for false
positives (Chesler et al., 2001) and other concerns with the precision of the technique
(Cervino et al., 2007), Burgess-Herbert et al. (2008) state that, under specific conditions, the
technique has proven useful.
2.F.6. Once a locus is established, how is the gene found?

With increasing frequency, mapping strategies such as those mentioned on previous pages can
narrow a trait locus to just a few candidate genesthose genes potentially responsible for the
phenotypic difference. Once the locus is narrowed, testing each candidate gene can begin. Such
studies include sequence analysis (determination of genetic polymorphisms in the candidate
genes themselves that could explain predicted functional differences) and expression analysis
(determination of whether differences in expression level of the product of the candidate genes
correlates with phenotypic differences across strains). While positive results from such studies
can enhance the candidacy of a gene, they do not constitute definitive proof that a candidate
gene is the responsible gene. However, if a new mutation has arisen on an inbred genetic
background and it is kept on that strain (making it coisogenic to the original strain), then
identification of the mutant-specific nucleotide change that maps within the critical interval is
often considered sufficient proof.
If the mutation or variant is not on a coisogenic strain, definitive proof requires
complementation testing or gene conversion. Complementation testing can be carried out when
the variant being tested is recessive and when another recessive allele exists that is known to
produce the same phenotype. Mice that carry the known allele (either heterozygously or
homozygously) are mated with mice that carry the allele being tested. If the phenotype does not
appear in any offspring, the allele being tested is said to be complemented by a wild-type
allele from the other parent. Complementation is taken as proof that the tested allele and the
known allele exist at different loci. If, on the other hand, the variant phenotype does appear in
the offspring, the alleles are called non-complementary, which means that the tested allele and
the known allele are at the same locus.
An alternative proof is gene conversion by homologous recombination. This may entail knockout or knock-down of a wild-type allele, or replacement of a critical sequence in a wild-type
allele with a putative mutant sequence. If such procedures convert a strain that does not express
the mutant phenotype to a strain that does (or vice versa, thus rescuing the phenotype), it is
taken as proof that the candidate gene is responsible for the mutant phenotype.
For QTL candidate gene analysis, complementation or homologous recombination studies are
difficult to perform because each locus typically has a relatively small impact on the phenotype.
However, the continued development of bioinformatics resources and techniques such as
interval-specific and genome-wide haplotype mapping, when combined with the development
of new animal resources such as the Collaborative Cross (see 3.D.2.d), should achieve sufficient
precision in gene mapping to permit scientists to routinely narrow the search to a limited
number of candidate genes for each QTL, and eventually, to unequivocally identify quantitative
trait genes through mapping studies alone.
2.G. Coat color genetics

The coat color of mice is under complex
genetic regulation; at least 50 genes are known
to influence coat color. The coat color genes
participate in a hierarchy of epistatic
relationships and include one of the most
polymorphic genes known in mice, the
nonagouti gene. Because of the availability of
coat color varieties and the simplicity of
scoring the phenotypes, coat color has been
studied as a model genetic system from the
beginning of modern mammalian genetics
(Cunot, 1902).
The complex genetics of coat color as a

model system.
The coat color system in mice is one of the
best-characterized genetic systems in
mammals. If the polymorphisms, the allelic
hierarchies, the epistatic interactions, and the
pleiotropic effects of the coat color genes
provides a typical example of how genes
function in a system to regulate phenotypic
expression, we can expect that sorting out the
genetic regulation of most traits will continue
to provide mammalian geneticists with
interesting challenges well into the future.
Coat color was an important marker in early mapping studies that established genetic linkage
groups. Coat color is used today as a powerful quality control marker for genetic contamination,
and as a marker for the segregation of linked genes in balanced stocks. (For an example of the
practical use of coat color to maintain a balanced stockthe BKS.Cg-m +/+ Leprdb/J [000642]
strain of JAX Micesee Appendix I, Using a Balanced Stock to Carry a Recessive Mutation
That Is Sterile or Lethal, Including Embryonic Lethal.)
Here, we present an overview of coat color genetics in mice
that illustrates how genes can interact in a system to regulate
the expression of a phenotype. Other genes for common coat
color mutants are listed in Appendix E, Coat Color Alleles for
Popular Strains of JAX Mice. For full detail on all the coat
color genes, visit the MGI website, www.informatics.jax.org.
2.G.1. The interactions of coat color genes
Coat color was one of the earliest

phenotypes studied by researchers.
th
In the 19 century, mouse fanciers bred mice

on the basis of coat color. Scientists studied
coat color because it was a heritable trait they
could identify easily, even if they did not
understand how it worked or how many genes
were involved (Silvers, 1979).
C. C. Little, the founder of The Jackson
Coat color is determined directly by the amount and type of

Laboratory, studied coat color at Harvard
beginning in 1907. It was this work that led him
melanin in the pigment granules and by the shape of the
to inbreed sisterbrother pairs of mice carrying
granules. Melanin pigment granules are produced in the
recessive genes for the dilution, brown, and
melanosomes, organelles of the melanocyte (the pigmentnonagouti genes, which resulted in the dbr
producing cell), and transported to skin and hair follicle
strain of inbred mice. (Later, the name of this
keratinocytes to provide skin and hair with color. Melanin
strain was changed to dba, after the three
recessive genes. In 1950 it was renamed
production is controlled by alpha melanocyte stimulating
DBA.)
hormone (!MSH), a hormone that binds receptors on the
melanocyte cell surface to initiate a signal transduction process
that activates tyrosinase. Tyrosinase is the enzyme that converts tyrosine to dopaquinone in the
melanosome and begins the synthesis of melanin. A series of reactions follow that ultimately
produce pheomelanins (yellow/red pigment) and eumelanins (black/brown pigment). The
melanin pigments are organized into granules, which can vary in shape and surface texture.
Granules are then transported out of the melanocyte to the keratinocytes.
Figure 2.2. The regulation of pigment synthesis in mice.
2.G.2. Five genes responsible for the most common coat color
variations in laboratory mice
Following is a brief discussion of five genes responsible for the most common varieties of coat
color in laboratory mice.
The nonagouti locus: a (Chr 2)

The nonagouti locus is named after the recessive allele that prevents expression of the agouti
protein. The agouti protein produced by the wild-type allele binds the !MSH receptor,
preventing !MSH-initiated signaling and providing different signals of its own that regulate a
eumelanin/pheomelanin switch. The result is an alternating pattern of pheomelanin (yellow/red)
and eumelanin (black/brown) bands on the hair shaftyellow on the distal portion and black on
the proximal portion. The overall appearance of the mouse is brown, but separation of the fur on
the skin surface reveals the black band of fur near the skin. The agouti allele (A) is dominant
over the nonagouti allele (a). The recessive nonagouti allele a permits unrestricted activation by
!MSH, resulting in fur that is entirely black. The nonagouti locus is highly polymorphic; at
least 15 additional alleles of the nonagouti locus exist.
The albino locus: Tyr (Chr 7)

The wild-type allele of the albino locus, Tyr+, produces tyrosinase, which converts tyrosine to
dopaquinone, initiating the series of reactions that produce melanin. The recessive allele Tyrc,
for which the albino locus is named, produces an inactive form of tyrosinase, and therefore
produces no melanin, resulting in albinism. Homozygosity for Tyrc results in masking epistasis
of all other coat color genes.
The brown locus: Tyrp1 (Chr 4)

The wild-type allele of the brown locus, Tyrp1+, produces tyrosinase-related protein 1 (TYRP1),
an enzyme that complexes with, and may stabilize, tyrosinase in the melanosome membrane.
TYRP1 catalyzes the last step in eumelanin production and promotes its polymerization into
melanin granules. The wild-type Tyrp1+ allele produces black eumelanin, and a recessive
mutant Tyrp1b allele produces brown eumelanin. The melanin granules produced in
homozygous Tyrp1b mice are more rounded, compared to the normal ovoid shape, and they
contain less eumelanin.
The dilute locus: Myo5a (Chr 9)

The wild-type allele of the dilute locus, Myo5a+, produces myosin Va protein, which is involved
with transport of organelles in cells. In mice homozygous for the recessive Myo5ad (dilute)
allele, melanosome trafficking defects result in uneven release of the melanin granules to
keratinocytes. As a result, the overall coat color of the mouse takes on a lighter (dilute)
appearance, whatever the color itself is. Thus, the dilute locus is considered a modifier of other
coat color loci.
The pink-eyed dilution locus: Oca2 (Chr 7)

The pink-eyed dilution locus in the mouse is named after the mutation p that results in
hypopigmentation of the eyes, skin, and fur. The gene in the mouse, Oca2, is named for the
deficiency in the homologous human protein that is associated with oculocutaneous albinism
type II. The function of the Oca2 gene product is not known, but it localizes to the melanosome
(and other organelle) membranes, and it may regulate the pH of the melanosome. The
eumelanin content of melanin granules in mice that are homozygous for Oca2p (the pink-eyed
dilute mutants) is greatly diminished, resulting in pink eyes and diluted coat color. The Oca2
gene is linked to the Tyr gene by < 20 cM.
2.H. For more information

Books accessible online from the Mouse Genome Informatics (MGI) website at
www.informatics.jax.org/resources.shtml:
The Anatomy of the Laboratory Mouse. Cook M. 1965. Academic Press. M.R.C. Laboratory
Animals Centre, Carshalton, Surrey, England.
Biology of the Laboratory Mouse. 1968. Green EL (ed). Dover Publications, Inc., NY.
The Coat Colors of Mice, A Model for Mammalian Gene Action and Interaction. 1979.
Silvers WK. Springer Verlag.
Mouse Genetics: Concepts and Applications. 1995. Silver L. Oxford University Press.
Origins of Inbred Mice. 1978. Morse HC III (ed). Academic Press. National Institute of
Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.
Other resources:
Festings characteristics of inbred mice:
www.informatics.jax.org/external/festing/search_form.cgi.
The Laboratory Mouse. Hedrich HJ (ed.) Elsevier, London.
The Mouse in Biomedical Research, 2nd edition. Fox JG et al. (eds). American College
Laboratory Animal Medicine.
2.I. References
Burgess-Herbert SL, Cox A, Tsaih S-W, Paigen B. 2008. Practical applications of the
bioinformatics toolbox for narrowing quantitative trait loci. Genetics. epub ahead of print:9
October 2008 (10.1534/genetics.108.090175).
Cervino ACL, Darvasi A, Fallahi M, Mader CC, Tsinoremas NF. 2007. An integrated in silico
gene mapping strategy in inbred mice. Genetics. 175:321333.
Chesler EJ, Rodrigues-Zas SL, Mogil JS, Usuka J, Grupe A, et al. 2001. In silico mapping of
mouse quantitative trait loci. Science. 294:2423.
Cunot L. 1902. La loi de Mendel et lhrdit de la pigmentation chez les souris. Arch. Zool.
Exp. Gen. 3:2730.
DiPetrillo K, Wang X, Stylianou IM, Paigen B. 2005. Bioinformatics toolbox for narrowing
rodent quantitative trait loci. Trends Genet. 21:683692.
Eicher E. 1971. The identification of the chromosome bearing linkage group XII in the mouse.
Genetics. 69:267271.
Human Genome Project Information. 2008.
www.ornl.gov/sci/techresources/Human_Genome/home.shtml (accessed October 2008).
Paigen K. 2007. The origins of experimental strategies in mouse genetics. Presentation given at
The Jackson Laboratorys Short Course on Medical and Experimental Mammalian Genetics.
Pennacchio LA. 2003. Insights from human-mouse genome comparisons. Mamm Genome.
14:429436.
Silvers WK. 1979. The Coat Colors of Mice: A Model for Mammalian Gene Action and
Interaction. Springer Verlag. (Available online at www.informatics.jax.org/wksilvers)
Yang H, Bell TA, Churchill GA, Pardo-Manual de Villena F. 2007. On the subspecific origin of
the laboratory mouse. Nat Genet. 39:11001107.
YoshikiA, Moriwaki K. 2006. Mouse phenome research: implications of genetic background.
ILAR J. 47:94102
25
Chapter 3: Categories of Laboratory Mice

Definitions, Uses, Nomenclature
Joanne M. Currer, Carol Linder, Jennifer Corrigan, Barbara Witham, Muriel Davisson,
Jennifer Merriam, Kevin Flurkey
About 100 years ago, C. C. Little began inbreeding mice for his studies on the genetics of
cancer. Since then, advancements in genetics and technology have allowed scientists to develop
derivitive inbred strains and strain panels that are tailored to specific research needs. Because of
the wide variety of these derivative strains and the ability to construct precise allelic mixes
combined with the inherent advantages of the inbred strainthe laboratory mouse continues to
be the most versatile and valuable tool in mammalian genetics a century after C. C. Little first
inbred his mice.
The objective of this chapter is to provide an overview of the various categories of laboratory
mice, including information about why and how they were developed and how they are used in
research. The chapter is organized as follows:
3.A. A few words about nomenclature and terminology................................. 26
3.A.1. Nomenclature ................................................................................ 26
3.A.2. Strain definition and breeding terminology ................................ 27
3.B. Inbred strains and crosses.......................................................................... 28
3.B.1. Inbred strains, substrains .............................................................. 28
3.B.2. Wild-derived inbred strains.......................................................... 36
3.B.3. F1 and F2 hybrids ......................................................................... 38
3.B.4. Multi-strain crosses....................................................................... 42
3.C. Strains with single-locus mutations .......................................................... 45
3.C.1. Spontaneous, induced, and genetically engineered
mutant strains ................................................................................ 46
3.C.2. Congenic and conplastic strains................................................... 54
3.D. Recombinant strain panels......................................................................... 59
3.D.1. Overview ....................................................................................... 59
3.D.2. Recombinant inbred (RI) strain panels........................................ 62
3.D.3. Recombinant congenic (RC) strain panels .................................. 65
3.D.4. Chromosome substitution (CS) strain panels and
genome-tagged mice..................................................................... 67
3.E. Mice with chromosomal aberrations ........................................................ 70
3.F. References .................................................................................................. 73
For details about these categories of mice, see
Silver (1995),
Berry and Linder (2007),
the Festing inbred strain database, available at
www.informatics.jax.org/external/festing/mouse/STRAINS.
For lists of JAX Mice organized by these categories, visit www.jax.org/jaxmice/type.
26 Section II: Using Mice in Research
3.A. A few words about nomenclature and terminology

3.A.1. Nomenclature
Mouse strain nomenclature provides two types of technical information: the background or
parental strains upon which the strain is based, and details about relevant genes and alleles. The
strain name can also include such information as who developed the strain, where it was
developed, and where it is currently maintained.
When publishing results, it is important that investigators use the full strain name at least once
so that readers can correctly interpret research results and precisely reproduce research.
Table 3.1 shows where to find information related to nomenclature throughout this handbook
and elsewhere.
Table 3.1. Sources of information about nomenclature.
Type of information
Location of information
Nomenclature guidelines
In this handbook
Discussions by category in this chapter
Summary in Appendix A, Strain Nomenclature Quick
Reference
On the web
Guidelines on interpreting nomenclature:
www.jax.org/jaxmice/faq/nomenclature_hints
Online nomenclature tutorial
www.jax.org/jaxmice/nomenclature
Other
Mouse strain and genetic nomenclature: an abbreviated
guide (Eppig, 2007)
Official nomenclature rules

(International Committee on
Standardized Genetic Nomenclature
for Mice)
Mouse Nomenclature Home Page:

www.informatics.jax.org/nomen
Official nomenclature for each strain

of JAX Mice
Individual strain datasheets

www.jax.org/jaxmice/query
Lab and investigator codes used within

strain names to denote developers and
holders of strains.
Institute for Laboratory Animal Research (ILAR), U.S.

National Academy of Sciences, Washington, DC:
http://dels.nas.edu/ilar
How to register the name of a new

mouse strain
Web form:
www.informatics.jax.org/mgihome/submissions/strains
Email assistance:
[email protected]
How to submit a proposed locus

symbol
Web form:
www.informatics.jax.org/nomen/nomen_submit_form.shtml
Email assistance:
[email protected]
How to submit the name of a new

mutation
Web form:
www.informatics.jax.org/nomen/allmut_form.shtml
Chapter 3: Categories of Laboratory MiceDefinitions, Uses, Nomenclature 27
3.A.2. Strain definition and breeding terminology

Throughout this handbook, we use very specific terminology related to strain definition and
breeding. Tables 3.2 and 3.3 provide definitions and, where necessary, examples.
Table 3.2. Strain definition terminology.
Term
Definition and comments
Stock
An isolated, interrelated breeding population.
Line
A pedigreed stock with a known lineage to a single breeding pair.
Inbred strain*
A line of mice that has been propagated by a single lineage of sisterbrother mating for
at least 20 generations. All mice of an inbred strain share the same 2 founders.
Subline
A stock of inbred mice that has been reproductively separated from the parental strain.
Inbred
substrain*
A subline of mice that has been separated from the parental inbred strain for 20
generations or that has any known, fixed genetic difference, even if that difference is at
one gene.
Coisogenic
strain
A variant inbred strain of mice that differs from an established inbred strain by a
mutation at only a single gene.
Unique nomenclature for lines of JAX Mice that have founders of 3 or more strains,
founders of unknown genetic background, or outbred founders. A line designated with
STOCK in the name mayor may notbe inbred. For example, as of 2006, STOCK
Tg(TIE2GFP)287Sato/J (003658) could not be called an inbred strain because only 15
generations of sister-brother mating could be confirmed.
*Definitions condensed from Silver (1995).
STOCK
Note: Sometimes the term strain is used as shorthand for inbred strain, and sometimes the
term strain is used to refer to an isolated breeding population that does not fulfill all
criteria for an inbred strain. A reader should not assume that strain refers to an inbred
strain unless it is stated explicitly.
Table 3.3. Breeding terminology.
Term
Definition
Examples
Incross
A cross of 2 animals of the same

homozygous genotype.
Breeding mice of the same inbred strain.
Outcross
A cross of 2 animals of unrelated

genotypes. Outcrossed stocks are
commonly referred to as outbred.
Breeding mice of 2 different inbred strains.

Breeding genetically different F1 hybrid mice.
Breeding any unrelated mice.
Intercross
A cross of any 2 animals that are

identically heterozygous at a particular
locus.
A cross between any 2 siblings that are
genetically different (that are not from
the same inbred strain).
Breeding mice of the same F1 hybrid

genotype.
Breeding siblings when creating an inbred
strain.
Backcross
A cross of 2 animals, one that is

heterozygous at a locus under
investigation, and one that is
homozygous for one of those
heterozygous alleles.
Breeding an F1 offspring back to a parental

genotype.
Breeding progeny back to the parental
background genotype when developing a
congenic strain.
Definitions condensed from Silver (1995).
3.B. Inbred strains and crosses

Inbred mouse strains and the crosses created from them are the workhorses of mammalian
genetics. They have been used by researchers since their creation early in the 20th century. Many
have been maintained for more than 200 generations. The inbred strain is such a powerful
research tool that, today, it is the foundation for most mouse models used in biomedical
research.
3.B.1. Inbred strains and substrains

Mice were originally inbred to make expression of a trait as consistent as possible by removing
genetic variance. The result is a strain of mice in which all members are genetically uniform. A
profound consequence of this genetic uniformity is that, when comparing two inbred strains
under controlled conditionsthe basic inbred strain experimentany phenotypic difference
between the strains must be due to a genotypic difference. Researchers have exploited the basic
inbred strain experiment to greatly accelerate the development of our understanding of
mammalian genetics. The homogeneity of the inbred strain also has enabled the derivation of
powerful genetic tools such as genetic crosses and inbred strain panels. This genetic
uniformity has become even more important with the advancement of genetic engineering.
Because noise from the genetic background is minimized, the expression of engineered genes
can be studied most effectively in inbred strains.
3.B.1.a. Definitions, characteristics, and value

3.B.1.a.1. Inbred strains
An inbred strain is a line of mice that has been inbred by intercross sibling (filial) mating for at
least 20 generations (F20). Although any generation might include a large number of mice, each
generation in the lineage of the strain comprises only two mice (one sisterbrother pair). With a
mean generation time of about three months, it generally takes about five years to create a fully
inbred strain by sibling matings. An acceptable alternative breeding scheme is offspringparent
mating, used infrequently because inbreeding progresses more slowly than with sibling mating.
3.B.1.a.2. Substrains
A substrain refers to an inbred strain that is reproductively isolated from its founder inbred
strain and that has any fixed genetic difference from that strain. This difference could be as
small as an allelic variant at a single gene. Any heritable change that has been identified by
either genetic or phenotypic analysis is sufficient to define a substrain. Whenever researchers
identify a substrain, they should use appropriately updated substrain nomenclature.
Even if a genetic difference from the founder strain is not explicitly identified, a reproductively
isolated population is considered a substrain when one of two conditions occur:
If, between the 20th and 40th generation of an inbred strain, a breeding pair is removed to
establish a new line (International Committee on Standardized Genetic Nomenclature for Mice,
2007). Typically, there is a greater than 50% likelihood that residual heterozygosity is still
present in the strain up to the 36th generation (Bailey, 1978), and about a 20% likelihood by the
40th generation. Thus, mice in the newly separated line are likely to be different enough to
create a new substrain even after just one generation of separation. (Beginning with the first
separated generation, the new line will differ permanently from the founder at, on the average,
12.5% of the segregating loci in the founder strain at the time of separation [Figure 3.2]).
If, after the 40th generation of an inbred strain, a subline is reproductively isolated for an
additional 20 generations (International Committee on Standardized Genetic Nomenclature for
Mice, 2007). At this point, genetic drift will have resulted in the fixation of, on the average,
twothree new alleles in the substrain and twothree different new alleles in the parental strain
(see sidebar, The rate of genetic drift in mice, in 3.B.1.d.2).
Festing (1979) points out that once a substrain is created, in theory, the parental strain should
also be considered a substrain, because both strains will continue to diverge from the generative
genotype at about the same rate due to genetic drift.
Besides the general advantages given on the previous page, inbred strains of mice share the
following characteristics and advantages:
Each inbred strain has a unique set of phenotypes that distinguishes it from other inbred
strains. Some phenotypes, such as coat color, are invariant. Other phenotypes, such as
circulating levels of glucose, are highly dependent on
environmental interactions.
What are inbred strain panels? How are they
used?
Phenotyping data for individual inbred strains and substrains
are cumulative and comparable within and between
An inbred strain panel is a collection of inbred
strains that is evaluated for one or more
laboratories (Festing, 1999).
phenotypes under controlled conditions (e.g., in
The phenotypic and genetic consistency of inbred strains
the same laboratory, at the same time, and at the
enhances the potential to identify
same age). Strain panels are of 2 types: 1) a
collection of independently-derived strains, or 2) a
genes that modify expression of specific mutations, and
collection of derivative strains developed from a
genetic interactions in diet, drug, and gene therapy studies.
cross of 2 or more founder strains (see 3.D,
With fixed major and minor histocompatibility loci, each
member of a given inbred strain is a perfect recipient for
tissue from any other member of the same sex. However, the
Y antigen, which is expressed only in males, can influence
whether or not transplanted tissue is accepted.
The use of inbred strains has enabled accumulation of
knowledge of the mouse genome over decades. This cumulative
knowledge provides synergies for new discoveries, making the
inbred mouse the preferable choice for current research.
3.B.1.b. Considerations
Recombinant strain panels). Both types of strain

panels are used for comprehensive analysis of
phenotypic variation and interrelationships, and
as tools for genetic mapping.
Strain panels enhance the advantages of inbred
strains. Once a new phenotype is characterized in
a number of well-chosen strains, its
interrelationship with other phenotypes can be
evaluated using previously published data for
those strains. A shared strain distribution pattern
among phenotypes suggests that the phenotypes
may be causally linked, and critical hypothesistesting experiments can be specified. In addition,
because extensive genetic and phenotypic data
for many strains are availableand are
continually accumulatingwell-chosen strain
panels provide the opportunity to investigate
phenotypegenotype relationships without the
need for additional DNA sequencing. Especially
useful is the potential for fine mapping of a
phenotype using established genetic information,
sometimes called in silico mapping.
Considerations for the use of inbred strains and substrains

include the following:
An inbred strain or substrain is representative of only a single
genotypenot laboratory mice in general. Thus, results of
research using individual strains may be idiosyncratic and
should not automatically be applied to all laboratory mice.
Although descended from the same inbred strain, substrains
may have very different phenotypes and genotypes. The
For more information on inbred strain
panels
greater the number of generations that separate the substrains,
the further apart they are genetically. Following are two
The Mouse Phenome Database (MPD) provides a
compilation of strain panel studies. See
examples that highlight the genetic differences that can occur
www.jax.org/phenome.
between even closely related substrains:
Strain panels and their applications are described
C57BL/6J (000664) mice carry a null mutation for the
in the Macroarray Resource Manual, available at
nicotinamide nucleotide transhydrogenase gene (Nnt).
www.jax.org/jaxmice/support.
Although pancreatic !-cell glucose sensing is affected
(Freeman et al., 2006), glucose clamp studies demonstrate
that glucose clearance is normal (Berglund et al., 2008) (For details see sidebar in 8.A.3.a.).
C57BL/6JEiJ (000924) and C57BL/6NJ (005304) mice carry the wild-type allele for Nnt.
The CBA/J (000656) strain is the only CBA substrain to carry the Pde6brd1 retinal
degeneration allele (Sidman and Green, 1965), which causes blindness by weaning age.
Also, CBA/J mice are not histocompatible with CBA/CaJ (000654) mice (Green and
Kaufer, 1965), although they share the same H2 haplotype. Either genetic drift or genetic
contamination (see 3.B.1.d for a discussion) could have caused these differences.
For substrain lineage charts of the most common inbred strains, see Appendix C, Origins and
Relationships among Common Strains and Substrains of Laboratory Mice.
During the process of domestication of the mice that were used to develop the classical strains
of laboratory mice, selection for early, high fecundity was almost inevitable, as was selection
for docility. Thus, even a range of inbred strains or substrains represents a biased
representation of genetic variance for mice (e.g., Yang et al., 2007).
The process of inbreeding diminishes individual genetic diversity and fixes deleterious
alleles, so that, in general, inbred strains and substrains suffer from inbreeding depression. A
dramatic example of this is the consistently poor breeding performance of inbred strains
compared to genetically mixed stocks.
3.B.1.c. Maintenance breeding strategies

Generally, inbred strains and substrains are maintained by continued sibling mating, even after
the 21st generation. But genetic drift, which will continue to affect the genome, must be
minimized (see discussion in 3.B.1.d.). Therefore, in production facilities such as The Jackson
Laboratory, inbred strains are maintained and expanded using foundation stocks, which tightly
controls the numbers and genetic quality of progenitors used to expand the inbred strain. An
additional strategy is to freeze embryos or gametes of a specific generation and refresh the strain
periodically using the frozen material. (For details on how we minimize genetic drift using both
strategies at The Jackson Laboratory, see Chapter 8, Genetic Quality ControlPreventing
Genetic Contamination and Minimizing Genetic Drift.)
In research facilities where investigators breed their own mice, it is surprising how easy it is to
lose the genetic homogeneity that distinguishes inbred mice. To produce enough mice for a
research project, investigators often expand an inbred strain by multiple matings. If these
matings are random, after a few generations, the genetic reliability of the inbred strain is lost.
The result is a stock of mice, not a substrain. If these matings are sibling matings, any single
lineage could be used to propagate the strain. However, if the parental strain exists elsewhere,
this single lineage would lead to a new substrain. To avoid these problems, we recommend
replacing the breeding line with new founders from the supplier (sometimes called refreshing
a strain) every five generations at a minimum. Figure 3.1 illustrates how on-site breeding
without replacement can inadvertently lead to new substrains.
Figure 3.1. How isolated breeding can inadvertently create substrains.
Assuming that the XYZ/S strain has no residual heterozygosity from the original founders (see 3.B.1.d),
mice shipped to Lab A are genetically virtually identical to all other XYZ/S mice of the same generation.
However, after 20 filial generations at Lab A, a new substrain will be created. At the rate of one newly
fixed mutation approximately every 7 generations (see sidebar, The rate of genetic drift in mice, in
3.B.1.d.2), mice of this new substrain, XYZ/SA will have, on the average, 56 fixed differences from their
XYZ/S contemporaries.
Certain inbred strainssegregating inbred strainsare maintained with forced heterozygosity.

This is usually done to keep both a mutant and wild-type allele on a consistent genetic
background. (See Section 3.C.1.c.3, Breeding strategies, for details.) Two examples:
129P3/J (000690), which is maintained by mating a light chinchilla (Tyrc/Tyrc-ch) with an
albino sibling (Tyrc/Tyrc) at each generation.
C57BL/6J-Ghrhrlit/J (000533), which is maintained by mating a heterozygote by homozygote
mutant at each generation.
3.B.1.d. Individuals in inbred strains are not completely genetically

identicalthe influence of residual heterozygosity, genetic drift, genetic
contamination, and copy number variation (CNV)
Except for the sex difference, mice of an inbred strain or substrain can be regarded as genetically
and phenotypically uniform. They are almost completely homozygous; that is, both alleles at
each locus are identical at virtually all loci. However, some real, and potentially changing,
genetic variation exists for all
Figure 3.2. Effects of inbreeding on homozygosity in individuals and in a
inbred strains due to residual
stock.
heterozygosity, genetic drift,
copy number variation (CNV),
and the possibility of genetic
contamination.
3.B.1.d.1. Residual
heterozygosity
Residual heterozygosity can be
defined as the proportion of
heterozygous loci in the original
cross that is not yet genetically
fixed at a given generation of
inbreeding (Bailey, 1978). In an
inbred line at F20, residual
heterozygosity is almost
certainly still present unless the
founders were closely related.
The likelihood that residual
heterozygosity has been
The solid lines show the difference in the percentage of original heterozygosity in the
eliminated in a cross of two
F1 that is lost at each generation for individuals (gray squares) vs. the lineage (gray
circles). The dashed line shows the likelihood of all original residual heterozygosity
unrelated founders does not
being eliminated from the line at any generation. Redrawn from Silver (1995).
reach even 0.5 until about F36
(dotted line in Figure 3.2). And,
it is not until F60 that this
likelihood reaches 0.99, when we can be confident that none of the heterozygous loci in the
founders are still segregating in the strain. As Bailey (1978) states, Purity is not easily attained.
The effect of inbreeding on homozygosity in individuals and in a lineage of a strain is shown in
Figure 3.2. The solid gray line (squares) indicates the percentage, on the average, of
heterozygous loci that existed in the original cross that are fixed
in each individual of a generation. At F20, typically 98.599.0% of
Residual heterozygosity in inbred mice at
generation F21: How did we compute the
the originally heterozygous loci are homozygous in each individual
number of genes to be 99?
mouse. Furthermore, there will be a slightly different set, and a
Number of structural genes
~25,500
slightly different total number, of heterozygous genes in each
parent. The residual heterozygosity that is permanently fixed to
Residual heterozygosity in the
ancestral founders for many inbred
homozygosity at each generation is represented by the solid black
strains (Bailey, 1978)
x 33%
line (gray circles). Note that if expansion of the inbred line occurs
Number
of
segregating
genes
in
at F21, the parents used for this expansion could easily still be
the ancestral founders
7,650
heterozygous at 99 genes (see sidebar).
th
Genes still segregating at the 20 generation of
sisterbrother mating:
One of the main points of inbreeding is to eliminate residual
Percentage (Silver, 1995)
1.3%
heterozygosity within a line. The actual differences in levels of
Quantity
99
initial heterozygosity combined with the random transmission of
alleles at each generation will determine when this is accomplished
Note: This estimate will vary directly with the
actual number of genes that are segregating in
for any given line (whether fewer or more than 20 generations of
the founding pair.
inbreeding is required). Figure 3.2 shows that, for a single locus
that is heterozygous in both parents, the likelihood that this locus
will be fixed to homozygosity for the lineage in one generation is 0.125.
Thus, if the parental strains differ in only three unlinked loci, there is a .1253 = .002 likelihood
(a one in 500 chance) that complete homozygosity will be accomplished in one generation.
Obviously, with increasing levels of residual heterozygosity, this likelihood diminishes. The
dashed line in Figure 3.2 illustrates the likelihood that original residual heterozygosity is
eliminated by a given generation when the original residual heterozygosity is more typical of
common crosses (more than 500 loci) and when linkage is considered.
The rate of genetic drift in mice.
The calculated rate of genetic drift depends on the
estimate of the spontaneous mutation rate. In mice,
this rate is difficult to measure accurately because of
the sample size needed for a reliable estimate. Drake
et al. (1998) calculated a mutation rate of about 1.1 x
-5
10 per zygote using data from control groups
(1,485,036 progeny) in the extensive radiation studies
performed at Oak Ridge, Harwell, and Neuherberg. In
these studies, female mice that were homozygousrecessive for 7 marker traits were mated with males
that were homozygous for all the corresponding wildtype alleles. Spontaneous mutations in the males
germ cells that inactivated one of these wild-type
alleles would produce offspring that expressed the
recessive trait, revealing the mutation.
Assuming 25,500 genes in the mouse genome, these
results indicate that the rate of spontaneous mutation
is 1 per 3.57 zygotes. Thus, new germline mutations
will arise at the rate of 1 every 1.8 offspring. With strict
sisterbrother mating, and assuming no selective
pressure, one quarter of these spontaneous mutations
will eventually be fixed to homozygosity in the strain;
the other three quarters will become extinct. The
result is that, on the average, one mutation that is
severe enough to alter the function of the gene
product will become fixed in an inbred strain about
every 7 generations due to genetic drift. This is an
underestimate of the actual rate because mutations
with inconspicuous effects were not included in the
estimate of the mutation rate.
Using a very different strategy, based on comparison
of mouse and rat sequence data at putatively neutral
sites (4-fold degenerate sites in exons and
unconstrained sites in introns), and an estimate of
80,000,000 generations separating the 2 species,
-9
Chamaray and Hurst (2004) estimate that 23 X 10
silent mutations occur per silent site (i.e., base pair),
per generation. Assuming the same rate for coding
9
sequence, and that 2% of the 2.7 X 10 base pairs in
the mouse genome are part of coding sequences, we
estimate a rate of genetic drift affecting coding
sequence of about one new mutation every 69
generations, an estimate that is remarkably similar to
the one based on Drake et al. (1998).
At The Jackson Laboratory, we address the issue of residual

heterozygosity by maintaining every inbred strain through a
single lineage of sisterbrother matings (our pedigreed
foundation stocks). Mice that are distributed (our
production mice) are from populations that were expanded
from this foundation stock. Thus, inbreeding of the parental
line continues in an unbroken lineage of sibling matings. As
a result, many of our inbred strains are well past generation
F60, with virtually no residual heterozygosity present.
3.B.1.d.2. Genetic drift

Random spontaneous mutations occur constantly. The
change in the genome of a breeding population due to the
accumulation of unselected random mutations over
generations is called genetic drift. Each new mutation is
propagated in the breeding population until it becomes either
extinct or fixed in the genome. Thus, even fully inbred
strains in which the original residual heterozygosity has
been eliminated will carry a background load of
constantly changing segregating loci, and their fixed
genomes will slowly change over time. The steady-state
level of segregating loci due to genetic drift in a closed
breeding population is determined by the background
mutation rate (see sidebar at left), the number of breeders
contributing to each generation, and the breeding scheme. If
a breeding stock is maintained through random matings, the
number of different segregating loci in an inbred strain will
be relatively high and fixation or extinction of new
mutations will be relatively slow. For inbred strains that are
maintained through a single line of sibling matings, a new
mutation either goes extinct or becomes fixed rapidly. In
each inbred strain, a new mutation will become fixed about
once every six to nine generations (sidebar).
At The Jackson Laboratory, we minimize the number of

breeders contributing to each generation by maintaining the
pedigreed foundation stock through a single lineage of strict
sisterbrother mating. This practice minimizes the steadystate level of heterozygosity and maximizes the rate of
extinction and fixation of new mutations. Thus, even though
we cannot prevent genetic drift, our production mice are
as genetically homogeneous as possible. An additional
strategy we use to minimize genetic drift for our most popular strains of JAX Mice is to freeze,
at a given generation, embryos and gametes, which are used to re-establish the strain every five
generations. Typically, the quantity of frozen stock is sufficient for at least 10 years, reducing
the rate of genetic drift more than 25 fold. (For details, see 8.B.2.b, Our Genetic Stability
Program.)
3.B.1.d.3. Genetic contamination

Probably the greatest source of heterozygosity in inbred strains is due to genetic contamination
caused primarily by human error (for example, by mistakenly mating the wrong mice together).
The Jackson Laboratory employs a rigorous Genetic Quality Control Program that minimizes
the chances a contamination event will occur, and, should one occur, to minimize the chances it
will be propagated through the inbred strain. (See Chapter 8, Genetic Quality Control:
Preventing Genetic Contamination and Minimizing Genetic Drift.)
3.B.1.d.4. Copy number variation (CNV)

Copy number variations (CNVs) are defined as genomic alterations involving duplication or
deletion of more than 1 kb of DNA (Freeman et al., 2006). CNVs can result in gene copy
number differences between individuals (i.e., zero, one, three, or four copies of a gene, rather
than two). CNVs have recently been implicated in a diverse group of human diseases, including
nervous system disorders (Lee and Lupski, 2006), mental retardation (Sharp et al., 2006), and
cancer (La Starza et al., 2007). Although some CNVs involve sizable fragments of a
chromosome and include many genes, CNVs are difficult to detect without specific tests. As a
result, their ubiquity in mammalian genomes was not fully realized until recently. In fact, CNVs
may arise quite frequently. For example, evaluation of CNV differences among monozygotic
twins (Bruder et al., 2008) demonstrates that, within every generation, a new CNV may appear
in 510% of the individuals.
Graubert et al. (2007) evaluated CNVs across mouse strains; they
identified an average of 22 CNVs per strain, with an average size
of 271.5 kb. Recent data, however, which are based on the higher
resolution platforms available for human studies, suggest that the
average CNV size may be much smaller, and that many CNVs
would have been undetected in the general screening studies
performed to date in mice. Full characterization of the extent of
inter-strain CNVs will require additional work with emerging
technologies.
What can researchers do to minimize the

impact of genetic drift and copy number
variation (CNV) on interpretation of results?
One way to help clarify the effect of genetic drift or
copy number variation (CNV) on interpretation of
published data is for researchers to cite the facility
that maintained the breeding colony of the mice
used in the study and to include the date when
the mice or the breeding stock were obtained. If
future studies identify mutations, including CNVs,
in the stock that affect the phenotype of interest,
and if the approximate date the mutation arose
can be identified, the original results can be
interpreted correctly by future investigators in this
new context.
Recently, Watkins-Chow and Pavin (2008) investigated copy

number variation within the C57BL/6J strain (000664). They
identified two CNVs, both on Chr 19, that were segregating within
the strain. They investigated one of the CNVs in more detail.
Thirteen percent of the mice were homozygous for this CNV; 64%
were heterozygous and 23% were negative. This ratio is in concordance with the HardyWeinburg equilibrium, which demonstrates that the CNV is freely segregating within the strain.
This identification of two CNVs in the small portion of the screened C57BL/6J genome
demonstrates that individual mice of highly inbred strains are not isogenic and that numerous
CNVs may be segregating within even carefully maintained inbred strains. Collectively, CNVs
such as the two reported could account for some of the phenotypic variability observed within
inbred strains and previously attributed to environmental, epigenetic, or stochastic differences.
Presumably, CNVs occur in all inbred strains. Although possible effects of CNVs on results of
experiments cannot be eliminated, they can be minimized. The same breeding and genetic
stability programs at The Jackson Laboratory that minimize segregating heterozygosity due to
genetic drift in inbred strains also minimize the number of segregating CNVs.
At present, CNVs must be treated experimentally as a source of random variation. As
information about CNVs accumulates for inbred mice, however, their stringently controlled
genetic backgrounds will make it possible to evaluate the often subtle influence of CNVs on
phenotypic expression. In the future, the similarity of CNVs between inbred strains of mice and
humans can be exploited to model the role of CNVs on phenotypic variation in humans.
3.B.1.e. Nomenclature
Inbred strains are designated using uppercase alphanumeric characters. Nomenclature for a
substrain reflects the inbred strain as well as information about how the substrain has diverged,
for example, the investigator or institution that developed the substrain and the institution that
currently maintains it. Table 3.4 provides several examples of inbred strain and substrain names
and their interpretation.
Table 3.4. Examples of nomenclature for inbred strains and substrains.
Name
Definition
Convention
C57BL
DBA
SJL
NZW
Inbred strains C57BL (line C, female 57,

BLack); DBA (Dilute Brown nonAgouti); SJL (Swiss, Jim Lambert);
NZW (New Zealand, White)
Uppercase alphanumeric characters,

starting with alphabetic character,
which may represent information about
parental strains, such as location of
origin, strain originator, phenotype.
129
201
Inbred strains 129 and 201.
Nomenclature exception: Numbers

starting the inbred strain name,
acceptable due to long-established use
before current nomenclature rules.
DBA/1LacJ
(001140)
Substrain of DBA/1J that was transferred

to The Laboratory Animal Center at
Carshalton, UK (Lac); now maintained at
The Jackson Laboratory (J).
CBA/CaGnLeJ
(001143)
Substrain of CBA inbred strain,

originated by T. C. Carter (Ca),
transferred to E. L. and M. C. Green
(Gn), and then transferred to P. W. Lane
(Le); now maintained at The Jackson
Laboratory (J).
Inbred strain name, forward slash (/),

and alphanumeric information
representing provenance. (Laboratory
and investigator codes are assigned by
the Institute for Laboratory Animal
Research [ILAR], U.S. National
Academy of Sciences, Washington,
D.C. The codes are available on their
website (http://dels.nas.edu/
ilar_n/ilarhome/search_lc.php).
C57BL/6NCrl
Substrain of C57BL/6J that was sent to

the National Institutes of Health (N); now
maintained at Charles River Laboratories
(Crl).
Often, abbreviations for inbred strain and substrain names are used in manuscripts and when
designating F1 hybrids. Table 3.5 lists the most common of these abbreviations.
Table 3.5. Abbreviations of inbred mouse strain and substrain names used in hybrid names.
Abbreviations and strains
129P
129P substrains
129X1
129X1/SvJ (000691)
CBy
BALB/cByJ (001026)
129P1
129P1/ReJ (001137)
A strains
D1
DBA/1 strains
129P2
129P2/OlaHsd
AHe
A/HeJ (000645)
D2
DBA/2 strains
129P3
129P3/J (000690)
AK
AKR strains
HR
HRS/J (000673)
129S
129S substrains
C57BL
C57L/J (000668)
129S1/Sv-Oca2+Tyr+KitlSl-J/J
B6
C57BL/6 strains
NZB
NZB strains
(000090)
B6Ei
C57BL/6JEi (000924)
NZW
NZW strains
129S1/SvImJ (002448)
B10
C57BL/10 strains
R3
RIIIS/J (000683)
129S2
129S2/SvPas
BR
C57BR/cdJ (000667)
129S4
129S4/SvJae
BALB/c strains
SJ or
J
SJL/J (000686)
129S5
129S5/SvEvBrd
C3
C3H strains
SM
SM/J (000687)
129S6
129S6/SvEvTac
C3Fe
C3HeB/FeJ (000658)
SW
SWR strains
129S7
129S7/SvEvBrd-Hprtb-m2
C3Sn
C3H/HeSnJ (000661)
NZW strains
129S8
129S8/SvEv-Gpi1c Hprtb-m2/J
(002027)
CB
CBA strains
CBACa
CBA/CaGnLeJ (001143)
Numbers in parentheses are JAX

Mice stock numbers.
129S1
3.B.1.f. Research examples

Variations in the effects of drugs among different inbred mouse strains: a contribution to drug
evaluation and the identification of genes that predict differences in drug efficacy.
Crowley et al. (2005) compared responses to the selective serotonin reuptake inhibitor
citalopram, an antidepressant, among eight inbred mouse strains using a tail suspension test.
DBA/2J (000671), BALB/cJ (000651), and BTBR strains from The Jackson Laboratory were
the most responsive, and C57BL/6J (000664) and A/J (000646) were the least responsive. The
strain distribution of the antidepressant-like activity did not correlate with the strain distribution
of effects on other behaviors, indicating that the patterns of sensitivity to citalopram are
behaviorally specific and unlikely to result from pharmacokinetic variables. This strain survey
identified the more appropriate strains for screening antidepressants and identified parental
strains that can be used to map quantitative trait loci (QTL) that regulate serotonin reuptake
inhibitors. In a follow-up study, Crowley et al. (2006) performed a mapping cross between a
citolopram-sensitive strain (BALB/cJ) and a citolopram-insensitive strain (A/J). Three QTLs
were identified (one each on Chr 7, Chr 12, and Chr 19). Three candidate genes at the Chr 19
QTL were sequenced. The researchers found two polymorphisms in the vesicular monoamine
transporter-2 gene, suggesting the possibility that this gene may regulate response differences to
anti-depressant serotonin reuptake inhibitors. Such QTL studies in mice identify possible genes
for human pharmacogenetic studies of therapeutic responses to anti-depressant drugs.
Identification of such genetic variants in humans patients would allow for more individualized,
rationally-designed, and ultimately, more successful drug treatments.
Interaction of dietary fat, body composition and bone mineral density characterized using strain
panels.
Strain comparisons provide an opportunity to identify possible genetic influences on
relationships among phenotypes and relationships between treatment and outcome variables.
Evaluations of such relationships in most genetically heterogeneous populations are complicated
because genetic and random sources of variance are confounded for each genotype. In contrast,
with inbred strains, random variation can be estimated directly, and its effect minimized,
because multiple copies of the same genotype can be sampled. Although studies using less than
six inbred strains generally are not sufficiently powerful for hypothesis testing, results from an
increasing number of large strain surveys are being made available to the public. For example,
the Mouse Phenome Database (MPD; www.jax.org/phenome) now provides data from hundreds
of strain comparison studies of a wide range of phenotypes.
Data from two of these studies, involving a total of 51 inbred strains, were used by Li et al.
(2008) to examine genetic effects on the relationships of dietary fat, body composition, and
bone density (BMD) in mice. Using structural equation modeling, the researchers demonstrated
that greater body fat is associated with lower BMD under conditions of a high fat diet, but not a
low fat diet. One lifestyle implication suggested by this model is that, to maintain or increase
BMD, lowering body fat, through exercise for example, may be more important for people on a
standard Western diet than for people on a very low fat diet.
3.B.2. Wild-derived inbred strains

Because the majority of standard inbred strains were developed from domesticated mice
originally obtained from mouse fanciers, genetic diversity was limited. To introduce allelic
diversity, some researchers have imported wild mice directly into the laboratory.
3.B.2.a. Definition, characteristics, and value

Wild-derived inbred strains originate from mice that are
trapped in the wild,
imported into the laboratory without domestication, and then
inbred by intercross sibling mating for at least 20 generations.
Most of the wild-derived strains used for research come from the subspecies Mus musculus
domesticus, M. m. musculus, M. m. castaneus, and M. m. molossinus, whereas standard
laboratory strains are primarily mixes of M. m. domesticus and M. m. musculus. (For detail on
the origins of laboratory mice, refer to 2.A, Origins and basic genetic characteristics of the
laboratory mouse.) Also see Silver (1995), Morse (2007), and Tucker (2007).
Other Mus species, such as M. caroli, are available as inbred strains; however, crosses of these
mice with the M. musculus species result in postfertilization defects. These defects limit the
usefulness of non-M. musculus species because they cannot be used with the powerful genetic
tools, such as those used for mapping, that require outcrossing. Examples of outcrossing
difficulties include the following: M. m. cervicolor x M. m. musculus embryos generated from
artificial insemination do not undergo the first cleavage event. M. dunni x M. m. musculus
hybrids fail to thrive at the blastocyst stage. Postnatal viability of M. caroli x M. m. musculus
pups is severely compromised. Crosses of M. spretus with M. m. domesticus produce viable
offspring; hybrid females are fertile, but hybrid males are sterile. (Silver, 1995).
Individuals of a given wild-derived inbred strain are genetically virtually identical, as in any
inbred strain. However, because their progenitors were so different genetically from the
progenitors of the classical inbred strains, the wild-derived inbred strains provide considerable
genetic diversity. It is this genetic diversitycompared to traditional inbred strainsthat makes
them such valuable tools for evolution and systematics research. Also, progeny from crosses
between wild-derived and common inbred strains are especially useful for genetic mapping. In
addition, several wild-derived inbred strains naturally carry fused chromosomes, called
Robertsonian chromosomes, which are used for mapping, genetic structure-function studies, and
to provide genetic markers. (See 3.E, Mice with chromosomal aberrations, later in this
chapter.)
Considerations for the use of wild-derived inbred strains include the following:
Little normative data exist for wild-derived inbred strains.
As with any inbred strain, any experimental result from a study of a single wild-derived strain
cannot be applied to all mice or even to all wild mice.
Wild-derived inbred mice are especially sensitive to variations in their environment caused by
noise, vibration, and replacement of regular caretakers. This may contribute to some of the
variation in breeding performances of wild-derived strains compared to standard inbred
strains.
One consideration relates specifically to handling: Because the mice retain many of their
wild alleles, they are very quick and take advantage of any opportunity to escape, which
makes them a challenge to care for.
For additional information on husbandry considerations for wild-derived inbred mice, see 9.C.3,
Caring for wild-derived inbred mice.

Often, the progenitors of wild-derived inbred strains are either one pair or a trio. Once a wildderived stock is fully inbred, it is maintained and monitored as any other inbred strain.
3.B.2.d. Nomenclature
Nomenclature for wild-derived mice follows conventions similar to those of inbred strains;
however, a wild-derived inbred strain name always designates the investigator who trapped or
introduced the wild mice into the laboratory and then inbred them. Even so, unambiguous
identification of a strain as wild-derived can be made only by reviewing the strain details. Table
3.6 provides examples of wild-derived strain names and their interpretation.
Table 3.6. Examples of nomenclature for wild-derived inbred strains.
Name
Definition
Convention
CAST/EiJ
(000928)
Inbred substrain of wild M. m. castaneus,

developed by E. M. Eicher (Ei); now
maintained at The Jackson Laboratory (J).
Uppercase alphanumeric characters,

starting with alphabetic character, which
represent information about parental
strains; forward slash (/); and ILAR
investigator and laboratory code(s)
(http://dels.nas.edu/
MOLD/RkJ
(000734)
Inbred substrain of wild M. m. molossinus

from Japan, developed by T. H. Roderick
(Rk); now maintained at The Jackson
Laboratory (J).
As above.
3.B.2.e. Research examples

Identification of loci that regulate lifespan.
Klebanov et al. (2001a) mapped genetic determinants of maximum lifespan, a life history trait,
using two 4-way cross populations, each of which included one wild-derived inbred strain
either CAST/EiJ (000928) or MOLD/RkJ (000734). These studies identified two significant
loci, Leg1 and Leg2, each of which accounted for at least 10% of the variance in maximum life
span. At each of these loci, the allele from only a single strainthe wild-derived strain within
the crossaccounted for the association of lifespan with the genotype at that locus. In both
cases, the allele from the wild-derived strain was associated with longer lifespans. No allele
from the six standard inbred strains in the study, at any locus evaluated, contributed a
comparable effect on lifespan. (Flurkey et al. [2007b] speculated that the inadvertent selection
for fecundity and other characteristics during domestication of the progenitors of standard
laboratory strains may have minimized genetic variation for life history traits such as lifespan.)
Unfortunately, the two wild-derived strains themselves are not particularly long-lived,
presumably because other genes limit their lifespan. Leg1 and Leg2 congenics, using genetic
backgrounds from long-lived strains, are currently being evaluated for lifespan.
Discovery of alleles in wild-derived mice for extended female reproductive lifespan.
Flurkey et al. (2007a), studying female reproductive aging, found that the very long
reproductive lifespan of mice imported from a South Pacific island (an outbred stock, Pohn,
mice from Pohnpei) diminished significantly within eight generations in the laboratory, even
though breeders in the Pohn stock were not sibling-mated. However, outcrossing late generation
Pohn mice to a standard laboratory strain (C57BL/6J [000664]) produced PohnB6F1 hybrid
mice with a longer female reproductive lifespan than previously reported for any M. musculus
F1 hybrid, including other hybrids of C57BL/6J. By using this F1 strategy, the researchers
unmasked alleles that delay female reproductive senescence.
3.B.3. F1 and F2 hybrids

A major advantage of inbred strains is the genetic homogeneity of its members. But what if a
researcher wants to study the interaction of different alleles of the same gene? Or work with an
animal that is more robust and that expresses hybrid vigor? Outcrossing two inbred strains to
create hybrids of the first and second filial generations (F1 and F2) produces mice that combine
the genetic consistency of inbred strains with controlled genetic diversity and hybrid vigor.
Evaluation of F1 and F2 hybrids is a critical first step in determining the genetic characteristics
of any phenotype, such as its mode of inheritance. (Even Mendel used this strategy with his
peas.) Although both F1 and F2 hybrids involve controlled genetic diversity, the different types
of diversity provide different types of information.
3.B.3.a. Definition, characteristics and value

3.B.3.a.1. F1 Hybrids
An F1 hybrid is the result of the first outcrossed generation of two inbred strains. F1 hybrids
from the same two parental strains are genetically identical to each other, with the exception of
the sex chromosomes (Figure 3.3). Reciprocal F1s, which are created by reversing the strains of
the dams and sires, differ phenotypically and genetically from each other. Differences include
Chromosome (Chr) Y, the males Chr X, mitochondria, maternal and paternal imprinting, and
other maternal influences (including litter size, composition of milk, and maternal behavior).
Figure 3.3. Genetic structure of F1 and F2 hybrids, using Chr 1 as an example.
F1 hybrids are particularly useful for the following:

To study heterosis, the expression of a phenotype that does not appear in either parent, but
that results from the interaction of two different alleles of a single gene. The most common
example of heterosis is hybrid vigor, which results from two processes:
Physiological buffering, the concept that an F1 hybrid presents a broader array of
responses to various stresses because each of the two alleles for a given gene may be
optimal for different environmental challenges.
Prevention of phenotypic expression of deleterious recessive alleles that are randomly fixed
in the parental inbred strains.
Thus, compared to their inbred parents, F1 hybrids generally live longer, breed better, and are
more disease resistant.
To determine the mode of inheritancewhether a phenotype is characterized by dominance,

additivity, or heterosis.
To create or enhance expression of polygenic diseases (such as lupus or diabetes), by
combining dominant or additive genetic determinants at different loci. This process is an
example of negative epistasis.
To study phenomena that affect the health of the mice, such as deleterious mutations or
radiation. F1 hybrids usually are more robust than either parental strain.
To minimize noise in bioassays, such as those involving nutrients, drugs, pathogens, or
hormones. The physiological buffering capacity of F1 hybrids minimizes the interactions with
non-relevant sources of variation that could interfere with the readout of the assay.
To maintain the health of mixed background mutant mouse stocks when the mutation
severely impairs health or fertility. This strategy is most often used with transgenic strains.
The stock may be either continuously or periodically refreshed through outcrosses of the
mutant carrier with an F1 hybrid. Within these crosses, females are often the F1 hybrid
because they tend to be good, productive mothers.
3.B.3.a.2. F2 Hybrids
An F2 hybrid is the first intercrossed generation of F1 hybrid siblings. Each F2 hybrid is
genetically unique, containing, on the average, a 50:50 mix of the genotype of each parental
strain, but in a random configuration (Figure 3.3). As a consequence,
genetic variance among individuals is produced, increasing the variance for a phenotype in
the population, and
recessive traits are expressed, permitting the study of recessive alleles on a mixed genetic
background.
F2 hybrids are particularly useful for the following:
To determine whether a phenotype is regulated by one or multiple genes and to characterize
its genetic complexity.
To map a trait.
As approximate controls for many targeted mutant stocks that are maintained on a mixed
genetic background (for example, outbred stocks with a mixed C57BL6 and 129 background,
commonly used for genetically engineered mice).
Considerations for the use of F1 and F2 hybrids include the following:
F1 hybrids are often used in tissue transplantation studies because they provide a common
environment for solid organs transplanted from either parental strain. However, transplanting
bone marrow, which contains hematopoietic stem cells (HSCs), is not straightforward due to
hybrid resistance. F1 hybrids may or may not accept HSCs from either parent, or they may
initially accept the HSCs but slowly reject the tissue. This rejection occurs, not because of
classic acquired immunity, but because of innate immune system differences determined by
natural killer cells (Kumar et al., 1997). Thus, when using F1s as hosts in bone marrow
transplantation studies, it is imperative to conduct preliminary tests to determine the extent of
hybrid resistance.
Normative data for F1 hybrids are much less extensive than for popular inbred strains.
A single F1 genotype represents a narrow range of the M. musculus genome in only one
configuration. As with any model based on a single genotypesuch as an inbred strain
experimental results from studies using a single F1 hybrid genotype should not be considered
typical of laboratory mice in general.
In F2 hybrids, heterozygosity is reduced by 50% compared to parental F1 hybrids. This
reduces hybrid vigor.
F2 hybrids and other segregating populations are often used for mapping studies, requiring
storage of tissue (at -80 C) for DNA analysis. It is advisable to keep the samples for possible
future analysis as new information (e.g., about mutations) or new technologies emerge.

Unlike inbred strains, F1 and F2 hybrids are not maintained as strains. Rather, they are
constantly recreatedF1 hybrids from their inbred parents, and F2 hybrids from their F1
parents and their inbred grandparents. Thus, a steady supply of F1 or F2 hybrids requires
maintenance of breeding colonies of the progenitor inbred strains.
Note: To meet the needs of researchers who use F1 and F2 hybrids and cannot or choose not to
maintain parental stocks, some suppliers of mice provide a selection of F1 and F2
hybrids for distribution. For information on hybrid mice available from The Jackson
Laboratory, call Customer Service at 1-800-422-6423 (North America) or 1-207-2885845 (International).
An F1 hybrid name is a combination of abbreviations of the parental strain names with an F1
designator; an F2 hybrid name is the same as the F1 but with an F2 designator. For all
hybrids, the abbreviation of the female strain is listed first. Because the abbreviations typically
do not designate substrains, when authors first mention an F1 or F2 in publications, they must
provide the full strain or substrain designation of both parental strains. Thereafter, use of an
abbreviation is acceptable. For a list of approved inbred strain and substrain abbreviations, refer
to Table 3.5, Abbreviations of inbred mouse strain and substrain names used in hybrid names,
presented previously in this chapter. Table 3.7 provides several examples of F1 and F2 hybrid
names and their interpretation.
Table 3.7. Examples of nomenclature for F1 and F2 hybrids.
Name
Definition
Convention
B6D2F1/J
(100006)
F1 hybrid of C57BL/6J (B6) female and

DBA/2J (D2) male; generated at The
Jackson Laboratory (J).
Inbred parental strain or substrain

abbreviations (female strain listed
first), F1, forward slash (/), and
ILAR investigator and laboratory
codes (http://dels.nas.edu/
CByD2F1/J
(100015)
F1 hybrid of BALB/cByJ (CBy) female

and DBA/2J (D2) male; generated at The
As above.
B6129SF1/J
(101043)
F1 hybrid of C57BL/6J (B6) female and

129S1/SvImJ (129S) male; generated at
As above.
B6129SF2/J
(101045)
F2 hybrid produced by breeding 2

B6129SF1 hybrids; generated at The
F1 hybrid name, with F2 replacing

F1.

Allelic diversity of F1 and F2 hybrids clarifies role of inheritance in cancer.
Within just a few years of the demonstration that Mendels laws were applicable to the
inheritance of at least some phenotypes in mammals, Little and Tyzzer (1916) used F1 and F2
hybrids of a stock of Japanese waltzing mice and stocks of common mice to investigate the
mode of inheritance of susceptibility to a transplantable tumor. All the Japanese waltzing mice
were susceptible, but none of the common mice were. All F1 offspring of crosses with the
Japanese waltzing mice were susceptible to the tumor, demonstrating that the susceptibility
phenotype was dominant. However, only 1.6% of the mice in the F2 generation were
susceptible. Little and Tyzzer illustrated how this non-Mendelian pattern of inheritance for
tumor-susceptibilityrevealed in the F2 generationcould result from influences on the
phenotype by multiple genes, each of which is inherited in a Mendelian fashion. This study was
the first to analyze phenotypic segregation in F2 hybrids to study the genetics of disease in
mammals. It established a standard strategy for genetic analysis that is routinely used even
today.
A single cross (F1 and F2 hybrids) illustrates polygenic inheritance and maternal effects.
Reifsnyder et al. (2000) demonstrated that the risk of type 2 diabetes was much greater in F1
hybrids of NZO/HlLtJ (002105) and NON/ShiLtJ (002423) mice than in purebred NZO/HlLtJ
mice. (NON/ShiLtJ mice do not develop diabetes although they express impaired glucose
tolerance.) This indicated that dominant or additive factors contributed by both parental strains
combined to enhance the expression of diabetes in the F1 mice. The distribution pattern of
diabetes frequency in the F2 generation confirmed that the induction of diabetes was polygenic.
An influence of the direction of the cross on diabetes outcome was identified in the F1: when
the dam was from the NZO/HlLtJ strain, the incidence of diabetes in the pups was greater than
when she was from the NON/ShiLtJ strain. Cross fostering studies showed that pups of either
cross gained weight more rapidly when the foster mother was NZO/HlLtJ rather than
NON/ShiLtJ. The more rapid weight gain was associated with a higher risk for development of
diabetes in F1 offspring from either cross. This maternal effect provides a model for the role of
juvenile obesity in the enhancement of diabetes risk. This model was discovered because of the
careful design of the breeding strategy.
3.B.4. Multi-strain crosses

Although F2 hybrids are typically used to study complex traits, their allelic diversity derives
from only two genotypes. To provide genetic diversity that more closely models a natural
population, researchers use multi-strain crossesstructured crosses involving more than two
parental strains. Multi-strain crosses are especially useful to comprehensively study the genetics
of complex traits such as behaviors and body composition.
3.B.4.a. Definition, characteristics, and value

Multi-strain crosses are structured, intercrossed generations of different F1 hybrids created in
various combinations from three or more inbred strains. An example of a multi-strain cross is a
4-way cross, in which two different F1 hybrids are outcrossed.
Exactly what are commercially available
outbred stocks? How do they differ from the
multi-strain crosses described here?
Commercially available, appropriately
outcrossed stocks, commonly called outbred
stocks, are maintained using breeding strategies
that maximize diversity. However, unlike multistrain crosses derived from inbred strains, mice
of an outbred stock have a varying and
uncontrolled genetic relationship to each other.
The main advantage of outbred mice is that they
are less expensive than strains that are
genetically well defined.
Although outbred stocks are sometimes used as
heterogeneous models, F1, F2, and defined
multi-strain crosses provide greater reliability as
well as opportunities to study the genetics of any
phenotype of interest. In addition, multi-strain
crosses actually provide a greater genetic
diversity compared to outbred stocks that are not
routinely refreshed.
Properly outcrossing a stock requires very
careful breeding of a large number of mice in
each generation. Without the addition of new
genetic diversity, as outcrossing proceeds, the
stock becomes progressively more inbred. In
fact, the majority of established outbred stocks
may be considered incompletely inbred stocks.
The first step in creating a multi-strain cross is to choose the

parental strains. Criteria are based on the nature of the study. For
example, to make a population of mice for a selection study,
investigators would choose strains with a wide range of values
for the target phenotype. To create a population that reflects a
broad variety of genetic influences, they would choose strains
that are as unrelated to each other as possible. The Mouse
Phenome Database (MPD) provides a comprehensive collection
of phenotypic data for mouse strain comparisons. For an
overview of the MPD, see 6.C.2, Other databases. Access the
MPD at www.jax.org/phenome.
Multi-strain crosses are created by
outcrossing the inbred parental strains (in various
combinations) to create an F1 generation, and
selectively intercrossing different F1s to create the first
segregating generation (which we call the S0 generation).
Sometimes, investigators are interested in generations of multistrain crosses subsequent to the S0 generation. For example, with
a 4-way cross, the S1 generation is the first generation in which a
segregating locus can be homozygous. To retain as much
diversity as possible in the S1 and subsequent generations, the
strategy would be to pair mice for breeding from the most
distantly related families.
The strength of a multi-strain cross depends on the careful choice

of the parental inbred strains that make up the F1 generation. By choosing strains that are
distantly related, the multi-strain cross population produces a wide range of genotypesin a
virtually infinite assortmentthat represents the species far more comprehensively than other
inbred or bilineal models.
Multi-strain crosses offer additional advantages:
They provide a population that avoids biases from idiosyncrasies of single genotypes.
The population can be reproduced from the parental strains at any time.
Their extensive heterozygosity promotes hybrid vigor (similar to F1 and F2 hybrids).
Figure 3.4 illustrates the differences in genetic diversity between a bilineal and a 4-way cross.
Figure 3.4. Differences in genetic diversity between crosses of two vs. four inbred strains.
Considerations for the use of multi-strain crosses include the following:
Because of the increased genetic variability, a larger sample size may be necessary to
maintain a given statistical power (Festing, 1999).
The use of multi-strain crosses generally precludes studies that require complete
histocompatibility.
Little background information is available for most multi-strain crosses.
Multi-way crosses are often used for mapping studies, requiring storage of tissue (at -80 C)
for DNA analysis. It is advisable to keep the samples for possible future analysis as new
information (e.g., about mutations) or new technologies emerge.

As with F1 and F2 hybrids, S0 and S1 generations must be continually created from progenitors.
However, multi-strain crosses are often maintained as stocks, especially when the population
was selected for a specific trait.
No specific nomenclature rules exist for segregating crosses from three or more inbred
progenitors. Thus, it is the responsibility of the researcher to clearly explain the crosses in
materials and methods and designate an appropriate abbreviation for use in the remainder of the
publication. Figure 3.4 provides an example of such nomenclature, which was defined in
Klebanov et al. (2001b).

Identification of genetic correlations between diverse phenotypes.
To resolve questions concerning the feasibility of artificial selection for increased lifespan in
mice and whether female reproductive longevity might provide an effective selection criterion,
Klebanov et al. (2001b) used the S0 and S1 generations of three 4-way crosses. The
investigators determined the heritability of lifespan and calculated genetic correlations between
maternal reproductive lifespan and total lifespan of parents and offspring. They found that, in
sufficiently diverse mouse populations, selection for increased longevity should be possible and
that the direct selection for parental lifespan will be a more efficient strategy than selection for
female reproductive lifespan.
An intervention study using a highly, genetically diverseyet reproduciblepopulation that
models the diversity of the human genome.
The Jackson Laboratory is currently participating in a multi-site program designed to assess the
effectiveness of treatments that may increase lifespan in mice. The National Institute on Aging
Interventions Testing Program (ITP) was established to evaluate agents that are proposed to
increase lifespan and delay the appearance of age-related disease in genetically heterogeneous
mice. Mice from the S0 generation of a 4-way cross (CByB6F1/J [100009] females x C3D2F1/J
[100004] males) are being used to test the treatments because these mice exhibit a broad range
of age-related pathologies that model a human population more accurately than inbred mice do.
Mice in the first cohort studied (Strong et al., 2008) were treated with one of four agents. Two
are anti-inflammatory agents: aspirin and nitroflurbiprofen. Two are anti-oxidents: 4-OH-alphaphenyl-N-tert butyl nitrone (4-OH-PBN) and nordihydroguaretic acid (NDGA). NDGA and
aspirin increased median lifespan of male mice significantly (12% and 8%, respectively), but
none of the treatments increased maximum lifespan. Nitroflurbiprofen and 4-OH-PBN had no
effect on lifespan. None of the treatments affected either mean or maximum lifespan among
female mice. Measures of blood levels of NDGA or aspirin and its salicylic acid metabolite
suggest that the observed lack of effects of NDGA or aspirin on lifespan in females could be
related to sex differences in drug disposition or metabolism. Although the effect of NDGA and
aspirin are small, further studies using a range of doses will determine if greater effects are
possible. If one, or even multiple, inbred strains or F1s had been used, results would have a
more limited relevance because of potential interactions of the treatment with the relatively
narrow range of age-related pathologies that characterize any homogenic population.
3.C. Strains with single-locus mutations (spontaneous,

induced, and genetically engineered mutant strains;
congenic and conplastic strains)
Researchers first studied genetic variants and observable, single-locus mutations that arose
spontaneously in non-inbred stocks. These phenotypic deviants provided a way for researchers
to study the function of the altered gene, especially its relationship to disease phenotypes. The
development of inbred strains made it even easier for researchers and technicians to identify and
study phenotypic deviants.
This observational approach is useful for
spontaneous mutations that affect visible
phenotypes, such as coat color, size,
morphology, and behavior. However,
spontaneous mutations are rare. Furthermore,
those with effects that are not obviously
visible can be discovered only by screening;
and, the costbenefit ratio of screening for
spontaneous mutations is very high. Thus, to
increase the rate of mutations so that screening
can be efficient and cost-effective, researchers
now often induce random mutations using
various techniques such as ionizing radiation
(e.g., X-rays) or chemical mutagenesis.
The development of technology to sequence
and manipulate DNA directly, combined with
the availability of the complete sequence of
the mouse genome, has provided researchers
with the tools to insert, delete, or alter
virtually any desired gene in the genome.
Consequently, researchers now often study
gene function using reverse genetics, i.e.,
altering known genes to produce precise
single-locus mutants, and then studying the
phenotypic consequences.
What is the relationship between single-locus

mutations and modifier genes?
The effect of a mutation is usually attributed
entirely to the locus where the mutation occurred,
suggesting that the phenotype is under the
regulation of that single locus. Often, however,
when the mutation is transferred to a different
genetic background (as when creating a congenic
strain), a variant of the phenotype appearsdue to
the presence of genes that interact with the
mutation to alter the phenotype on the new
background. These genes are usually called
modifier genes.
Of course, the same genes exist in the original
strain as well, but with different alleles. In the
original strain, however, the mutant phenotype is
attributed entirely to the mutation. It is only when
the mutation is transferred to a new background,
and when a different phenotype appears, that we
notice the interaction of the mutation with the
modifier genes. For the sake of illustration, assume
that a mutation was discovered in strain A. When
the mutation was transferred to strain B, a different
phenotype appeared and modifier genes were
identified. If, however, the mutation had arisen on
strain B, the modified mutant phenotype would
have been attributed exclusively to the mutation
and not to interaction with modifier genes. If this
mutation was then transferred to strain A, the
existence of modifier genes would have been
recognized.
For purposes of discussion in this handbook,

Indeed, researchers should keep in mind that the
consequence of any mutation on any genetic
we group strains with single-locus mutations
background is almost always the product of both a
as follows:
direct effect of the mutation and interactions of the
Mice with spontaneous and induced
mutation with specific genes at other loci. This is
mutations and mice that are genetically
true even on the genetic background on which the
mutation arose or was originally created.
engineered (knockout, knockin, transgenic).
In this category, the mutations are carried
on the genetic backgrounds on which they arose or were engineered.
Congenic and conplastic mice. In this category, the mutations or variant alleles are transferred
through directed breeding to a new genetic background.
3.C.1. Spontaneous, induced, and genetically engineered mutant

strains
3.C.1.a. Definitions, characteristics, and value
3.C.1.a.1. Spontaneous and induced random mutations
The random nature of spontaneous and induced mutations has a very distinct implication:
Researchers can make discoveries about the genetic regulation of a phenotype without the bias
of a hypothesis. This permits novel discoveries of unanticipated genetic relationships.
Creating new mouse strains based on
spontaneous mutations: The Phenotypic
Deviant Search program and the Mouse
Mutant Resource at The Jackson Laboratory
Animal care technicians at The Jackson
Laboratory are trained to identify unexpected,
deviant phenotypes, which could indicate the
occurrence of a spontaneous mutation.
Technicians set aside these deviant mice and
their littermates, and researchers meet weekly to
view the selected mice. Phenotypes of interest
are tested for heritability by individual
researchers or by the Mouse Mutant Resource
group, which also registers mutations from
investigators outside of The Jackson Laboratory.
Following further characterization, the mice are
offered to the global research community. To
date, more than 500 strains of JAX Mice have

been developed from mice identified via the
deviant search.
We are very serious about recognizing the
contribution our caretakers make to our deviant
search program. Animal care technicians who
discover mutations that result in publications
receive formal acknowledgment in the
manuscripts.
For more information about the Mouse Mutant
Resource, visit http://mousemutant.jax.org/index
or email [email protected].
Spontaneous mutations
Spontaneous mutations that cause observable phenotypes
generally are discovered by conscientious animal care
technicians or researchers who are very familiar with the
phenotypes of specific strains and who observe something
unique in a specific mouse. If a phenotype is of interest, the
mouse and its relatives are bred to determine whether the
phenotype is heritable.
Induced random mutations
Induced mutations in mice are typically produced by such
treatments as chemicals or ionizing radiation. For chemicallyinduced mutations, male mice are injected with a chemical that is
known to cause point mutations (N-ethyl-N-nitrosourea [ENU],
for example). For radiation-induced deletions, males are
irradiated. Following treatment, the males are bred with nontreated females, and their offspring are screened for phenotypes
of interest. Because treatment produces numerous mutations in
each mouse, a desired phenotype often is produced by complex
genetics. These phenotypes are generally lost as the line is
propagated and the critical constellation of mutations is broken
up. As a result, if a line still expresses a deviant phenotype after
about five generations, this usually indicates that this deviant
phenotype is driven by a single locus mutation.
3.C.1.a.2. Genetically engineered mutations
Genetic engineering technology allows researchers to create

mice with specific mutations for designated genes. In this
handbook, we organize genetically engineered mice into two categories:
Targeted mutant mice produced using homologous recombination, in which a targeted
endogenous gene is altered. This classification includes knockout (KO) mice, in which a gene
is made non-functional, and knockin mice, in which the function of a gene is altered.
Transgenic mice, in which a functional exogenous genepossibly from another speciesis
inserted randomly into the genome of a mouse.
Targeted mutant mice by homologous recombination
Homologous recombination involves genetic modificationseither knocking out an exon or
knocking in a novel DNA sequence or geneto the genome of embryonic stem (ES) cells.
Successfully modified ES cells are identified through a selection process and injected into host
embryos. Embryos are then transferred into pseudopregnant host females. When the ES cells
contribute to the cellular makeup of the developing fetus, the result is a chimera. Chimeras
comprise both ES-derived cells and cells from the original embryo. These chimeras are usually
bred with the host strain to test for germline transmission of the targeted mutation. When a
chimera produces progeny with the mutation, it is called going germline. Germline chimeras
produce heterozygotes for the targeted mutation. Thus, these heterozygotes must be intercrossed
to produce a homozygous knockout or knockin mouse.
Transgenic mice
To create transgenic mice, multiple copies of a
genetically-engineered transgene are injected into a
fertilized egg. The transgene usually includes the
structural components of the gene and a promoter
region that specifies when and where that gene is
expressed. For example, a promoter could specify that
a gene would be expressed only in fat cells, and only
when the animal was under stress. Often, an intron is
included in the engineered transgene, which helps
stabilize the gene once it is inserted. Typically, a
transgene will insert as multiple tandem copies. Two
or more different transgenes also can be co-injected
simultaneously. Co-injected transgenes typically
insert in the same genome location.
A few words about 129 strains, ES cells, and

nomenclature
A large number of mutant mice produced through homologous
recombination involve embryonic stem (ES) cells from 129
inbred strains. When using a 129 substrain, it is critical that the
genotype match that of the 129 ES cells and the DNA library
used for the construct. Failure to do so results in mixed 129
genotypes. For a list of the 129 strains from which the principal
ES cells were derived, see Appendix B, 129 Strains
Nomenclature and Related ES Cell Lines.
Because of the complex history of the 129 strains,
nomenclature was problematic, which hampered replication of
studies (Simpson et al., 1997; Threadgill et al., 1997). In 1999,
Festing et al. developed new nomenclature to distinguish the
129 parental lines and related 129 strains. The International
Committee on Standardized Genetic Nomenclature for Mice
approved the new nomenclature. For an overview of the new
rules, refer to Appendix B, 129 StrainsNomenclature and
Related ES Cell Lines. For full nomenclature details, visit
www.informatics.jax.org/mgihome/
nomen/strain_129.shtml.
Examples of genetically engineered mutant mice

T cell receptor (TCR) transgenic mice are used to
study interactions of the T lymphocyte with specific
antigens (von Boehmer et al., 1988). Most T
lymphocytes in the TCR transgenic mice target a
single antigen that is specified by the researcher
when the transgenic mouse is created. This enables researchers to study the interaction of a
specific antigen with T lymphocytes because it greatly amplifies a cellular-level phenomenon
impossible to observe by other means. However, the repertoire of the T cell system is
artificiallyand extremelyrestricted in these mice. Most of their T cells react with the
same antigen, and no other antigens. Therefore,
these mice are very immunocompromised.
Creating humanized mice: compounding mutations to
enable human tissue transplants
Tissue-specific knockouts can be achieved with a
Cre-lox strategy, involving both homologous
Despite the similarities between mice and humans at the
genetic, physiologic, and anatomical levels, some human
recombination and transgenic technologies. A
diseases can be studied only in human tissue. (Viruses, for
structural component of the gene to be knocked out
example, are typically species-specific.) Humanized mouse
is surrounded by loxP sites using homologous
models meet the need for hosts of human tissue. Such
recombination. The loxP sites are targets of a Cre
models are severely immunocompromised, permitting the
recombinase, which cuts the DNA strand at that site.
transplantation and survival of human tissue in mice so that
pathogenesis and treatment of uniquely human diseases can
The Cre recombinase can excise, invert, or
be studied. Leonard Shultz has spent much of his research
translocate the floxed fragment (the fragment
career at The Jackson Laboratory constructing a succession
flanked by the lox sites), depending on the
of immunodeficient mouse models, each of which was a
orientation of the loxP sites. The gene for the
better host for human tissue than the one before.
scid
tm1Wjl
recombinase is physically linked to a tissue-specific
His most recent model, the NOD.Cg-Prkdc Il2rg
/SzJ
promoter, and a mouse is made transgenic for this

strain of JAX Mice (005557), is arguably the most versatile
immunodeficient mouse model available. This strain and
construct. A Cre-lox mouse is produced by
other similar humanized mouse models are now being used
crossing mice that have a tissue-specific Cre
for studies of human hematopoiesis, innate and adaptive
recombinase with mice that have a target gene
immunity, infectious diseases, cancer biology, regenerative
flanked by loxP sites (a floxed locus). It is
medicine, and autoimmunity, including type 1 diabetes (Shultz
important to note that, although all cells of the
et al., 2007; Pearson et al., 2008).
mouse carry the engineered gene, expression of the
Such humanized mice illustrate the value of a broad
recombinase is limited only to the tissue designated
understanding of the various types of mutant mice. The NOD
mouse has inherent immunodeficiences in its innate immune
by the promoter. As an example, to restrict
system, representing strain variation. The scid mutation,
expression of a transgene to the brain and other
which severely impairs adaptive immunity, was a
neuronal tissue, a promoter for a neuron-specific
spontaneous mutation. The Il2rg knockout was specifically
protein, nestin, can be used. Figure 3.5 provides a
engineered to produce immunodeficiency. It is because of the
schematic overview of Cre-lox technology.
combination of these complementary deficiencies that such
unique mouse models could be created.
Figure 3.5. Schematic of Cre-lox technology illustrating an excision of a target site.
The FLP-FRT system is similar to the Cre-lox System. It involves the use of flippase (FLP)
recombinase, derived from the yeast Saccharomyces cerevisiae (Sadowski, 1995). FLP
recognizes a pair of FLP recombinase target (FRT) sequences that flank a genomic region of
interest.
A more recently developed (and simpler) way of suppressing expression of an endogenous
gene is by constructing an RNA-mediated interference (RNAi) transgenic. When a transgene
produces a strand of RNA that is complementary to an endogenous mRNA, the
complementary strand hybridizes with the endogenous RNA; the double stranded RNA is
degraded by endogenous mechanisms, leading to post-transcriptional suppression of gene
expression. RNAi transgenic technology permits tissue- or temporal-directed suppression of
gene expression, without the requirement to outcross to another strain that carries a targeted
mutation, as with Cre-lox and FLP-FRT systems (Dykxhoorn et al., 2003). RNAi technology
holds great promise for mammalian application (Behlke, 2006), but it currently has some
drawbacks. The most serious is that, often, insufficient RNAi is produced to completely
suppress the target gene.
3.C.1.b. Considerations
Considerations for the use of spontaneous, induced, and genetically engineered mutant strains
A mutant phenotype of the strain may necessitate special husbandry.
For strains based on random mutations, initially the gene is unidentified, and it will remain so
until it is positionally cloned or tested by complementation.
When inducing random mutations, the initial mutational load can impair breeding.
For transgenic mice
Multiple copies of the transgene frequently insert, sometimes at multiple sites. Because the
site of insertion is random, endogenous genes might be knocked out, which could create a
cryptic KO mouse. This happens in approximately 1015% of transgenics.
The expression of the transgene may be lost through generations of breeding, typically as a
result of DNA methylation or copy number loss. The best strategy to minimize this loss is
to maintain the line in forced hemizygosity.
Over-expression of a transgene, including marker transgenes, may have unintended
consequences, including cell lethality (Leiter et al., 2007).
A successfully inserted transgene may not be expressed. To increase the probability of
expression, it is helpful to include an intron in the transgene.
For mice used in a bigenic system:
It may be necessary to maintain parental strains. For example, with Cre-lox models, often
both the Cre and loxP parental strains must be maintained.
Genotyping sometimes is complicated by a need to differentiate homozygotes from
hemizygotes (e.g., typically floxed genes must be homozygous
for the system to work).
Dont some inbred strains carry mutations?
Why arent the mutations part of the name?
For Cre-lox Systems, both the Cre and the loxP lines must be
Probably all inbred strains carry fixed mutations.
genotyped; however, even the presence of both Cre and loxP
The mutations might have been in the
sites is no guarantee that the Cre-lox System will work.
progenitors, or they might have arisen during
Similarly, the fact that the Cre-lox System worked in one
inbreeding or strain maintenance. For example, in
generation is no guarantee that it will work in subsequent
the C3H family, most strains carry the retinal
rd1
degeneration 1 mutation (Pde6b ), which causes
generations.
blindness; a few carry the toll like receptor 4
Lps-d
The promoter driving the Cre may give only mosaic cell
mutation (Tlr4
), which causes
expression in a tissue.
immunodeficiency.
3.C.1.c. Breeding mutant mice and selecting

controls
When developing and expanding a line of mutant mice, several
issues must be clarified:
The heritability and mode of inheritance of the phenotype.
The genetic background of the new mutant strain.
The breeding scheme used to expand and maintain the mutant
strain and perhaps create controls.
Also, as with any breeding of inbred strains, preventive measures
must be taken to guard against genetic contamination and
minimize genetic drift.
3.C.1.c.1. Heritability and mode of inheritance
Neither mutation is specified in C3H strain names,

such as C3H/HeJ (000659), which carries both
mutations, or C3HeB/FeJ (000658), which does
Lps-d
not carry Tlr4
. (This is yet another reason why
it is so important to learn the genetic details about
the mice you are studying. For JAX Mice, such

details are provided on the strain datasheets,
available at www.jax.org/jaxmice/query.)
Historically, when a mutation arises
spontaneously in the parental lineage and
becomes homozygous, it becomes part of the
genotype of the parental lineage, and the name of
the strain is not changed. However, when a new
strain is specifically created to carry a mutation,
even if the strain is coisogenic to the parental
strain, the mutation is designated in the new
strain name.
Regardless of the origin of a random mutation, the first step in

development of a mutant mouse line is to determine heritability
of the phenotype, whether it is monogenic, and whether it can be
carried homozygously. Heritability is proof that a phenotype is genetically determined.
Analysis of heritability also includes determining the mode of inheritancedominant, recessive,

or additiveand the degree of the penetrance. (For details about heritability, refer to 2.B.1,
Terminology.)
3.C.1.c.2. Strain background considerations

Once investigators have characterized the heritability of a mutation, they must consider the
genetic background they will use to carry the mutation. If the mutation arose or was created on a
well-characterized strain, and if the strain characteristics do not interfere with the study of the
mutation, it can be maintained on the original strain. If, however, the original background is
mixed or not well characterized, or if the strain characteristics could interfere with the study of
the mutation, it can be moved to another background, creating a congenic (see 3.C.2).
Generally, C57BL/6 is the preferred background because it is a well-characterized, robust strain.
3.C.1.c.3. Breeding schemes and choices for controls.

When choosing a breeding scheme, an important consideration is whether the priority is to
create as many mutant mice as quickly as possible or to expand the line more slowly but create
littermate controls at the same time. Table 3.8 describes the breeding options, several of which
can be used to produce control animals along with the mutant mice.
Note: Transgenic mice that are hemizygous are usually maintained by backcrossing to the
parental strain.
Table 3.8. Expansion and maintenance breeding schemes for strains with single-locus
mutations.
Conditions related to the mutation
Fertility
Mutants of both genders

are fertile
Mode of inheritance
Dominant or
semi-dominant
Mutants of neither
gender are fertile
Offspring
Heterozygous mutant x
homozygous wild-type
(M/+) x (+/+)
(M/+), (+/+)*
heterozygous mutant
(M/+) x (M/+)
(M/M), (M/+), (+/+)*
Homozygous mutant x
homozygous mutant
(M/M) x (M/M)
(M/M)
Heterozygous carrier x
heterozygous carrier
(m/+) x (m/+)
(m/m), (m/+)*, (+/+)*
Homozygous mutant x
homozygous mutant
(m/m) x (m/m)
(m/m)
(M/+) x (+/+)
(M/+), (+/+)*
Homozygous mutant x
(M/M) x (+/+)
(M/+)
Recessive
Homozygous mutant x
(m/m) x (m/+)
(m/m), (m/+)*
Dominant or
semi-dominant
Not applicable
Recessive
Mutants of only one

gender are fertile
Applicable breeding schemes

Description (genotypes)
Dominant or
semi-dominant
Recessive
Heterozygous carrier x
(m/m), (m/+)*, (+/+)*
(m/+) x (m/+)
M = dominant mutant allele; m = recessive mutant allele; + = wild-type allele.
* Can be used as littermate controls. See Table 3.9 for details.
If fertile ovaries can be obtained from mutant females, ovarian transplants can be used to expand the
mutant stock. This may be more efficient than intercross matings because fewer animals are needed. (For
more detail on ovarian transplants, see 13.E.2, Assisted reproductive techniques [ARTs].)
For breeding schemes that do not produce controls, other options exist. Table 3.9 highlights
these options.
Table 3.9. Choices of controls for specific mutant genotypes.
Mutant genotypes
Suitable controls
(M/M)
If a mutants genetic background is an inbred strain, that inbred strain

(coisogenic to the mutant strain) is a suitable control as long as the
mutant strain has not become a substrain.
If the mutants genetic background is mixed, F2 hybrids between the 2
parental strains are approximate controls. Although it is unlikely that an
F2 hybrid population will have the same genetic mix as the mutant line,
an F2 control is the best option if littermate controls cannot be used.
(M/+)
Same as for (M/M), plus

Wild-type (+/+) littermates are ideal controls.
(m/m)
Same as for (M/M), plus

For fully recessive mutations, heterozygote (m/+) siblings or wild-type
(+/+) littermates are suitable controls. (Typically, these controls are
designated (+/?) because they cannot be distinguished from each other
without genotyping.)
A recessive mutation that is fatal or that causes a critical phenotype such as sterility also can be
carried in a balanced stock, in which the mutation is linked to a marker gene (often one for coat
color) so that mutant mice and carriers of the mutation can be identified by sight. Balanced
stocks are infrequently used today because of the prevalence of genotyping; however, once a
balanced stock is created, it is very convenient to use. Several strains of JAX Mice are
maintained as balanced stocks. For details on breeding a balanced stock, refer to Appendix I,
Using a Balanced Stock to Carry a Recessive Mutation That Is Sterile or Lethal, Including
Embryonic Lethal.
3.C.1.c.4. Breeding considerations to minimize genetic drift

When maintaining a mutant strain, breeding strategies must minimize the creation of genetic
differences between the mutant strain and the background strain on which is resides. Use these
guidelines:
If the mutation is on a stable inbred strain, backcross to the parental strain about every 10
generations. This will prevent creation of a substrain.
If the mutation must be kept on a mixed background, choose breeders to minimize inbreeding
at each generation, and backcross offspring to the F1 hybrids between the two parental strains
about every 10 generations. This will prevent creation of recombinant inbred lines.
To learn when a specific strain of JAX Mice was most recently refreshed, contact Technical
Support at 1-800-422-6423 (North America) or 1-207-288-5845 (International).
3.C.1.d. Nomenclature
Nomenclature for strains with single locus mutations includes information about the background
strain or substrain followed by information about the gene and mutant allele. Note that the
designation for the mutation is the same whether it is carried homozygously or heterozygously.
For full strain details, check with the supplier of the strain. For JAX Mice, refer to the strain
datasheet (www.jax.org/jaxmice/query). Table 3.10 provides several examples of nomenclature
for single locus mutations.
Table 3.10. Examples of nomenclature for strains that carry single locus mutations.
Name
Definition
Convention
w-J
C57BL/6J-A /J
(000051)
Substrain of C57BL/6J (000664), in

which the agouti gene (A) is
homozygous for the mutated Aw-J allele;
maintained at The Jackson Laboratory
(J).
Background strain, hyphen (-),

symbol for the mutated allele
(italicized), forward slash (/),
and ILAR code(s)
(http://dels.nas.edu/
C3H/HeJ-Mgrn1md/J
(000223)
Segregating inbred strain, in which the

Mgrn1 gene is heterozygous for the
Mgrn1md allele; maintained at The
As above.
B6129PF1/J-Aw-J/Aw
(100409)
F1 hybrid, created from a

C57BL/6J-Aw-J/J (000051) female and a
129P3/J (000690) male (which is
homozygous for the Aw allele); the A
gene in the F1 is heterozygous for the
Aw-J allele and the Aw allele; generated
at The Jackson Laboratory (J).
As above, with optional allelic

information following ILAR
code(s).
B6;129S4-Nos1tm1Plh/J
(002633)
Targeted mutation one of the Nos1 gene

(Nos1tm1Plh), on a mixed C57BL6/J and
129S4/SvJae background (B6;129S4);
developed by P. L. Huang (Plh);
(J).
Background strain (strain

abbreviations separated by a
semi-colon [;] indicate less
than 5 or unknown number of
filial generations); hyphen (-);
gene (italicized), number of
targeted mutation (tm#) and
allele (italicized superscript);
forward slash (/), and ILAR
code(s) (http://dels.nas.edu/
ilar_n/ilarhome/search_lc.php)
C57BL/6-Tg
(CAG-EGFP)1Osb/J
(003291)
Transgenic mouse (Tg) on a C57BL/6

background, with insert of gene
enhanced green fluorescent protein
under the direction of promoter for beta
actin, (CAG-EGFP); 1st line created at
the Research Institute for Microbial
Diseases, Osaka University (Osb);
(J).
Background strain; transgene

symbol Tg; insert
designation, line number and
developer; forward slash (/);
and ILAR code(s)
(http://dels.nas.edu/ilar_n/
ilarhome/search_lc.php).
STOCK-Tg
(B19-RNAi:Il3)241Ckn/J
(002182)
Transgenic (Tg) mouse on a

background derived from 3 or more
founder strains (STOCK), in which an
Il3 antisense RNA transgene is
expressed under control of the B19
parvovirus promoter; 241st line created
by D. A. Cockayne (Ckn); maintained at
As above, with STOCK

designation to represent mixed
background of 3 or more
founder strains.
3.C.1.e. Research examples

A spontaneous mutation used to study the role of leptin in autoimmunity.
A spontaneous mutation in the leptin receptor (Leprdb-5J) of NOD/ShiLtJ (001976) mice, which
are prone to type 1 diabetes, resulted in a new strain: NOD/ShiLtJ-Leprdb-5J/LtJ (004939).
Research with this strain led to the demonstration that altered leptin signaling suppressed the
progression of type 1 diabetes in NOD mice (Lee et al., 2005). Had these investigators not been
so observant of the new phenotype, they would have missed the opportunity to discover the
surprising role of a fat tissue hormone (leptin) in the modification of an autoimmune disease.
ENU technology used to create a model for hyperlipidemia.
To discover new mouse models of cardiovascular disease, Svenson et al. (2008) used ENU
mutagenesis followed by high-throughput phenotyping. The researchers identified a new
missense mutation in the LDL receptor (Ldlr), which they named Wicked High Cholesterol
(WHC). When they compared mice bearing the WHC mutation to the widely used Ldlr
knockout (KO) mice, they observed notable phenotypic effects of the mutation, such as
accelerated atherosclerotic lesion formation and reduced hepatosteatosis in the WHC mutant
after a short exposure to an atherogenic diet. The WHC mutant carries, on a C57BL/6J (000664)
genetic background, a single-base mutation in the Ldlr gene that substitutes a G with an A in
exon 14 at nucleotide 2096. As a result, cysteine V at amino acid residue 699 is substituted by a
tyrosine (C699Y) in the extracellular EGF-precursor homology domain of the LDL receptor.
Although the EGF precursor homology domain does not participate in lipid binding, the
physiological effects of this mutation demonstrate that this domain influences the function of
the receptor, presumably through influences on tertiary structure. The WHC mutant provides a
useful new tool for understanding the pathophysiology of atherosclerosis and for evaluating
additional genetic modifiers regulating hyperlipidemia and atherogenesis. The creation and
discovery of WHC provides a good example of how ENU mutagenesis technologygenerating
single nucleotide mutants that do not appear naturallyhelps researchers understand structure
function relationships as well as overall function of the genes that are mutated.
Cre-lox technology used to demonstrate the relationship of fat to insulin metabolism.
Blher et al. (2003) used a Cre-lox System to study the influence, on energy metabolism, of
insulin signaling in fat tissue. They created mice in which the insulin receptor was floxed, i.e.,
in which an exon of the insulin receptor was surrounded by lox sites. By crossing these mice
with mice bearing a Cre-recombinase transgene under the regulation of the AP2 promoter,
which limits expression of the recombinase to white fat, the researchers produced mice in which
white fat had no insulin receptors. As a result, the amount of fat tissue was greatly diminished.
Because these Cre-lox mice were more insulin-sensitive than normal, a role for white fat in the
development of insulin resistance, which promotes type 2 diabetes, was demonstrated.
Interestingly, these Cre-lox mice also lived about 15% longer than the various controls (mice
with only the Cre-recombinase transgene, mice with only the floxed insulin receptor, and mice
of the same mixed genetic background with neither mutation), demonstrating a role for even
normal levels of white fat in limiting lifespan.
3.C.2. Congenic and conplastic strains

A congenic strain is one in which a short chromosomal segmentcontaining a gene with an
allele of interestis transferred to a different genetic background through selective breeding
using either phenotypic or genotypic screening. It is important to note that this chromosomal
segment contains other linked genes as well.
Historically, congenic strains were generated to
help understand the effects of genetic variants on
transplantation biology. Most strains were major
histocompatibility complex (H2), minor
histocompatibility complex (H), nonhistocompatibility alloantigen, and cellular marker
congenics. Today, uses include the study of
mutations on a standardized genetic background.
Why are there so many B6.129 congenic

strains?
A large number of congenic mice are produced
using knockout and knockin mutants that were
created from 129 ES cells. Chimeras often are
made by combining genetically engineered 129
ES cells with embryos from a strain that can be
distinguished from 129 by coat color. C57BL/6J
(000664) is such a strain. When the chimeras
are mated with C57BL/6J mice, the chimeras
that have gone germline produce agouti
offspring, which are B6129F1 hybrids. The
chimeras that have not gone germline produce
only black offspring, which are C57BL/6J inbred
mice.
Congenic mice are particularly useful for the

following purposes:
To clean up a genetic background. By putting
the allele of interest on a standardized inbred
strain, researchers can quantify the effects of the
When the B6129F1s are mated together to
allele on a well-defined and reproducible
propagate and expand the stock, a genetically
background.
mixed background is produced. To move the
mutation to a standardized genetic background,
To study an allelic series on the same genetic
often a congenic is made on the C57BL/6J
background. This allows researchers to directly
backgroundresulting in a B6.129 congenic.
compare the effects of the various alleles for a
specific gene on one, well-defined background.
To study the effect of a given allele on multiple, standardized backgrounds (i.e., C57BL/6J
[000664], C3H/HeJ [000659], DBA/2J [000671]. This allows researchers to study the effects
of modifying genes.
To support gene mapping and positional cloning studies.
We include conplastic strains in this discussion about congenics because a conplastic strain is a
mitochondrial congenic, a mouse that contains the nuclear genome of one strain and the
mitochondrial genome of another.
3.C.2.a. Definitions, characteristics and value

3.C.2.a.1. Congenic strains
Congenic strains are produced by
transferring a chromosomal segment (including the allele of interest) from a mouse of one
strain or stock to an inbred strain through outcrossing (generation N1, which is the same as an
F1 generation), and then by
backcrossing mice with the allele or phenotype of interest for nine more generations (N2
N10), generally reversing the gender of the inbred strain and the carrier breeders at least once
to assure that both Chr Y and the mitochondrial chromosome are the recipient type.
A congenic strain has been backcrossed for at least 10 generations. Statistically, at this point,
99.8% of the allelic differences between the donor and recipient strains that are unlinked to the
congenic locus are expected to be the recipient type in the congenic (Figure 3.6) (Silver, 1995).
Note that the amount of donor genome linked to the selected gene or marker is reduced at a
much slower rate, approximately equivalent to 200 cM/N, where N is the number of backcross
generations for N > 5 (Silver, 1995).
It can take up to three years to create a fully congenic strain (N10). Therefore, researchers
sometimes use incipient congenics (N5N9) in their initial studies because at that point in the
backcrossing process, at least 94% of the genetic background, on the average, is recipient type.
After N10, the breeding strategy depends on whether the congenic strain is to be kept as a fully
inbred congenic strain, in which the donor allele is homozygous, or as a segregating inbred
congenic strain, in which the donor allele is kept heterozygous at the congenic locus. (A
segregating inbred congenic strain is useful when the congenic allele is dominant or additive
and a researcher wishes to produce carriers and non-carriers within the same cross.)
A fully inbred congenic strain requires a filial intercross (F1) after the N10 generation, followed
by filial breeding (F2) of offspring that are homozygous for the donor allele. Note that although
the genetic background for the inbred congenic strain is virtually completely recipient type, the
congenic locus includes passenger genes that will be donor type.
A segregating inbred congenic strain is maintained after N10 by continued backcrossing to the
parental strain. In the segregating congenic, the genes that are linked to the congenic locus, and
that have allelic differences between the donor and recipient, will also be heterozygous.
Figure 3.6. Effects of backcrossing on homozygosity and heterozygosity.
The effects of
backcrossing on
homozygosity and
residual heterozygosity
(unlinked to the
congenic locus)
throughout the process
of creating congenic
mice. The symbols
represent residual
heterozygosity at any
given generation,
expressed as the percent
of the original
heterozygosity in the N1
generation. The filled
triangles and diamonds
represent mean values.
For any individual
mouse, the value will
probably differ from the
mean.
It takes only 10 generations to create an inbred congenic, while it takes 20 generations to create
a standard inbred strain. This is because in creating a congenic, one of the parents is always
100% homozygous for the recipient genotype. Figure 3.7 illustrates this comparison.
Figure 3.7. Effects of backcrossing vs. intercrossing (inbreeding) on percentage of original
heterozygosity that is homozygous for all future generations.
By the 10th generation of backcrossing, the
congenic strain is homozygous (recipient
type) for 99.8% of the original genetic
differences from the donor strain that are
not linked to the congenic locus. For
inbreeding by sibling mating, it takes 30
generations of inbreeding to reach that
percentage of homozygosity.
Creating a congenic strain using phenotyping

Today, because genetic markers are available for most mutations, congenic mice are commonly
created using selective breeding based on genotyping. Traditionally, however, congenics were
created for a known monogenic trait by selecting for the desired phenotype at every generation.
This approach is sometimes used today, especially when a genetic marker is unavailable.
Selection based on phenotypes requires multiple strategies, based on the characteristics of the
mutation. These strategies are described in Appendix H, Transfer of a Mutant or Variant Allele
to a New Genetic Background by Phenotypic Selection.
Creation of speed congenics using marker-assisted backcrossing
Speed congenics are congenic mice created using a breeding strategy that reduces the number of
backcross generations necessary to fix (to the recipient type) the required 99.8% of the genetic
differences between the donor and recipient strains. This strategy involves genotyping using
single nucleotide polymorphism (SNP) markers and/or microsatellite (SSLP) markers to select
the most suitable mice, i.e., those with the
greatest amount of the recipient genotype, for
Are speed congenics worth the expense?
backcrossing. At The Jackson Laboratory, we
A drawback with creating congenics using
recommend placing markers about every 10 cM.
traditional backcrossing is that the process takes
about 2.53 years. This can be a major
Speed congenic technology can reduce the
impediment to progress of a research program. In
number of required backcrosses from 10 to 5
contrast, creating a speed congenic takes just
and save 1-1/2 years. Speed congenics provide
about 1.5 years. Although the process to create a
another benefit: any residual heterozygosity is
speed congenic is more expensive, the time
well-defined.
savingsand the fact that the strain is so well-
3.C.2.a.2. Conplastic strains
definedmight make a speed congenic the

preferred option.
For information on the speed congenic service at

A conplastic strain has the nuclear genome of
The Jackson Laboratory, visit
one strain and the mitochondrial genome of
www.jax.org/jaxservices/speedcongenic. Or call
another. Conplastic strains are used mostly to
us at 1-800-422-6423 (North America) or 1-207study the role of mitochondrial genes in energy
288-6294 (International). We will analyze your
balance and disease risk.
needs and help you determine whether a speed
congenic is the right choice for your research
A conplastic strain is developed by
program.
initial outcrossing of a female mitochondrial
donor with a male recipient (generation N1)
followed by
continued backcrossing, mating one female of each generation (the mitochondrial donor) to a
male of the recipient strain for at least 9 additional generations (N2N10).
The effects of backcrossing on homozygosity and residual heterozygosity of conplastic strains is

the same as for congenics (Figure 3.7), except that for conplastic strains, few, if any, passenger
genes are involved because only the small number of genes encoded by the mitochondrial DNA
are transferred.
3.C.2.b. Considerations
In a congenic strain, a short chromosomal segmentcontaining multiple genes rather than a
single geneis transferred to an inbred strain by successive backcrossing. Along with the allele
of interest, this segment includes donor-type alleles that are commonly referred to as passenger
genes or linked genes. The transfer of these donor-type alleles has important implications for
research:
Although the congenic strain is very closely related to the recipient strain, the strains will
differ at locations in addition to the gene of interest. Therefore, the strains are not coisogenic.
Variants of phenotypic expression in the congenic strain might result from an interaction of
the recipient background with the allele of interest or from an interaction of the recipient
background with passenger genes from the donor. Thus, a variant phenotype observed in a
new congenic strain cannot be attributed exclusively to an interaction of the target gene with
the recipient genotype.
3.C.2.c. Maintenance breeding strategies

Following the creation of an inbred congenic strain or segregating inbred congenic strain,
maintenance of congenic strains is the same as for single locus mutations (see 3.C.1.c.3, Table
3.8, Expansion and maintenance breeding schemes for strains with single-locus mutations.
Conplastic strains are maintained by backcrossing females of the conplastic strain to males of
the recipient strain.
For detailed information on breeding strategies for specific congenic or conplastic strains of
JAX Mice, refer to the strain datasheet, available at www.jax.org/jaxmice/query.
3.C.2.d. Controls
For congenic mice, the selection of controls is based on the nature of the mutation.
Considerations are the same as those specified for random mutations (see 3.C.1.c.3, Table 3.9,
Choices of controls for specific mutant genotypes). For conplastic mice, controls are the
recipient inbred strain.
3.C.2.e. Nomenclature
Nomenclature for congenic strains includes information about recipient and donor strains as
well as the locus of interest. Nomenclature for conplastic strains includes names of the
mitochondrial donor strain and the recipient strain. Numbers of generations of backcrossing and
inbreeding (designated by N for backcross generation and F for filial generation) generally are
not reflected in the name, but are important pieces of information that should be provided by the
supplier. For example, N6F20 designates that a strain has been backcrossed 6 times followed by
20 generations of sisterbrother mating. A question mark indicates that data are not available.
For example, N(?)F25 means that the number of backcross generations is unknown, but the
mice have been inbred for 25 generations. Table 3.11 provides several examples of congenic
and conplastic strain names.
Table 3.11. Examples of nomenclature for congenic and conplastic strains.
Name
Definition
Convention
B6.129P1-Lama2 /J
(000631)
Congenic strain, where locus of

interest (Lama2dy) of the 129P1
donor strain has been
backcrossed to recipient strain
C57BL/6J (B6) at least 5 times
(.) at The Jackson Laboratory
(J).
Abbreviation of recipient strain, period

(.), abbreviation of donor strain, hyphen
(-), locus of interest (in italics), forward
slash (/), and ILAR code(s)
(http://dels.nas.edu/ilar_n/ilarhome/
search_lc.php).
Note: Congenic strain names, which
include a period (.), are assigned at
backcross generation 5 (N5). Congenics
from N5 to N9 are called incipient
congenics. A full congenic requires 10
backcross generations. For details about
the number of backcross generations for
a particular strain, check with the
supplier. For JAX Mice, refer to the
strain datasheet at
www.jax.org/jaxmice/query.
B6.Cg-Ay/J
(000021)
Congenic strain, where locus of

interest (Ay) from a mixed donor
stock (Cg) was backcrossed to
recipient strain C57BL/6J (B6)
at least 5 times (.) at The
As above, with Cg representing a

mixed donor stock.
C57BL/6J-mtPWD/Ph/ForeJ
(0005761)
Conplastic strain, in which the

mitochondrial genome (-mt) of
PWD/Ph was transferred to
C57BL/6J by J. Forejt (Fore);
maintained at The Jackson
Laboratory (J).
Strain of nuclear genome, mitochondrial

symbol (-mt), strain of mitochondrial
genome (superscripted), ILAR code(s)
search_lc.php).
dy
3.C.2.f. Research examples

Use of congenic strains in discovery of function of Lith1 and Lith2 genes.
Congenic strains were instrumental in the discovery of Lith1 and Lith2 genes, both of which
determine cholesterol gallstone formation (Paigen et al., 2000). Researchers started with two
inbred strains, C57L/J (000668) and AKR/J (000648) that differed with respect to gallstone
formation (C57L/J forms gallstones readily when fed a lithogenic diet; AKR/J does not). They
created an F1 hybrid from the two strains and backcrossed it to the resistant strain, AKR/J. They
fed these mice a lithogenic diet and mapped the phenotype gallstone formation. Two loci
were identified: Lith1, which mapped to Chr 2; and Lith2, which mapped to Chr19.
Confirmation that these genetic regions actually contained a gene or genes that regulates
gallstone formation required further work. By moving the chromosomal regions containing the
gallstone formation genes from the C57L/J strain to the AKR/J strain, i.e., by constructing the
congenic strains AK.L-Lith1C57L/J and AK.L-Lith2C57L/J, the researchers conferred susceptibility
to the previously resistant AKR/J strain. This directly demonstrated that the Lith1 and Lith2 loci
contained genes that controlled gallstone formation. Once the genes underlying these QTLs are
identified, the roadmap for discovery of orthologous human LITH genes will be available,
and the putative roles in cholesterol gallstone formation can be tested in selected human
populations.
Use of conplastic strains to modify free radical production.
Gusdon et al. (2007) used conplastic strains of mice to study the affect on mitochondrial
function of a variant in a mitochondrially encoded gene that retards the development of type 1
diabetes. The researchers transferred the a variant of the NADH dehydrogenase subunit 2
gene (mt-Nd2a), carried by mitochondria from ALR/LtJ (003070) mice, to the NOD/ShiLtJ
(001976) genetic background by creating the NOD/ShiLtJ-mtALR/LtJ/Mx conplastic mouse. They
also created the reciprocal ALR/LtJ-mtNOD/ShiLtDvs/Mx conplastic, which places mitochondria
with the common mt-Nd2c variant on the ALR background. Gusdon et al. (2007) demonstrated
that mitochondria carrying the mt-Nd2a variant produced a lower level of free radicals in vitro
than mitochondria with the mt-Nd2c variant, whether the nuclear genome was ALR- or NODtype. This work demonstrates that conplastic strains with ALR/LtJ mitochondria may be
valuable as a means of determining if reduction of free radical generation can moderate other
diseases such as atherosclerosis and hypertension, as well as type 1 diabetes.
3.D. Recombinant strain panels

3.D.1. Overview
Three of the categories of laboratory mice are associated with strain panels that are developed
from outcrosses of inbred strains: recombinant inbred (RI); recombinant congenic (RC); and
chromosome substitution (CS; also called consomic) strains, including genome tagged strains.
These strain panels generally are based on the outcrossing of two founder strains to create an F1
generation, followed by intercrossing or backcrossing or a combination of both to create a set of
new inbred strains. The mice of each inbred strain panel contain portions the genetic makeup of
the founder strains recombined in multiple, uniqueand very well-definedconfigurations.
RI, RC and CS inbred strain panels extend the advantages of standard inbred strains:
Because the founders are well-characterized inbred strains, investigators can take advantage
of previous research and accumulated data to choose phenotypes that are differentially
regulated in the founder strains, and, therefore, whose genetics can be studied using the panel.
Because each of the multiple strains within a panel is inbred, investigators can take advantage
of the powerful research capabilities afforded by inbred strains. In particular, researchers can
draw on the accumulated information about phenotypes and genotypes for each of the strains
in the panel.
Because extensive genetic data and maps exist for most recombinant strain sets, mapping a
newly-characterized trait often requires no additional genotyping.
Because the genotype of a euthanized mouse is not lost, phenotypes that require terminal
but multiplesampling can be studied. For example, longitudinal information on invasive
measures can still be generated for a given genotype.
Because data acquired for a recombinant strain set are cumulative, researchers can compare
their results for one phenotype with information for other phenotypes from the same set of
strains to identify phenotypes that are genetically correlatedwithout mapping.
For mapping studies, specific recombinant strains identified as critical for initial mapping can
be crossed for fine mapping. This approach requires less phenotyping and genotyping than
more traditional fine mapping strategies.
Quantitative trait loci (QTLs) that are mapped using recombinant strain sets can be quickly
verified and refined by generating sets of either intercross or backcross lines between the
strains with recombinations in critical QTLs.
Data obtained from several recombinant strain sets can be compared or combined,
particularly if the sets have a founder strain in common or if they segregate for alleles of
common origin in the genomic region(s) of interest.
A recombinant panel can be used to map a quantitative trait that has a great deal of nongenetic variance. Because many copies of each genotype are available, a precise mean
value of the phenotype for a given genotype can be determined by evaluating multiple
individuals for each recombinant strain of the panel. The same principle applies for
phenotypes with incomplete penetrance.
Table 3.12 provides an overview and comparison of RI, RC, and CS panels. Detail on each
panel type follows the table.
Table 3.12. Comparison of recombinant inbred (RI), recombinant congenic (RC), and chromosome
substitution (CS) panels.
Panel type
Development scheme
Specific uses and limitations
Recombinant inbred (RI):

Set of inbred strains, in
which about 50% of the
genome of each RI strain is
from each founder strain in
unique combinations.
Outcross 2 inbred strains to

create F1s.
Intercross F1s to create
F2s.
Intercross sibling pairs
from F2 generation into
multiple inbred lines.
Continue intercrossing to
F20.
Uses:
Determining whether one or multiple genes regulate a
phenotype.
Mapping for monogenic traits without genotyping.
Easy identification of genetic correlations by comparison of
the strain distribution of a new phenotype with the published
strain distributions of other phenotypes.
Mapping a phenotype with large non-genetic variation or
incomplete penetrance.
Limitations:
Less useful for complex traits because allele combinations
that are needed for expression of the trait are broken up
within each RI line.
Recombinant congenic (RC):

Set of inbred strains in
which a small amount25%
or lessof the genome of
each RC strain is from a
donor strain. For each RC
strain, this amount is
randomly drawn from the
donor genome.

create F1s.
Backcross N2 and N3
generations.
Intercross N3 sibling pairs
for 14 more generations
(F1F14) into multiple
inbred lines.
Uses:
Mapping for monogenic and complex traits.
Constructing a single-locus congenic strain (from a single
RC strain).
Limitation:
Few RC strain panels exist.
Chromosome substitution
(CS):
Set of inbred strains in
which individual
chromosomes have been
replaced by homologous
chromosomes from the
donor strain.

create F1s.
Starting with F1s,
backcross progeny for 9
additional generations.
With each backcross, use
marker-assisted selection
for a single, complete
donor chromosome.
After N10, intercross until
all markers for the target
chromosome are donortype.
Uses:
Rapid mapping of phenotype to a chromosome.
Analysis of complex traits (multiple QTLs can be
identified).
Fine mapping of QTL using one CS strain as a parent and a
founder strain as the other parent.
Identification of modifier genes.
Limitations:
Initially, a phenotype is mapped to an entire chromosome.
Initially, cannot discriminate between single and multiple
QTLs when they are on one chromosome.
Few CS strain panels exist.
3.D.1.a. Considerations
Considerations for the use of recombinant strain panels include the following:
Phenotypic variance for a complex trait may emerge among strains of a recombinant panel,
even when the founder strains do not express the variance, because unique combinations of
alleles can produce epistatic effects within one or more of the recombinant strains. This
epistatic variance then can be analyzed by performing crosses involving the individual
affected strains and the founder strains.
Coat color provides a very clear example of how this epistatic variance can affect phenotypic
expression. When RI lines are constructed, coat color alleles that differ between the founder
strains at multiple loci, and which may or may not be expressed, assort randomly. Thus, coat
colors of mice from different strains within a panel may vary, and some may even differ from
either founder strain.
During propagation of recombinant lines, mutations may occur spontaneously and be bred by
chance to homozygosity, as with any inbred strain. This possibility may confound genetic
analyses because the mutation is not shared by other strains of the panel or by either of the
founder strains. As a preventive measure, The Jackson Laboratory preserves many RI lines as
cryopreserved embryos.
Initial characterization of a phenotype across inbred strains of a panel involves the assessment
of numerous strains, ideally at the same age and at the same time. It is usually impossible to
use such a balanced design, however, because acquisition and breeding of the strains is
difficult to completely synchronize. The best alternative is to include mice of a readily
available control strain (usually a parental strain of the panel) every time any mice of the
panel are tested. Thus, the degree of uncontrolled variation in the phenotype over time can be
evaluated and statistically controlled. This strategy increases the number of control mice that
must be evaluated, but minimizes misleading results.
3.D.1.b. Comparison to F2 hybrids

Mice from an F2 generation also provide genetic diversity and genome reorganization.
Therefore, sometimes their use is compared with that of RI, RC or CS strain panels. But the two
categories have very different characteristics: Mice of each F2 generation must be created from
an F1 generation, which must be created from two inbred strains. The genome of each F2 hybrid
is unique and is not reproducible; it must be evaluated for each F2 mouse. In contrast, the
genomes of individual mice within any inbred strain of a panel are identical by definition and
perpetually renewable. The genome of each strain need be determined only once.
3.D.2. Recombinant inbred (RI) strain panels

3.D.2.a. Definition, characteristics and value
A recombinant inbred (RI) strain panel comprises a set of inbred strainsRI lineseach of
which contains genetic contributions from two different inbred founder strains in a unique,
random distribution throughout the genome. The genome of each line comprises 50% of the
genome of each founder strain, but in a unique combination (Bailey, 1971; Taylor, 1978).
Figure 3.8 provides an overview of creation of an RI strain panel and an example of the genetic
variance that can occur on Chr 1.
Figure 3.8. Creation of recombinant inbred (RI) lines; example of effect on Chr 1.
Due to inbreeding depression, not all strains survive. Thus, some line numbers are missing in the final
panel. For example, in the illustration, line AXB2 did not survive.
The original purpose of the RI strain panel was as a mapping tool to enable rapid mapping of a
phenotype at a time when this process was very difficult. Researchers created RI panels from
founder strains with phenotypic differences that were already mapped (C57BL/6J [000664] and
DBA/2J [000671], for example), which provided a scaffold of genetic markers with known map
locations and associated strain distribution patterns. They could then evaluate any new
phenotype in the RI lines and compare its strain distribution to those of known markers. Strain
distributions that correlated between a new and a known marker would designate the map
location of a gene that regulated the phenotype. Thus, if a trait differs between two inbred
strains for which an RI panel exists, it may be possible to map a gene regulating that trait
without additional genotypingsimply by phenotyping the lines in the panel. Furthermore, if
enough strains are available, an RI panel can have about four times the resolution of an F2 cross
(because of recombinations that occurred when the RI line was created).
Today, researchers also use RI lines to test hypotheses of causality between phenotypes. If two
phenotypes (for example, obesity and mammary tumor incidence) appear in Strain A, but not in
Strain B, an investigator might propose that the two phenotypes are causally relatedthat
obesity promotes mammary tumor formation. They could test this hypothesis by evaluating an
RI panel for the two phenotypes. If the strain distributions of the two phenotypes differ, they
would conclude that the phenotypes are not directly related and that their association in the
founder strains may be coincidental. If the strain distributions coincide in a sufficient number of
strains to provide statistical significance, researchers would conclude that the phenotypes are
genetically linked. Although this does not prove that the phenotypes are regulated by the same
gene, it does provide a basis for proposing that they are. Three possibilities exist: one phenotype
may be directly caused by the other; both phenotypes may be regulated by the same gene; or the
phenotypes may be regulated by closely linked genes. Additional studies, such as fine mapping,
targeted mutagenesis, or phenotypic modification, are necessary to distinguish among these
possibilities.
As with any genetic mapping resource, the greater the number of different samples (in this case,
the number of RI strains in a set) that are used to analyze a trait, the more precisely the trait can
be mapped. Thus, large sets of RI strains offer obvious advantages over small ones. It is
generally observed that, when mapping a single locus trait, at least 13 RI strains within a panel
must be evaluated to obtain statistical significance.
Variations:
Sometimes, RI panels are created from crosses other than F1 hybrids of two inbred parental
strains. Examples:
Advanced intercross lines, generated from multiple generations of intercrosses before
inbreeding, which breaks the genome into smaller segments than in a traditional RI strain and
which allows for more precise mapping.
Multi-strain crosses (for example, an 8-way cross), which provide much greater genetic
diversity but require more lines in the mapping panel.
3.D.2.b. Maintenance breeding strategies

RI lines are maintained by sibling incrossing, as other inbred strains are. Due to genetic
variation and inbreeding depression, it is not unusual for reproductive performance to vary from
line to line within an RI panel. Some lines may reproduce very poorly.
3.D.2.c. Nomenclature
Nomenclature for RI strains includes abbreviations for the two founder strains, separated by an
X, the number of the RI line, and other information. The abbreviation of the female strain used
in the initial cross is listed first. All members of an RI set are serially numbered, regardless of
how many laboratories produced them. Many abbreviations used for RI strains differ from those
used for hybrid strains. For clarification, refer to strain information from the supplier. Table
3.13 provides several examples of RI strain names and their interpretation.
Table 3.13. Examples of nomenclature for recombinant inbred (RI) strains.
Definition
Convention
BXD1/TyJ
(000036)
BXD2/TyJ
(000075)
BXD5/TyJ
(000037)
Name
The first (1), second (2) and fifth (5)

lines in an RI panel derived from a cross
between a C57BL/6J (B) female and a
DBA/2J (D) male; developed by B. A.
Taylor (Ty); maintained at The Jackson
Laboratory (J).
Abbreviation for strain of female founder,

X, abbreviation for strain of male
founder, line number in the panel, forward
slash (/), and ILAR code(s)
search_lc.php)
Note: Not all lines survive inbreeding;
thus, gaps in the sequence of line numbers
sometimes appear.
CX8B/EiJ
(001568)
CX8D/EiJ
(001569)
The (B) and (D) lines in an RI panel

created by crossing a Balb/cWt (C)
female with a C58/J (8) male;
developed by E. Eicher (Ei); maintained
at The Jackson Laboratory (J).
As above with grandfathered exception:

line designated by alphabetic letter.
3.D.2.d. Research examples

An RI panel used to study the genetics of angiogenesis.
Rogers et al. (2004) used composite and multiple interval mapping in a BXD RI panel (based on
a C57BL/6J [000664] and DBA/2J [000671] cross) to identify novel QTLs on Chrs 4, 13, 5, and
18 that regulate the induction of angiogenesis by the vascular endothelial growth factor (VEGF).
Polymorphisms in the associated genes may influence individual susceptibility to angiogenesisrelated diseases such as cancer, macular degeneration, atherosclerosis, and arthritis.
An RI panel used to discover loci that control transcript expression of acute phase proteins.
Vazquez-Chona et al. (2005) used mice from two panels of RI strains based on C57BL/6J and
DBA/2J inbred strains. One RI panel was developed at The Jackson Laboratory, the other by
Peirce et al. (2004). Vazquez-Chona and colleagues found three loci that control transcript
expression of acute phase proteins in the brains of these mice. The genotype at one locus, on
Chr 12, was highly correlated with the expression of classic acute phase genes. Within this locus
they identified the inhibitor of DNA binding 1 (Id2) as a candidate upstream regulator.
The Collaborative Crossan RI panel used to map complex traits across inbred lines.
The Collaborative Cross, designed specifically for complex trait analysis, is an RI panel
developed by crossing eight, genetically diverse, inbred strains of JAX Mice (Churchill et al.,
2004). About 1,000 strains will be produced to complete the project; 650 lines are presently in
production (Chesler et al., 2008). The project is under the supervision of The Complex Trait
Consortium, an international group of scientists that includes several from The Jackson
Laboratory. With a defined, stable, and reproducible population of about 135,000
recombinations, mapping resolution will be high enough to dissect virtually any complex trait
and characterize its epistatic and gene-environment interactions. By providing a large, common
set of genetically defined mice, the Collaborative Cross will become a focal point for
cumulative and integrated data collection on diverse phenotypes, facilitating a systems approach
to mammalian genetic analysis. The availability of mice from a fully genotyped panel is
expected to greatly reduce the barrier to entry for new studies, particularly for nongeneticists.
As another component of the project, F1 (RIX) progeny, as a group, will be a source of virtually
unlimited, yet reproducible, combinatorial diversity that will represent the genetic structure of
human populations far better than any other conventional mouse crosses.
3.D.3. Recombinant congenic (RC) strain panels

3.D.3.a. Definitions, characteristics and value
Although RI panels are very useful for studying monogenic traits, the most common human
diseases are polygenicrequiring a specific allelic configuration of multiple genes. To apply
the advantages of inbred strains to the study of polygenic traits, researchers developed
recombinant congenic (RC) strain panels (Demant and Hart, 1986). An RC strain panel
comprises a set of inbred strains, each of which contains small segments of an inbred donor
genome transferred to an inbred recipient genome. The creation of an RC strain panel is very
similar to that of an RI panel, with one major
Figure 3.9. Chr 1 in four lines of the CcS RC strain
difference: following the initial outcrossing of the
panel.
donor and recipient strains, lines of the RC strain panel
are backcrossed, typically for two generations, before
intercrossing (Demant and Hart, 1986). In an RC panel
of 18 strains created using two backcross generations,
about 90% of the donor genome is represented, but in
each individual strain, only about 12.5% of the donor
genome, on the average, is represented. As a result, an
allele that participates in determining a complex trait
can be separated from the other alleles influencing that
trait, and its effect can be studied in isolation. In
principle, the RC panel transforms a multigenic trait
The CcS RC panel was constructed from the BALB/cHeA
(recipient) and STS/A (donor) inbred strains. Adapted from
into a series of single gene traits. Figure 3.9 provides an
Groot et al. (1992).
example of the genetic variation among RC strains.
An important consideration in using RC strains is that, in comparison to RI strains, less of the
donor genome is represented in each RC strain. Therefore, to obtain the same degree of
coverage of the donor genome, a greater number of RC strains is necessary.
Variations:
RC panels also can be developed using alternative strategies:
The number of backcrosses can vary. Increasing the number of backcrosses decreases the
proportion of the donor genotype in each strain. Note: Because backcrossing increases
homozygosity twice as fast as does sibling intercrossing, an RC strain is considered inbred
when the sum of the number of intercross (F) generations plus twice the number of backcross
(N) generations (including the initial cross) is at least 20.
During development of an RC strain panel for a particular
Standard inbred strains can be considered a
large RC panel.
complex trait, selection strategies are used to identify breeders.
As with congenic strain development, selection can be based
Recently, some in the scientific community have
started to think of the classical inbred strains as a
either on phenotype or genotype. But unlike congenic strain
set of recombinant congenics that developed with
development, for which selection is made on only the donor
a majority of genetic material (~8595%) from M.
genotype or phenotype, selection for RC strains can involve
domesticus and a small amount (~515%) from M.
phenotypes or genotypes of the recipient as well as the donor.
musculus. This concept permits the potential to
When selecting on phenotype, because the trait is complex,
apply recombinant congenic analysis for mapping
to any phenotype that has been characterized for a
multiple loci will be involved in producing the trait. These loci
large number of inbred strains (Yang et al., 2007).
will be isolated (along with some irrelevant loci) in the RC
strains. Further mapping studies and crosses of specific RC
strains can then be used to identify the genetic interactions that
regulate the phenotype. When selecting on genotype, loci regulating the trait are identified in
a preliminary cross. These loci are selected in various combinations during backcrossing to
produce the RC strain panel. Phenotypic variation among the individual RC strains can then
be related to a particular combination of loci within that strain.

RC strains are maintained by sibling incrossing, as other inbred strains are. Reproductive
performance may vary among strains within a set.
Nomenclature for RC strains includes the two founder strains and the line number. The strain of
the female is listed first. Table 3.14 provides several examples of RC strain names and their
interpretation.
Table 3.14. Examples of nomenclature for recombinant congenic strains.
Name
Definition
Convention
NONcNZO5/LtJ
(004455)
NONcNZO10/LtJ
(004456)
The fifth (5) and tenth (10) lines of an

RC panel derived from a cross between
a NON/ShiLtJ (NON) female and a
NZO/HiLtJ (NZO) male; developed by
E. Leiter (Lt); maintained at The
Abbreviation for strain of female

founder, c, abbreviation for strain of
male founder, line number in the panel,
forward slash (/), and additional
information, including ILAR code(s)
search_lc.php).
Note: Not all lines survive inbreeding;
thus, gaps in the sequence of line
numbers may appear.
CBcNO7A/LtJ
(003052)
The (A) subline of the seventh (7) line

of an RC panel derived from a cross
between a CBA/JLsLt (CB) female and
a NOD/Shi (NO) male; developed by E.
Leiter (Lt); maintained at The Jackson
Laboratory (J).
As above, with uppercase alphabetic

subline indicator (A).

Use of an RC panel to characterize the polygenic regulation of induced-colon cancer.
The genetic regulation of 1,2-dimethylhydrazine (DMH)-induced colon tumors was analyzed
using an RC panel between BALB/cHeA (resistant) and STS/A (susceptible). An RC panel was
used because the trait is polygenic. The CcS/Dem RC strains differed widely in the development
of DMH-induced colon tumors, indicating that a limited number of genes with a major effect are
responsible for the high susceptibility of the STS/A strain. The data for the number of tumors
and the size of the tumors had different strain distribution patterns, indicating that these subphenotypes were regulated by different sets of genes (Moen et al., 1991). Further studies of the
susceptible strains identified four loci (susceptibility to colon cancer loci: Scc-1, -2, -3, -4) that
mapped to four different chromosomes (Groot et al., 1992).
Use of an RC panel to characterize control of a trait by genes with low penetrance.
The genetic regulation of N-ethyl-N-nitrosourea-induced lung cancer was studied in an RC
panel derived from B10.O20 (resistant) and O20 (susceptible) inbred strains. From F2 crosses of
five OcB strains with O20 mice, 730 F2 hybrids were typed and scored for tumor number and
size. Thirty lung cancer susceptibility (Sluc) loci (14 of which were previously reported) and 25
two-way interactions between loci were identified. Thus, advanced crosses of specific RC lines
with one of the parental strains elucidated the genetic complexity of lung cancer and identified
many new loci and interactions among loci (Tripodis et al., 2001).
Use of an RC panel to study the interaction of genetic elements that regulate a complex trait.
To study genetic interactions affecting type 2 diabetes (T2D), a series of 10 RC strains was
constructed between NZO/HlLt mice, which develop a polygenic T2D, and NON/Lt mice,
which express genetically determined risk factors for T2D, but do not develop frank diabetes.
The strains were constructed on the NON/Lt background by selecting for combinations of NON
and NZO loci that were known QTLs for obesity and diabetes. All ten strains gained
significantly more weight than the NON/Lt founder strain, but none were as obese as the
NZO/HlLt founder strain. Strain-specific T2D incidence ranged from 0100% and was
influenced by the number of specific diabetogenic QTL. Some obese strains did not develop
T2D, demonstrating that obesity alone does not cause T2D; other conditions are necessary. In
contrast, the NONcNZO10/LtJ (004456) strain manifested a 100% incidence of T2D without
the extreme obesity of the NZO founder strain. Thus, this RC panel captures alleles that interact
with obesity to either enhanceor diminishrisk for T2D, and models the polygenic nature of
T2D in humans (Reifsnyder and Leiter, 2002).
3.D.4. Chromosome substitution (CS) strain panels and genome

tagged mice
3.D.4.a. Definitions, characteristics and value
3.D.4.a.1. Chromosome substitution (CS) strains
A CS strain (sometimes called a consomic strain) is an inbred strain in which one of its
chromosomes is replaced by the
Figure 3.10. Chromosomal differences among strains
homologous chromosome of
of a CS strain panel.
another inbred strain via a series
of marker-assisted backcrosses
(Nadeau et al., 2000; Table 3.12).
In principle, a complete CS panel
consists of 22 strains, each with
the same background genotype,
but each having one of 22
replacement chromosomes (Chr 1
19, Chr X, Chr Y, or the
mitochondrial chromosome) from
a single donor genotype (Figure
3.10). Occasionally, replacement
of a specific chromosome results
in infertility; therefore, multiple
strains, each with a portion of the
donor chromosome, are produced.
Sometimes investigators develop a
single CS strain to study one donor
chromosome on a recipient
background.
When constructing a CS strain,
progeny must be genotyped at
every backcross generation to
ensure that recombination has not
Each strain in the CS strain panel differs from the recipient
occurred between the donor
strain by one chromosome only. The 22-strain panel includes
chromosome and its recipient
replacements of all 22 chromosomes, one per strain. In the
counterpart. Traditionally, Chr Y
figure, black represents the recipient; gray represents the
has been transferred onto a new
replacement from the donor. Not represented in the figure is the
strain without genotyping because
conplastic CS strain, which differs only at the mitochondrial
chromosome.
recombination of Chr Y is rare.
After 10 backcross generations, a
CS line will be homozygous and recipient-type for 99.8% of the differences between the
foundersexcluding the substituted chromosome.
Analysis of a CS strain panel allows researchers to rapidly associate regulation of a phenotype

with a particular chromosome or chromosomes. The term used to identify the mapped trait is
quantitative trait chromosome (QTC). A QTC may carry more than one locus that affects a trait.
Other considerations when using a CS strain panel include the following:
CS strain panels are useful for analysis of Mendelian (monogenic) traits as well as complex
(polygenic) traitsmultiple QTCs can be identified in a single screen. In contrast, RI panels
can be used for direct mapping of monogenic traits only (Nadeau et al., 2000).
CS panels facilitate fine mapping. Once a QTC is identified, mice from the appropriate CS
strain can be backcrossed to the host strain, and progeny with recombinations in the donor
chromosome can be identified. Using this method, the location of a QTL can be resolved
(fine-mapped) relatively easily compared to mapping with F2 hybrids.
CS strain panels can be used to identify modifier genes that affect the phenotypic expression
of a mutation by crossing mutant mice to mice of different strains of the CS panel.
Differences in phenotypic expression among the different F1 hybrid progeny would identify
the location of a modifying locus.
Because genetic background noise inherent to genotyping crosses is minimized in CS strain
panels, and because non-genetic variance can be minimized by phenotyping multiple mice
from each strain, efficient confirmation of weak QTCs is possible, and tests for dominance or
additive modes of inheritance are efficient.
CS strain panels are particularly sensitive to errors that are introduced by unbalanced designs,
i.e., by an uneven distribution of mice from each strain among different sampling times. For
example, if a majority of the control mice (mice of the parental strain) were evaluated for the
phenotype in the first month of the study, and a majority of mice from some of the CS strains
evaluated in the fourth month, effects of evaluation-time differences will be confounded with
the genetic differences between the control and CS strains. Sampling-time variance can result
from seasonal effects, unrecognized variations in the phenotyping tools or procedure, and
random differences in environmental variables. Both false positive and false negative results
will occur. Studies using a CS panel are especially prone to this problem because of the
difficulty in coordinating breeding among the 2025 strains of the panel. The best solution is
to include a sufficient number of control mice at each evaluation time to provide an
appropriately-sized group for statistical comparison. If this strategy is prohibitive, the
distribution of control mice among sampling times should be as balanced as possible. If these
conditions cannot be met, results of a CS panel survey in which different mice were evaluated
at different times must be considered preliminary until they can be confirmed by direct
comparison of the control group with the affected CS strain(s).
Mice of a CS strain that exhibit the trait can be used to produce, within a few generations, a
series of congenic strains that subdivide the chromosome into segments and thus refine the
position of the causative locus. This is achieved by backcrossing to mice of the recipient
strain, identifying recombinant progeny in an N2 generation, and determining which regions
of the chromosome are associated with the variant phenotype.
The CS strain panel (C57BL/6J Chr #PWD/Ph/ForeJ), developed from a wild-derived founder
(PWD/Ph) and a standard laboratory strain (C57BL/6J [000664]) provides greater genotypic
varianceand potentially greater phenotypic variancethan other recombinant panels.
3.D.4.a.2. Genome tagged mice

Genome tagged mice are similar to CS strains, except that a portion of a chromosomerather
than an entire chromosomefrom a donor strain is maintained on a standard recipient
background. Genome tagged mice are created to provide greater precision with regard to the
locus of interest. However, a greater number of strains are required for a complete panel. A set
of genome-tagged mice for a given chromosome can easily be produced from a single CS strain.

CS strains and genome-tagged mice are maintained with sibling intercrossing, as with other
inbred strains.
Nomenclature for CS strains includes the name of the recipient strain and the number and donor
of the transferred chromosome. (The superscripted donor name is distinguishable from an allele
symbol because it is capitalized and non-italic.) Table 3.15 provides several examples of
consomic strain names and their interpretation.
Table 3.15. Examples of nomenclature for consomic strains.
Name
A/J
Definition
Convention
C57BL/6J-Chr 1 /NaJ
(004379)
C57BL/6J-Chr XA/J/NaJ
(004398)
Two strains of a CS strain panel, in

which Chr 1 and Chr X from strain
A/J (Chr 1A/J, Chr X A/J) were
transferred to C57BL/6J by J.
Nadau (Na); maintained at The
Recipient strain, hyphen (-),

chromosome number, donor
strain (superscripted), forward
slash (/), ILAR code(s)
ilarhome/search_lc.php).
BALB/cByJ-Chr YC57BL/6By/J
(001452)
CS strain, where Chr Y from

C57BL/6By was transferred to
BALB/cByJ; maintained at The
As above.

A CS panel used for the discovery of a QTL for pubertal timing.
The genetic regulation of pubertal timing in mice is poorly understood, at least partly because
relatively large non-genetic effects amplify variance. Krewson et al. (2004) used a C57BL/6JChr #A/J/NaJ CS strain (CSS) panel to identify QTCs for the more rapid pubertal development in
A/J (A; 000646) compared to C57BL/6J (B6; 000664) mice. In an initial survey, a total of 420
females per CS strain, from at least two litters per strain, were evaluated for the timing of
vaginal opening (VO). CSSs for Chr 6 and Chr 13 each displayed an earlier time of VO than B6
mice. From these initial studies, appropriate sample sizes for accurate estimates of the timing of
VO were determined. Additional studies then confirmed these two differences. F1 mice (B6 X
CSS) for Chr 6 and Chr 13 displayed phenotypes that were intermediate between the CSS and
B6 strains, indicating that the trait was inherited in a codominant manner. Nathan et al. (2006)
studied the C57BL/6J-Chr 6 A/J/NaJ (B6-6A; 004384) strain in greater detail. Linkage analysis of
N2 mice from a B6 X B6-6A cross identified a QTL on the distal end of Chr 6 that regulates VO
in mice. The QTL was confirmed and its location refined by generating and phenotyping a panel
of 12 congenic strains from a B6 X B6-6A cross. Additional analysis of the QTL demonstrated
that the effects of the responsible gene(s) are gender specific and without parent-of-origin
effects. These results demonstrate that the genetic regulation of a phenotype with large nongenetic variance can be studied reliably using mice of a CSS panel.
Genome tagged mice used to explore the genetics of behavioral variation.
Gale et al. (2008) studied a panel of genome-tagged mice that consisted of more than 60
congenic strains, each carrying a different, small (2030 cM) segment of the DBA/2J (000671)
genotype on the C57BL/6J (000664) background. The panel was designed to cover almost the
entire DBA/2J genotype. A total of 97 loci were mapped for a variety of complex behavioral
traits including hyperactivity, anxiety, avoidance, and conditional fear. This study mapped a
much larger number of loci, many to a greater precision, than generally is possible with standard
mapping crosses. In addition, more than half the strains with significant QTLs exhibited
phenotypes that differed from either of the parental strains. These results indicate that, in
traditional mapping crosses such as an F2 cross, epistasis can interfere with detection of loci for
complex traits because its effects differ for each individual mouse, increasing the variance and
decreasing the sensitivity for detection of loci that influence complex traits. In contrast, as with
any inbred strain, epistatic effects are constant within a strain of genome tagged mice.
3.E. Mice with chromosomal aberrations

Chromosomal aberrations are rearrangements of the normal chromosomal structure. They occur
spontaneously or can be induced, and can generally be observed cytologically. Most
chromosomal aberrations carried on laboratory mice were discovered in wild mice.
3.E.1. Definitions, characteristics and value

Six types of chromosomal aberrations are preserved in inbred strains:
Inversions: rearrangements of DNA segments within chromosomes, where the segment is
reversed end to end.
Insertions: the insertion of a fragment from one chromosome into another.
Robertsonians: two different chromosomes joined at their centromeres to produce a bi-armed
chromosome.
Reciprocal translocations: exchanges of DNA segments between two different chromosomes.
Generally reciprocal translocations produce either semi-sterility or complete male sterility.
Trisomies: deviations from the normal diploid number of chromosomes in which triplicate
copies of one chromosome or a portion of that chromosome exists in the cell.
Chr Y aberrations.
Figure 3.11 provides simple examples of two types of chromosomal aberrations.
Figure 3.11. Schematic: inversion and reciprocal translocation.
Chromosomal rearrangements have

been used as dominant markers for
linkage studies and for marking tissues
in experiments involving chimeras or
transplantations. Today, many strains
with chromosomal aberrations are used
in fluorescence in situ hybridization
(FISH) gene mapping studies and in
meiotic nondisjunction studies.
Chromosomal aberrations are also used
to study the relationship of
chromosomal structure or gene
location to gene function. And, some
chromosomal aberrations in the mouse
are useful for modeling the effect of
chromosomal aberrations on fertility.
Mice with chromosomal aberrations

are also used to create other research
models. Robertsonian chromosomes in
combination can be used to produce whole chromosome trisomies for specific mouse
chromosomes. An example is the mouse used to study Down syndrome, B6EiC3Sn a/ATs(1716)65Dn (001924).
Often, chromosomal aberrations are transferred to a standard inbred background for study just
as other mutations are. Sometimes the aberrations are carried and studied on an undefined stock.
To produce mice trisomic for a specific chromosome, a combination of different strains is
required.
3.E.2. Maintenance breeding strategies

Some strains that carry a chromosomal aberration can be maintained either as homozygotes or
heterozygotes that segregate for the aberrant chromosome. Several have fertility and sterility
problems; these strains require special breeding schemes and handling. For details on specific
strains of JAX Mice with chromosomal aberrations, refer to the strain datasheet
(www.jax.org/jaxmice/query).
3.E.3. Controls
Appropriate controls for segregating aberrations are wild-type littermates; controls for
homozygous aberrations maintained on standard inbred backgrounds are mice of the specific
inbred strain background. Because of their origin from wild mice, Robertsonian chromosomes
maintained homozygously, and not on a standard inbred background, do not have a genetically
similar control.
3.E.4. Nomenclature
Nomenclature for mice with chromosomal aberrations includes the type of aberration and
chromosome(s) involved, an aberration series number, and the researcher or laboratory that
discovered or produced the aberration. Table 3.16 provides several examples of nomenclature of
mice with chromosomal aberrations. Table 3.17 provides the aberration codes used in
nomenclature for strains of JAX Mice. For information on JAX Mice with chromosomal
aberrations, visit www.jax.org/jaxmice/type/chromosomal_abberati. For a complete list of
aberration codes, refer to the full nomenclature rules at
www.informatics.jax.org/mgihome/nomen/anomalies.shtml.
Table 3.16. Examples of nomenclature for strains with chromosomal aberrations.
Name
Definition
Convention
STOCK In(5)30Rk/J
(000852)
An undefined stock (STOCK)

carrying an inversion (In) in Chr 5
(5); the 30th inversion found by T.
Roderick (Rk); maintained at The
Background strain or stock,

abbreviation of aberration (see
Table 3.17 for code
translation), affected
chromosome(s), series number
of the aberration, ILAR
code(s)* of discoverer or
developer, forward slash (/),
and ILAR code(s).
ilarhome/search_lc.php.)
STOCK Rb(6.16)24Lub
(000885)
An undefined stock (STOCK)

carrying the Robertsonian
translocation (Rb), where Chr 6 and
Chr 16 are joined (6.16); the 24th (24)
translocation found at Medizinische
Hochschule Lubeck (Lub).
As above.
B6EiC3Sn a/A-Ts(1716)65Dn
(001924)
Mutant strain B6EiC3Sn, segregating

at the agouti locus (a/A), carrying a
trisomy (Ts) for the centromeric end
of Chr 17 and the distal telomeric end
of Chr 16 (1716); the 65th (65) trisomy
found by M. T. Davisson (Dn).
As above.
CBA/CaH-T(14;15)6Ca/J
(000655)
Inbred strain CBA/CaH carrying a

reciprocal translocation (T) for Chr
14 and Chr 15 (14;15); the 6th (6)
translocation found by T. C. Carter
(Ca); maintained at The Jackson
Laboratory (J).
As above.
Table 3.17. Abbreviations of chromosomal aberrations used in strain names of JAX Mice.
Abbreviation and definition
Abbreviation and definition
In
Inversion
Reciprocal translocation
Is
Insertion
Ts
Trisomy
Rb
Robertsonian chromosomes
(translocations)
Chr Y abnormality
3.E.5. Research examples

A trisomy model used to test Down syndrome drugs.
Researchers at a University of Colorado at Denver and Health Sciences Center (UCDHSC;
Costa et al., 2007) have successfully treated a mouse model of Down syndrome with an FDAapproved drug used to improve memory retention of patients with Alzheimers disease. The
treatment has the potential for treatment of children and adults with Down syndrome. The strain,
B6EiC3Sn a/A-Ts(1716)65Dn (001924) was developed by Dr. Muriel Davisson at The Jackson
Laboratory (Davisson et al., 1993). This strain has a mixed trisomy for part of Chr 17 and part
of Chr 16, which results in symptoms of Down syndrome.
An undetected inversion that interfered with mapping.
During construction of a strain congenic for a segment of Chr 6 (B6.C3-6T), Rosen et al. (2004)
noted that recombination was suppressed in the central region of Chr 6, as suggested by lack of
recombination in more than 600 N10F2 mice. This absence of recombination frustrated attempts
to fine map a quantitative trait locus (QTL) for bone density on Chr 6. Akeson et al. (2006)
subsequently demonstrated the existence of an inversion, In(6)1J, in C3H/HeJ (000659) mice
that encompasses about 20% of Chr 6 from ~73 Mb to ~116 Mb. As a result, linkage crosses
using C3H/HeJ mice will show no recombination in this region of Chr 6. Because this inversion
will hold this segment of Chr 6 intact, it could be useful for mutagenesis or breeding studies
(Akeson et al. 2006).
3.F. References
Akeson EC, Donahue LR, Beamer WG, Shultz KL, Ackert-Bicknell C, Rosen CJ, Corrigan J,
Davisson MT. 2006. Chromosomal inversion discovered in C3H/HeJ mice. Genomics. 87:311
313.
Bailey DW. 1971. Recombinant inbred strains, an aid to finding identify, linkage, and function
of histocompatibility and other genes. Transplantation. 11:215327.
Bailey DW. 1978. Sources of subline divergence and their relative importance for sublines of
six major inbred strains of mice, in Origins of Inbred Mice. Morse HC III (ed). Academic
Press, NY. pp 197215.
Behlke, MA. 2006. Progress towards in vivo use of siRNAs. Mol. Ther. 13:644670.
Berglund ED, Li CY, Poffenberger G, Ayala JE, Fueger PT, Willis SE, Jewell MM, Powers AC,
Wasserman DH. 2008. Glucose metabolism in vivo in four commonly used inbred mouse
strains. Diabetes. 57:17901799.
Berry ML, Linder CC. 2007. Chapter 4, Breeding systems: considerations, genetic
fundamentals, genetic background, and strain types, in the Mouse in Biomedical Research,
Volume 1, 2nd edition. Fox JG, et al, (eds). American College Laboratory Animal Medicine.
Academic Press. pp 5378.
Blher M, Kahn BB, Kahn CR. 2003. Extended longevity in mice lacking the insulin receptor in
adipose tissue. Science. 299:572574.
Bruder CEG, Piotrowski A, Gijsbers AACJ, Andersson R, Erickson S, Diaz deStahl T, Menzel
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77
Chapter 4: Characteristics of Popular Strains of

JAX Mice, Including Reproductive Performance
Currently, The Jackson Laboratory strain database contains complete phenotypic and genotypic
information for more than 4,000 strains of JAX Micewhat it is about each strain that makes
it unique and valuable to researchers for specific uses. Our objective for this chapter is to
provide a summary of information for the most commonly used strains. This information
includes the official and common strain names, the JAX Mice stock number, relevant genes
and alleles, and the most common characteristics and uses.
Information for each strain also includes technician notes whenever available. Technician
notes, which are most often anecdotal, are contributed by animal caretakers and technicians at
The Jackson Laboratory. Technician notes are important for two reasons: First, they often
provide helpful hints for handling the mice. Second, they represent visual observations of
specific phenotypes that may be unusualbut perfectly normalfor a specific strain. This
knowledge can often prevent misidentification of normal mice as abnormal or ill.
4.A. Strain characteristics ............................................................................ 78
4.B. Reproductive performance.................................................................138
4.C. References...........................................................................................140
For additional details on strains of JAX Mice, see the following:
Full details on all strains of JAX Mice, as well as links to other strain-related information.
www.jax.org/phenome
Experimental data on many commonly-used strains of JAX Mice.
www.informatics.jax.org/external/festing/search_form.cgi
Festings characteristics of inbred mice and rats.
Acknowledgments: We would like to thank Barbara Witham for providing valuable information
for this chapter, Pat North-Hughes for collecting and organizing updated technician notes, Dan
Smith for collecting and organizing the reproductive performance data provided in Table 4.1,
Linda Washburn for providing information on wild-derived strains, and David Higgins and
Linda Neleski for their careful fact checking.
4.A. Strain characteristics

129P1/ReJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001137

Generation: F155 (18-OCT-06)
n/a
129/ReJ;
Inbred strain
Pink-eyed, light bellied chinchilla; related genotype: Aw/Aw Oca2p Tyrc-ch/Oca2p Tyrc-ch
H2 haplotype:
Genes/alleles:
Cdh23ahl: cadherin 23 (otocadherin); age related hearing loss 1

common names: Cdh23753A; mdfw;
Disc1del; disrupted in schizophrenia 1; deletion
common name: Disc1129S6;
Polid ; polymerase (DNA directed), iota; deficient
common name: Poli-
Strain origin:
Source:
Developed by Dunn (1928) from crosses of coat color stocks from English fanciers and a
chinchilla stock from Castle. Common origin with strain 101. Dunn to WL and ES Russell
(1945), to Hunt, Wynder, and Runner at JAX (1947). After the 1947 Bar Harbor fire, Hunt
returned a chinchilla pink-eyed (Oca2p Tyrc-ch/Oca2p Tyrc-ch) substrain to JAX (1948) and
Wynder returned an albino pink-eyed (Oca2p Tyrc / Oca2p Tyrc) substrain (1948). The
original coat color genotype was reconstituted by crossing females of the former and males
from the latter. Offspring of this cross were used to establish the R1 (WL Russell), Re (ES
Russell), and Rr (MN Runner) substrains.
This non-dystrophic substrain descended from the 129/Re-Lama2dy/+ subline and was
established from tested offspring of full-sib Lama2dy/+ x Lama2dy/+ mating. Russell to JAX
(1969), to barrier facility (1978) by fostering on C57BL/6J at F71. For a complete history, see
Simpson et al., (1997).
Characteristics
and uses:
Homozygous for Cdh23ahl, age-related

hearing loss 1 mutation; onset between
35 months of age.
Co-isogenic with 129P1/ReJ-Lama2dy/J
(000641).
5% spontaneous testicular teratoma.
High frequency of venous congestion in
adrenals and uteri in old females.
High frequency of urinary calculi (Russell,

1966).
Highly susceptible to Sendai virus (Parker et
al., 1978).
Widely used in production of targeted
mutations due to availability of embryonic
stem (ES) cell lines. 129 substrain must be
matched to the ES cell line.
Research applications: cancer, neurobiology,
reproductive biology, sensorineural.
Technician
notes:
Very good parents; dont need anything

special to breed well.
Large, docile mice.
Chapter 4: Characteristics of Popular Strains of JAX Mice, Including Reproductive Performance 79
129P3/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000690

Generation: F178 (03-JAN-08)
n/a
129/J; changed 15-DEC-04
Inbred strain, segregating inbred strain
Pink-eyed, light-bellied, light chinchilla; related genotype, Aw/Aw Oca2p Tyrc-ch/Oca2p Tyrc
Albino; related genotype: Aw/Aw Oca2p Tyrc/ Oca2p Tyrc
H2 haplotype:
bc (see Fischer Lindahl K, 1997)
Genes/alleles:

common names: Cdh23753A, mdfw
Disc1del: disrupted in schizophrenia 1; deletion
common name: Disc1129S6
Polid : polymerase (DNA directed), iota; deficient
common name: Poli-
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
LC Dunn, Columbia University, NY in 1928 from crosses of coat color stocks from English
fanciers and a chinchilla (Tyrc-ch) stock from WE Castle. This strain has a common origin with
strain 101.
To WL Russell at JAX, to Runner at JAX. Russell sent stock to Hunt (1947), and Runner sent
stock to Wynder (1947). Hunt to JAX (1948), an Oca2p Tyrc-ch/Oca2p Tyrc-ch substrain; and
Wynder to JAX (1948), an Oca2p Tyrc/ Oca2p Tyrc substrain. The original coat color genotypes
were reconstituted by crossing these two substrains. Offspring of the cross were used (1948) to
establish the Rr, Re, and RI substrains. The JAX substrain was separated from the Rr substrain
(1951) at F5 after the cross. For a complete history, see Simpson et al., (1997).
hearing loss 1 mutation; onset prior to 3
months of age.
Low tumor frequency; not susceptible to
MMTV.
5% frequency of spontaneous testicular
teratomas.
High frequency of venous congestion of
adrenals and uterus.
Highly sensitive to estrogen.
Highly resistant to radiation.
Useful for ovary transplant and ova
transfer studies.
Carries a Type 1A Chr Y of Asian M.m.
musculus origin (Tucker et al., 1992).
Suppurative conjunctivitis and ulcerative

blepharitis is common; corynebacterium have
been found on conjunctival examination. This
rare condition has been found only in 129P3/J
and BALB/c substrains (Sundberg et al.,
1991).
Maintained by matings of Oca2p Tyrc-ch/
Oca2p Tyrc x Oca2p Tyrc/ Oca2p Tyrc , which
produce chinchilla and albino progeny.
Research applications: cancer, cardiovascular,
neurobiology, reproductive biology,
sensorineural.
Very nervous and jumpy; gentle mice.

Poor breeders. Around " of first litter
born dead or die shortly after. Many
missing litters. But good sized litters.
Loud noises cause them to chew or eat
litters; often find babies with missing
limbs.
Reduce amount of shavings to avoid mice

pushing them in a pile under the water bottle,
possibly drowning themselves.
Change cages weekly; this seems to avoid
diarrhea that occurs when cages changed less
often.
129S1/SvImJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 002448

n/a
129/SvImJ
129S1/Sv-p+ Tyr+ Kitl+
129S3/SvIm
129S3/SvImJ
Inbred strain
White-bellied agouti; related genotype: Aw/Aw
H2 haplotype:
Genes/alleles:

Gnat2cpfl3: guanine nucleotide binding protein, alpha transducing 2; cone photoreceptor
function loss 3
common name: Gnat2
Development:
129S1/SvImJ was developed to serve as a control inbred strain for many of the steel-derived
ES cell lines (e.g. W9.5 and CJ7). SSLP marker analysis indicates that 129S1/SvImJ is
identical to 129S1/Sv +p +Tyr-c KitlSl-J /+ except for the region surrounding the Kitl gene on
Chr 10. 129S1/SvImJ was derived from 129S1/Sv-+p +Tyr-c KitlSl-J/+ (000090). The steelJackson mutation (KitlSl-J, formerly MgfSl-J) is segregating in 129S1/Sv-+p +Tyr-c KitlSl-J/+.
KitlSl-J was removed in 1995, at F26, by selective breeding to produce 129/Sv-+p +Tyr-c
+Kitl-Sl-J (002448; see Simpson et al., 1997). This name was later shortened to 129/SvImJ.
Subsequently designated 129S3/SvImJ (Festing et al., 1999), this strain was renamed
129S1/SvImJ in February 2001 to emphasize its relationship to Stock No. 000090.
Characteristics
and uses:
Homozygous for Gnat2cpfl3, cone

photoreceptor function loss 3, which
affects bright light (photopic) vision.
In response to challenge, develop immunemediated nephritis characterized by
proteinuria, glomerulonephritis, and
tubulointerstitial disease (Xie et al., 2004).

Research areas: cancer, neurobiology,
reproductive biology.
Technician
notes:
Chew a lot of grain and leave it on the

bottom of the cage; may have to add grain
to the wean cages more often than normal.
May build up shavings under water bottle,

especially when building nests, resulting in
wet/drowned mice. It may be necessary to
remove some shavings.
129X1/SvJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000691

n/a
129X1 (changed: 06-JUN-07)
129/SvJ (changed: 19-APR-07)
Inbred strain
Pink-eyed, light-bellied, light chinchilla; related genotypes: Aw/Aw, Oca2p Tyrc-ch/Oca2p Tyrc
Albino; related genotypes: Aw/Aw, Oca2p Tyrc / Oca2p Tyrc
H2 haplotype:
bc
Genes/alleles:

Polid ; polymerase (DNA directed), iota; deficient
common name: Poli-
Strain origin:
As 129/ReJ. 129/J, 129/ReJ, and 129/SvJ have a common origin.
Source:
Runner to JAX (1947) and subsequently distributed to other members of the JAX staff,
including ES Russell, Murray, Hummel, and Dagg. Hummel to Stevens in approximately
1953.
Characteristics
and uses:

months of age.
Testicular teratomas >1% (Stevens, 1973).
Non susceptible to MMTV.
Highly sensitive to estrogen at all ages.
Maintained by mating mice of different
colors, Oca2p Tyrc-ch/ Oca2p Tyrc X Oca2p
Tyrc/ Oca2p Tyrc, which produces both
chinchilla and albino offspring.

Useful for ovary transplant and ova
transfer studies.
Research applications: cancer,
neurobiology, reproductive biology,
sensorineural.
Technician
notes:
Gentle mice.
Very crawly; sometimes hang off cage
cover.
Sometimes chew through filter hoods.
Poor breeders. First 23 litters may be born
dead or eaten; then they start breeding.
Use Nestlets with all new litters.

Mice take shavings and push under water
bottle, causing wet boxes; decrease
shavings to avoid.
A/HeJ
Stock No. 000645
Common name:
Former name:
Strain type:
Appearance:
AHe; A Heston
n/a
Inbred strain
Albino; related genotype: a/a Tyrp1b/Tyrp1b Tyrc/Tyrc
H2 haplotype:
Genes/alleles:
Hc0: hemolytic complement; deficient

common names: C5-, C5-d, C5-def, C5-deficient, hco
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Developed by LC Strong in 1921 from a cross between a Cold Spring Harbor albino and a Bagg
albino; thus, it is related to BALB/c (Strong, 1936). Majority of sublines trace to stock that
Bittner obtained from Strong (1929). Some of this stock was sent to Heston (1940).
Heston to JAX (1948) at F77.
Low frequency of mammary and lung
tumors in virgin females, but high
percentage of mammary adenocarcinomas
(large proportion acinar type) develop in
multiparous females.
High frequency of renal disease in older
animals.
Primary cleft palate sometimes found in
newborns; easily induced with a variety of
agents, including cortisone.
Lung tissue very susceptible to induction of
tumors by methylcholanthrene and urethane
(Malkinson et al., 1985).
Hyperactive airway response to various
chemicals (Ewart et al., 1994; Levitt et al.,
1995; Takahashi et al., 1995).
Carries a Type 1A Asian M.m. musculus

Chr Y (Tucker et al., 1992).
Small percent (4%) of nonproductive males
are hermaphrodites; additional 17% of
nonproductive males have abnormally small
testes containing no sperm.
In The Jackson Laboratory substrains,
observation of rare spontaneous
myoepitheliomas arising from myoepithelial
cells of various exocrine glands.
Low inter- and intra-strain aggression
(Carlier et al., 1991).
developmental biology, reproductive
biology, immunology and inflammation.
Pretty, white coat.

Very quiet, docile; a little curious, but in a
shy way.
Very easy mice to work with.
Very non-productive, but if they have 1
litter, they seem to continue to breed.
Often have eye problems. Sometimes, one

or both eyes appear closed, but a week later
they open.
Sometimes born with their eyes open, which
can result in damage.
A/J
Stock No. 000646
Common name:
Former name:
Strain type:
Appearance:
A
n/a
Inbred strain
H2 haplotype:
Genes/alleles:

common names: Cdh23753A; mdfw
Dysf prmd: dysferlin; progressive muscular dystrophy
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Strong (1921) from a cross of an albino from Cold Spring Harbor stock and a Bagg albino;
given to Cloudman (1928). A/HeJ and A/J have a common origin.
Cloudman to JAX (1947) at F73.
hearing loss 1 mutation; onset between 35
months of age.
Moderate mammary tumor frequency; high
percentage of mammary adenocarcinomas
(large proportion of acinar-type) in
multiparous females.
Primary lung tumors in 50% of mice; lung
tumors readily develop in response to
carcinogens.
High frequency of renal disease in older
animals.
Homozygous retrotransposon insertion in the
dysferlin (Dysf) gene causes late onset (45
months) progressive muscular dystrophy (Ho
M et al., 2004).
Dysferlin mutation not present in RI lines
with A/J mice (Ho M et al., 2004).
Primary cleft palate sometimes found in

newborn; easily induced with a variety of
agents (Azziz and Ladda, 1990; Kalter,
1981).
Lower percentage of granulocytes than
A/HeJ.
Low frequency of osteoporosis (Silberberg
and Silberberg, 1962).
myoepitheliomas arising from
myoepithelial cells of various exocrine
glands.
Research application: cancer,
cardiovascular, developmental biology,
internal/organ, neurobiology, sensorineural,
immunology and inflammation.
Unusually long gestation length
(unpublished communication, Corrow DJ)
Gentle mouse; easy to handle.

Very clean.
Small eyes, often with secretion that looks
like they have a cold.
Males prone to rectal prolapses.

Large litters, good breeders. But breeders
tend to bite pups. Breeders have some hair
loss.
A/WySnJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000647

Generation: F264 (05-DEC-07)
A Woolley Snell
n/a
Inbred strain
Albino; related genotype: a/a Tyrp1b/Tyrp1b Tyrc /Tyrc
H2 haplotype:
Genes/alleles:

Tnfrsf13cBcmd1-A/WySnJ: tumor necrosis factor receptor superfamily, member 13c; B-cell
maturation defect 1, A/WySnJ
common names: Bcmd1A/WySnJ
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Developed by LC Strong (1921) from a cross between a Cold Spring Harbor albino and a Bagg
albino. A/HeJ, A/J and A/WySnJ have a common origin. Strong to Bittner at JAX (1927).
Bittner (1942) to Woolley at JAX (1942) to Snell at JAX (1951) at F8486.
hearing loss 1 mutation; onset after 10
months of age.
Frequency of facial clefting in A/WySnJ is
2030%. Clefting reporting to be a 2 locus
system: clf1 and clf2 (Juriloff and Mah,
1995). Highly susceptible to induction of
congenital cleft palate by cortisone.
myoepitheliomas arising from myoepithelial
cells of various exocrine glands.
High incidence of spontaneous lung

adenomas; lung tumors readily develop in
response to carcinogens.
High percentage of mammary
adenocarcinomas (large proportion acinartype) develop in multiparous females.
Unlike A/J mice, A/WySnJ mice carry a
spontaneous mutation in Tnfrsf3c and
exhibit a significant loss of mature B cells
(Miller and Hayes, 1991; Lentz et al., 1996;
Shulga-Morskaya et al. 2004)
developmental biology, immunology and
inflammation, neurobiology, sensorineural.
Appear to be nice, fat, calm and cleancoated mice.
AKR/J
Stock No. 000648
Common name:
AK
Former name:
n/a
Strain type:
Appearance:
Inbred strain
Albino; related genotype: a/a Tyrc/Tyrc Soat1ald/Soat1ald hid/hid
H2 haplotype:
Genes/alleles:

Obq3AKR/J: obesity QTL 3; AKR/J
Obq4AKR/J: obesity QTL 4; AKR/J
Rmcfs: resistance to MCF virus; MCS sensitive
Soat1ald: sterol O-acyltransferase 1; adrenocortical lipid depletion
common names: Acact-, ald
Thy1a: thymus cell antigen1 theta: a variant
common names: Thy-1.1, Thy1.1, Thy1a
hid: hair interior defect
Strain origin:
Source:
Detwiler to Furth (192836) as high leukemia strain. Random bred at Rockefeller Institute for
several generations (Furth, 1946), followed by 9 generations of inbreeding by Mrs. Rhoades and
an additional 12 by Lynch at the Rockefeller Institute (Lynch, 1954). Based on allele
distribution, possibly shares a genetic origin with the RF strain (Atchley and Fitch, 1993).
Lynch to JAX (1948) AT F22.
Characteristics
and uses:
High spontaneous frequency of lymphatic

leukemia before 1 year; high viremic strain
(DiFronzo and Holland, 1993).
Viremic from birth, and express the
ecotropic retrovirus AKV in all tissues.
hid (hair interior defect) mutation causes
alterations in hair development that is
evident only microscopically.
Mutation in Soat1ald leads to truncated
SOAT1 protein and adrenal cortical lipid
depletion.
Relatively resistant to aortic lesion

formation on semi-synthetic high fat diet;
hyporesponsive to diets containing high
levels of fat and cholesterol.
Low induction of colon carcinogenesis with
1,2dimethylhydrazine (DMH) (Rosenberg
and Liu, 1995).
diabetes and obesity, endocrine deficiency,
internal/organ, metabolism, neurobiology,
Technician
notes:
Heavy cage soiling.

Gentle, easy to handle; but sometimes they
will squeal when picked up.
Occasionally non-productive, but good

parents.
B6.129P2-Apoetm1Unc/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 002052

Generation: N12F17 (03-JAN-08)
ApoE-KO; apoE-; apoE0; epsilon-;

n/a
Congenic, mutant strain, targeted mutation
Black; related genotype: a/a
H2 haplotype:
Genes/alleles:
Apoetm1Unc: apolipoprotein E; targeted mutation 1, University of North Carolina

Common names: AopE(-), APOE KO, apoE-, ApoE-KO, Apoetm1Un, apoE0, epsilon-
Development:
The Apoetm1Unc mutant strain was developed in the laboratory of Dr. Nobuyo Maeda at The
University of North Carolina at Chapel Hill. The 129-derived E14Tg2a ES cell line was used.
The plasmid used is designated as pNMC109 and the founder line is T-89 in the primary
reference. The C57BL/6J strain was produced by backcrossing the Apoetm1Unc mutation 10
times to C57BL/6J mice. Previously mice backcrossed 6 times (N6) to C57BL/6J mice were
distributed solely. Mice from the N6 generation are homozygous for pink-eyed dilution Oca2p,
giving them pink eyes and a silver coat color. The E14Tg2a ES cell line carries this recessive
mutation, which remained linked to the targeted Apoe gene on Chr 7 at this backcross
generation. Mice from the N6 colony are no longer available for distribution. The pink-eyed
dilution mutation was bred out of this strain by N12, the current backcross generation.
Characteristics
and uses:
Mice homozygous for Apoetm1Unc

mutation show marked increase in total
plasma cholesterol levels unaffected by age
or sex.
Fatty streaks in proximal aorta found at 3
months of age. Lesions increase with age
and progress to lesions with less lipid but
more elongated cells, typical of a more
advanced stage of pre-atherosclerotic
lesion.
Moderately increased triglyceride levels
reported in mice with this mutation on a
mixed C57BL/6 x 129 genetic background.
Aged APOE deficient mice (>17 months)

develop xanthomatous lesions in the brain
consisting mostly of crystalline cholesterol
clefts, lipid globules, and foam cells. Smaller
xanthomas seen in the choroid plexus and
ventral fornix.
Recent studies indicate that APOE deficient
mice have altered responses to stress,
impaired spatial learning and memory,
altered long term potentiation, and synaptic
damage.
Research applications: diabetes and obesity,
neurobiology (Alzheimers), cardiovascular,
atherosclerosis, lipid metabolism.
Technician
notes:
Good parents.
Chewed ears may appear in breeders about
4 months of age.
Malocclusion and hydrocephalus relatively

common. Check for malocclusion in
weanlings.
B6D2F1/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 100006

Generation: n/a
B6D2F1
n/a
F1 hybrid
Black; related genotype: a/a Tyrp1b/+ Myo5ad/+
H2 haplotype:
b/d
Genes/alleles:
See C57BL/6J (000664) and DBA/2J (000671)
Development:
Hybrid strain created by crossing C57BL/6J (B6; 000664) female and DBA/2J (D2; 000671)
male.
Characteristics
and uses:
Technician
notes:
Mixed haplotype enables mice to accept

tissue transplants from both parental strains.
Useful as a genetic background for
transgenic/knockout creation as well as other
deleterious mutations.
Research applications: radiation,

behavioral; drug safety and efficacy testing;
bioassays of nutrients, drugs, pathogens,
and hormones.
Easy to handle.
Parental breeding pairs are good producers.
When having large litters, have increased
appetite.
May have small eyes, missing eye,

cataracts, missing fur, occasional white
belly spots.
BALB/cByJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001026

CBy; BALB Bailey; BALB/c Bailey J;

n/a
Inbred strain
Albino; related genotype: A/A Tyrp1b/Tyrp1b Tyrc/Tyrc
H2 haplotype:
Genes/alleles:
Acadsdel-J: acyl-Coenzyme A dehydrogenase, short chain; deletion, Jackson

common name: Bcd-1c
Hld: hippocampal lamination defect
Mdmg1BALB/cBy , mandibular morphogenesis 1
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Halsey J Bagg albino to LC Strong in 1920 (Strong, 1978). The history of the BALB/c
substrains has been well document (Potter, 1985), and the genetic difference between the
BALB/c substrains characterized (Hilgers et al., 1985). Subline of BALB transferred from
MacDowell, Cold Spring Harbor, to Muller, University of Texas, to Snell, University of Texas,
(1932) to Scott (JAX), to Andervont (1935) to NIH (1951) at F72, to Bailey (1961) at F99.
Bailey to JAX (1975) at F136 by hysterectomy derivation and fostering on C57BLKS/J.
Low spontaneous mammary tumor frequency
in females, but susceptible to MMTV.
Higher reproduction rate than BALB/cJ.
Carries an Asian M.m. musculus-origin Chr
Y (Tucker et al., 1992).
Suckling young susceptible to diarrhea in less
than optimum environment.
Males much less aggressive than BALB/cJ
(Les, 1987).
Spontaneous dystrophic cardiac calcinosis.
High liver triglyceride levels.
Increased wound healing time.
Mid-range bone density levels.

Moderate increase in food intake and
weight on high-fat/high-calorie diet.
Susceptible to toxoplasmosis.
Differs from all other BALB/c sublines at
the Acads (acyl-CoA dehydrogenease,
short chain) locus by having a null allele.
Useful for production of plasmacytoma,
forming basis for development of ascites
tumors and monoclonal antibodies.
immunology and inflammation,
neurobiology, sensorineural.
Good sized litters; good parents.

Higher reproductive rate than BALB/cJ.
Pair or trio matings work well.
Heavy cage soiling.
Easy to handle.
Occasionally jumpy due to weather.
Eat a lot.
Females may have ulcerated eyelids, rough
appearing coats.
Alopecia.
BALB/cJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000651

C; BALB
n/a
Inbred strain
Albino; related genotype: A/A Tyrp1b/Tyrp1b Tyrc/Tyrc
H2 haplotype:
Genes/alleles:
Hld: hippocampal lamination defect
Strain origin:
Source:
BALB/cByJ and BALB/cJ have a common origin. Bagg acquired progenitors of this strain (then
called BALB) in 1913 from an Ohio dealer. Bagg to Little and MacDowell, Cold Spring Harbor
(1922), MacDowell to Muller at University of Texas at F12, Muller to Snell (who added the /c)
(1932) at F25, Snell to Scott at JAX (1947).
Scott to JAX (1947) at F41.
Characteristics
and uses:
Low spontaneous mammary tumor

frequency, but susceptible to MMTV.
Relatively resistant to the induction of colon
carcinogenesis (Moen et al., 1996).
Prone to other cancers later in life, including
reticular neoplasms, primary lung tumors,
and renal tumors.
Rare spontaneous myoepitheliomas arising
from myoepithelial cells of various exocrine
glands.
Very sensitive to radiation.
Susceptible to chronic pneumonia.
Plasmacytomas easily induced using

pristane or silicone gels (Potter and
MacCardle, 1964; Potter et al., 1995).
Lower reproductive performance than other
BALB substrains due to vaginal septa,
which may cause dystocia.
Extremely high inter- and intra-strain
aggression and lower reproductive
performance than that found in BALB/cByJ
mice (Les, 1987).
cardiovascular, immunology and
inflammation, neurobiology.
Technician
notes:
Highly aggressive; may kill cage mates. But

easy for technicians to handle.
Coat may have an oily, look, appearing
dirty, yellowed, and unkempt.
Lumps, tumors.
May have temporary hair loss. Hair loss at
weaning age resolves itself by 6 weeks of
age.
With age, mice often develop a slight
swelling around the edge of the eyelids.
Heavy cage soiling.

Urination often soaks fur around genital
area, resulting in difficulty with sexing.
Moderate productivity rate. Good mothers.
Timed pregnancy and superovulation
difficult with this strain. Many matings are
not fertile although plugs are deposited.
If feed hopper is overfilled, mice will knock
out large amounts of food.
BTBR T+ tf/J
Stock No. 002282
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain, mutant strain

Black and tan, tufted; related genotype: a t/at T+/T+ tf/tf
H2 haplotype:
Genes/alleles:
T+, brachyury; wild-type

tf, tufted; tufted
Strain origin:
n/a
Source:
n/a
Characteristics
and uses:
Technician
notes:
Generation: F?+34 (11-JAN-08)
Compared to other inbred strains, exhibit

several symptoms of autism, including
reduced social interactions, impaired play,
low exploratory behavior, unusual
vocalizations, and high anxiety. (McFarlane
et al., 2008; Moy et al., 2007).
Exhibit 100% absence of the corpus

callosum and a severely reduced
hippocampal commissure. (Wahlsten et al.,
2003).
Research applications: dermatology,
developmental biology, neurobiology.
n/a
BUB/BnJ
Stock No. 000653
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain
Albino; related genotype: a/a Tyrc/Tyrc
H2 haplotype:
q2 (see Fischer Lindahl K, 1997; Shen et al., 1982)
Genes/alleles:

Gpr98frings: G protein-coupled receptor 98; frings
common names: frings, Mass1frings
Pde6brd1: phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide; retinal degeneration 1
common names: rd, rd-1, rd1, rodless retina
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
From albinos of unknown ancestry developed by JW Wilson at Brown University, with

selection against circling which appeared at about F4 (Curtis, 1956).
Brown University to S Bernstein (Bn) at JAX at F46 and then to production facility in 1968.
Carries the Pdebrd1retinal degeneration allele
(Sidman and Green 1965).
76% of males immunized at 68 weeks of
age develop severe type II collagen induced
arthritis with clinical and pathological
features resembling rheumatoid arthritis in
the human (Ortman et al., 1994).
Relatively nicotine resistant (Pauly et al.,
1990; Marks et al., 1991).
Homozygosity for Gpr98frings results in
susceptibility to audiogenic seizures prior to
25 days of age (Skradski et al., 2001) and
early onset hearing impairment by 34
weeks of age (Johnson et al., 2005).
No detectable endogeneous ecotropic

MuLV DNA sequences (Jenkins et al.,
1982).
High serum complement activity.
In response to challenge, BUB/BnJ mice
develop immune-mediated nephritis
characterized by proteinuria,
glomerulonephritis, and tubulointerstitial
disease (Xie et al., 2004)
Carries a Western European Type 3 M.m.
domesticus Chr Y (Tucker et al., 1992).
Research applications: immunology and
inflammation, neurobiology, sensorineural.
Docile, large mice.
Breeders occasionally chew ears.
C3H/HeJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000659

C3; C3H Heston;

n/a
Inbred strain, spontaneous mutation
Agouti; related genotype: A/A
H2 haplotype:
Genes/alleles:
Gria4spkw1: glutamate receptor, ionotropic, AMPA4 (alpha 4); spike wave discharge 1
Tlr4Lps-d: toll-like receptor 4; defective lipopolysaccharide response
common names: lpsd, TlrLps-d, TLR4-Mu, Tlr4-, Tlr4d
In(6)1J: inversion, Chr 6, Jackson 1
Strain origin:
Source:
LC Strong originated the C3H strain in 1920 from a cross of a female Bagg albino x DBA male,
with selection for high mammary tumor frequency (Strong, 1935). Significant differences among
substrains. To Andervont, NCI (1930). A spontaneous mutation occurred in C3H/HeJ sometime
between 1960 and 1968 at lipopolysaccharide response locus (mutation in toll-like receptor 4
gene, Tlr4 Lps-d) making C3H/HeJ mice endotoxin resistant while the other 3 C3H strains are
endotoxin sensitive.
Andervont to Heston, NCI (1941) at F35; Heston to JAX (1948) at F48.
Characteristics
and uses:
Tlr4Lps-d makes the strain susceptible to

gram negative bacterial infections.
Carries Pde6brd1 retinal degeneration
allele, which causes blindness by weaning
age.
Frequency of mammary tumors in both
breeders and virgins lower than that of
other C3H substrains (Outzen et al.,
1985).
Does not carry MMTV; but virgin and
breeding females still may develop
mammary tumors later in life.
Hepatomas (7291% in males at 14
months, 59% in virgin females, 3038%
in breeding females).
High mortality in males exposed to
turpentine or chloroform fumes.
Carries Chr Y of M.m. domesticus origin
(Tucker et al., 1992).
When fed an atherogenic diet, fail to develop

atherosclerotic aortic lesions.
Low red and white cell counts.
Lipopolysaccharide hyporesponsive because
homozygous for Lpsd mutation, which occurred
between 1960 and 1969 (Glode and
Rosenstreich, 1976).
Carries the In(6)1J inversion, encompassing
about 20% of Chr 6 from ~73 Mb to ~116 Mb.
Inversion has no apparent effect on phenotypes
(Akeson et al., 2006).
Spontaneously develop alopecia areata (AA) at
a reported incidence of approximately 0.25%
by 18 months of age. AA can be surgically
induced by grafting a small piece of skin from
an older, donor animal with AA onto a
younger, isogenic C3H/HeJ recipient.
immunology and inflammation, neurobiology,
sensorineural.
Technician
notes:
Active; can be jumpy; two-week-old mice

very active. Aggressive; curious.
Blind after 3 weeks of age.
Fair amount of bent tails.
Eat a lot; get fat as they age.
Females sexually mature very early (25 days).

Pair matings work best.
Hair loss in older breeders.
Cages wet from urine.
C3H/HeOuJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000635

C3Ou; C3H Outzen

n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
C3H/HeJ, C3H/HeOuJ, and C3HeB/FeJ have a common origin. The C3H parent strain was
developed by LC Strong in 1920 from a cross of a Bagg albino female with a DBA male
followed by selection for high incidence of mammary tumors. Separated from C3H/HeJ in 1952
before occurrence of Tlr4Lps-d mutation.
Normal littermates of C3H/HeJ-KitW-x in JAX Foundation Stocks to Outzen at JAX (1981) at
F93.
Strain carries Pde6brd1 retinal degeneration
gene; mice will be blind by weaning age.
Does not carry MMTV, but virgin and
breeding females may still develop some
mammary tumors later in life.
Does not carry the Tlr4Lps-d mutation.
High incidence of hepatomas in C3H mice

(reportedly 7291% in males at 14 months,
59% in virgin females, 3038% in breeding
females).
sensorineural.
Mice get fat as they age.

White spots.
Occasional hair loss in older breeders.

Good breeders. Pair mating.
C3H/HeSnJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000661

C3H Snell; C3Sn
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Strain origin:
C3H/HeJ, C3H/HeOuJ, C3HeB/FeJ, and C3H/HeSnJ have a common origin. Strong (1920) to
Andervont (1930) to Heston (1938) at F35.
Source:
Characteristics
and uses:
Technician
notes:
Heston to Dickie (JAX) (1947) at F48 to Snell in approximately 1964, to JAX.

Parental substrain for Snell congenic strains.
Does not carry MMTV.
CD8+ T-cell depletion.

Does not carry the In(6)1J inversion found
in C3H/HeJ (000659) (Akeson et al., 2006).
Research applications: neurobiology,
sensorineural.
Jumpy, curious; get frightened if

surroundings are noisy.
Good breeders. Good parents.

Large sized mice at weaning.
C3HeB/FeJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000658

C3Fe; C3H Fekete; HeB
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Pde6brd1: phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide; retinal degeneration 1;
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
C3H/HeJ, C3H/HeOuJ, and C3HeB/FeJ have a common origin. C3H/HeJ ova transferred to
C57BL/6 by Fekete at JAX (1948). Original transplant animals to Hummel at JAX.
Hummel to JAX (1950) at F3.
Does not carry MMTV. Low frequency of
mammary tumors.
Calcareous heart deposits in almost all retired
breeders.
Does not carry the In(6)1J inversion found in
C3H/HeJ (000659) (Akeson et al., 2006).

Ovarian tumor frequency after 19 months
about 65% in female breeders, 22% in
virgins.
Research applications: sensorineural.
Jumpy.
Mature breeders tend to be chubby.
C57BL/6ByJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001139

C57 Bailey; B6By; Black 6 Bailey;
B6 Bailey
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
n/a
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Generation: F200+F5 (28-DEC-07)
C57BL/6J, C57BL/10J, and C57BL/6ByJ have a common origin. C57BL/6N was separated
from C57BL/6J in 1951; C57BL/6ByJ was separated from C57BL/6N in 1961 (Bailey, 1978).
C57BL/6ByJ carries a Type1A Asian M.m. musculus Chr Y (Tucker et al., 1992).
Histologically normal retinas found in this substrain (Sidman and Green 1965).
Bailey to JAX (1979) at F111.
Carries the Xmmv64a allele; C57BL/6J the
Xmmv64o.
Immunosuppression occurred in female
C57BL/6J mice administered the kselective agonist, U50,488H opioid,
whereas C57BL/6ByJ were not suppressed
(Eisenstein et al., 1995).
C57BL/6J and C57BL/6ByJ have different
isoforms of the Std (sulfotransferase,
DHEA preferring ) gene (Chapman, 1994).
Testis size in C57BL/6ByJ and C57BL/10J
significantly smaller than in C57BL/6J
substrain; based on 0.38% of body weight
determined for 21 inbred strains (Chubb,
1992).
Low plasma cholesterol and triglyceride
levels (Jiao et al., 1990).
High level of plasma serotonin (1.72.2
mg/ml), more than twice the level found in
BALB/cBy; they carry the plasma
serotonin level Splh allele mapped to Chr 1
(Eleftheriou and Bailey, 1972).
Preference for ethanol, high preference for

other sweet and sour compoundssucrose,
saccharin, acesulfame, dulcin, glycine, 1glutamine and d-phenylalanineand low
preference for salty compounds (Bachmanov
et al., 1996).
Intermediate tyrosine hydroxylase activity
level compared to high activity in BALB/cJ
and low activity in CXB-9/ByJ (Vadasz et
al., 1987).
All C57BL substrains are homozygous for
Bsp (black spleen), thought to result in
lipofuscinosis (melanosis, or blackening, of
the anterior portion of the spleen), which is
found in 457% of young C57BL mice
(Chrichton and Shire, 1982). The
pathological relevance is obscure (van der
Heijden et al., 1995.
5 SNP differences distinguish C57BL6ByJ,
C57BL/6J, and C57BL/6NJ (Petkov et al.,
2004).
Calm mice, although 2- to 3-week-old

mice can be jumpy. Jumpy if in noisy
surroundings.
Occasionally poor breeders. Generally
good parents.
Tend to get very large at end of breeding

rotation.
Occasional barbering.
Prone to dermatitis.
C57BL/6J
Common name:
Former name:
Strain type:
Appearance:
H2 haplotype:
Genes/alleles:
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Stock No. 000664

C57 Black; B6; B6J; Black 6
n/a
Inbred strain
b
Generation: F226p (11-JAN-08)

Gluchos1C57BL/6J: glucose homeostasis QTL 1; C57BL/6J
NntC57BL/6J: nicotinamide nucleotide transhydrogenase; C57BL/6J
Little (1921) developed this strain from mating of littermates female 57 x male 52, from Miss
Lathrops stock. Sublines 6 and 10 separated prior to 1937 (Russell, 1978).
Little to Fekete to Hall at F22, back to JAX (1948) at F24.
months of age.
Mammary tumor frequency of 1% in
breeders, none in virgins.
Resistant to irradiation.
Resistant to C57BL/10J transplantable
tumors.
High preference for alcohol, morphine, other
opioids (Chadha et al., 1991; Phillips et al.,
1994; Berrettini et al., 1994; Belknap et al.,
1995; Grahame et al., 1995; Watzl et al.,
1992).
Highly susceptible to development of
atherosclerotic lesions (Nishina et al., 1993).
Frequency of eye defects about 12%
(Robinson et al., 1993). Includes
anophthalmia, microphthalmia, and cataracts.
Frequency of hydrocephalus in weanlings is
1%, of malocclusion, 3%.
5 SNP differences distinguish C57BL6ByJ,
C57BL/6J, and C57BL/6NJ (Petkov et al.,
2004).
Occasionally hyperactive but easy to handle.
Active barberers.
Males may be aggressive in overcrowded
cages or if cohorts are mixed after weaning.
Occasional white spots in fur. Sometimes
mice appear to have a dirty blue coat color.
May have some yellow/tan hairs around the
base of the tail, base of ears, and corners of
eyes. This is considered normal.
Occasional rectal and uterine prolapse.
Carries a Type 1A Asian M.m. musculus

Presence of Nnt mutation, which diminishes
initial insulin response to injected glucose
(Toye et al., 2005), does not affect steadystate glucose clearance (Berglund et al.,
2008) or impede development of dietinduced obesity with a high-fat diet (JAX
Services, 2008).
Alopecia-areata like hair loss due to
whisker chewing and barbering is common
(Thornburg et al., 1973; Militzer and
Wecker, 1986), especially in older breeders
and in crowded cages. Juvenile alopecia is
common at about 45 weeks of age (first
molt), but usually resolves itself by 6
weeks of age.
Most widely used inbred strain. Commonly
used for generation of congenics carrying
both spontaneous and induced mutations.
Other research applications:
diabetes and obesity, hematological,
Females may die bearing first litter or may
cannibalize first litter. Not handling pups
less than 7 days old may reduce this.
Male spermatogenesis is slow; therefore,
males do not breed well in polygamous
matings. Pair or trio matings
recommended.
Sometimes build up shavings around water
drip holes, resulting in leakage.
Older males may gain weight and
sometimes become non-productive.
C57BL/10J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000665

n/a
Inbred strain
H2 haplotype:
Genes/alleles:
n/a
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Black 10; Black 10 J
C57BL/6J and C57BL/10J have a common origin. Little (1921) developed this strain from
mating of littermates male 57 x female 52 from Miss Lathrops stock. Sublines 6 and 10
separated prior to 1937 (Russell, 1978). Little to Scott at JAX.
Scott to JAX (1947) at F32.
Low tumor frequency; resistant to some
C57BL/6 tumors.
Preference for alcohol, morphine and
other opioids.
Overall tumor incidence is 33% in males
and 31% in females, most of which is
due to lymphoma.
Prone to dermatitis, a common problem
in the C57BL strain.
High lymphocyte phytohaemagglutinin
response, good immune response to
ovalbumin, poor response to DNPkeyhole limpet haemocyanin; resistant to
induction of passive cutaneous
anaphylaxis (IgG1- and IgE-mediated).
Susceptible to immunosuppression of contact

hypersensitivity by ultraviolet light;
moderately susceptible to experimental
allergic encephalomyelitis.
Frequency of eye defects about the same as in
C57BL/6J (Pierro and Spiggle, 1967; 1969).
Frequency of both malocclusions and
hydrocephalus is rarer than in C57BL/6J.
Often used as a background strain for
histocompatibility congenics.
Hair loss in weanlings very common.

Hydrocephaly and white belly spots.
Good mothers and fathers.

Weanlings can be active, but breeders not
active.
C57BL/10SnJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000666

B10 Snell J; Black 10 Snell J
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
n/a
Strain origin:
Source:
Generation: F62 (1995)
C57BL/6J, C57BL/10J and C57BL/10SnJ have a common origin. Little (1921) strain from
mating of littermates male 57 x female 52 from Miss Lathrops stock. Sublines 6 and 10
separated prior to 1937.
Little to WL Russell, to Scott at JAX at F26. Scott to Snell at F3536 to JAX by hysterectomy
derivation and fostering on C57BL/6J.
Characteristics
and uses:
Low tumor frequency.

Resistant to some C57BL/6J tumors.
Eye defects same as C57BL/6J.
Frequency of both malocclusions and
hydrocephalus is rarer than in C57BL/6J.
Often used as a background strain for

histocompatibility congenics.
Technician
notes:
Barbering in weanlings and breeders.

Entire litters may be missing at weaning.
Weanlings slightly to very jumpy.
Eat a lot.
Occasional hydrocephaly noticed at 4

weeks of age.
Occasional rectal and vaginal prolapse.
C57BLKS/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000662

C57BL/Ks; C57Kaliss; Black Kaliss J

n/a
Inbred strain
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
C57BL/6J sent to Biesele at Sloan-Kettering (1947). Pen bred 1 generation and returned to
Kaliss at Sloan-Kettering. Taken to JAX (1948) and inbred.
Kaliss to JAX (1965) by hysterectomy derivation and fostering on C3HeB/FeJ at F67. Genomic
analysis of the C57BLKS inbred strain shows that 84% of the alleles in this strain are shared
with C57BL/6 and 16% are shared with DBA/2J, indicating genetic contamination early in the
strains history (Naggert et al., 1995).
Characteristics
and uses:

months of age.
High frequency of congenital malformation
of toes.
High frequency of polycystic kidneys,
microphthalmia (Dagg, 1963).
Diet-induced atherosclerotic lesions much
more severe in C57BLKS/J than in
C57BL/6J or many other inbred strains
(Mu et al., 1999).
The mutations diabetes (Leprdb) and obese

(Lepob) each express a much more severe
phenotype on the C57BLKS/J background
than on the C57BL/6J background.
The Cpefat mutation causes severe obesity,
hyperinsulinemia, and hyperglycemia on the
C57BLKS/J background rather than the
hyperinsulinemia, and mild obesity without
hyperglycemia found on the HRS/J
background (Collins et al., 2005).
Technician
notes:
Quiet; easy to handle.

Barbering is common.
Malocclusion and hydrocephalus relatively
common.
Poor breeders. Trio mating works; good

parents.
Small litter size.
C57BR/cdJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000667

BR; Brown cd; C57 Brown;

n/a
Inbred strain
Brown; related genotype: a/a Tyrp1b/Tyrp1b
H2 haplotype:
k2 (Fischer Lindahl K, 1997; Shen et al., 1982)
Genes/alleles:

Rmcf s: resistance to MCF virus; MCF sensitive
Strain origin:
Source:
Little (1921) developed this strain from a mating of littermates female 57 and male 52 that gave
rise to C57BL and C57BR. Black and brown lines separated in the 1st generation. Substrain cd
established in generation 13 from a cross of 2 brown branches, one of which had previously
given rise to strain C57BR/a. Some given to Cloudman at JAX, to Heston at JAX (1938).
Characteristics
and uses:

hearing loss 1 mutation; results in earlyonset hearing loss that is moderate at 7
weeks of age, severe by 20 weeks, and that
progresses with increasing age (Henry,
1982; Zheng et al., 1999).
Low mammary tumor frequency; some
hepatomas in females.
Carries a Chr Y of Asian M.m. musculus
origin (Tucker et al., 1992).
Highly atherogenic (Paigen et al., 1990;

Kuan et al., 1992).
Research applications: cardiovascular,
Technician
notes:
White belly spot.

Poor breeders: small litters; missing litters.
Need to be delayed mated; mating at wean
age does not work very well.
Occasionally, one pair will be very

productive, with large litters.
C57L/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000668

L; C57 Leaden; leaden

n/a
Inbred strain
Leaden (grey); related genotype: a/a Tyrp1b/Tyrp1b Mlphln/Mlphln
H2 haplotype:
bc (Shen et al., 1982)
Genes/alleles:

Mlphln: melanophilin; leaden
common names: leaden, ln
Obq3C57L/J: obesity QTL 3; C57L/J
Obq4C57L/J: obesity QTL 4; C57L/J
Rmcfs: resistance to MCF virus; MCF sensitive
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Murray at JAX (1933) mutation to leaden (ln) in F22 of a C57BR subline of which the
nonleaden (brown) branch is now extinct. Stock was maintained by Cloudman at JAX.
From Cloudman to Heston at JAX (1938), to JAX (1947) at F45.
months of age.
High incidence of Hodgkin's-like reticulum
cell neoplasm at 18 months of age;
pituitary tumors in old multiparous
females.
Highly susceptible to experimental allergic
encephalomyelitis (EAE).
Frequent congenital cystic ovaries (Jagiello
and Ducayen, 1973).
Highly susceptible to diet-induced
atherosclerosis and diet-induced
cholelithiasis (gallstones) (Khanuja et al.,
1995).

Carries no detectable endogenous ecotropic
MuLV DNA sequences.
Low mammary tumor frequency.
Extremely high hematocrit.
Research applications: general purpose,
cancer, cardiovascular, dermatology,
Calm mice.
May have white spot on belly.
Like to have nesting material for litters.
Poorfair breeders. May become nonproductive suddenly.
C58/J
Stock No. 000669
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Generation: F280 (27-NOV-06)
Inbred strain
H2 haplotype:
k2 (Fischer Lindahl K 1997; Shen et al., 1982)
Genes/alleles:

Strain origin:
MacDowell, Cold Spring Harbor (1921) from mating of littermates female 58 and male 52 of
Miss Lathrops stock.
Source:
MacDowell to Brandenburg (University of California, Berkeley) at F75, Brandenburg to JAX

(1948) at F77.
Characteristics
and uses:
Technician
notes:

months of age.
Aplasia of kidney in about 10% (Hummel et
al., 1966).
Very high frequency of leukemia prior to
one year of age (Mucenski et al., 1988).
Exhibit intermediate susceptibility to
developing atherosclerotic aortic lesions on
an atherogenic diet.
Carries a Chr Y of Asian M.M. musculus

A high viremic strain (Jenkins et al., 1982).
Frequent polyovular follicles (Fekete,
1950).
cancer, cardiovascular, neurobiology,
sensorineural.
Small size at weaning.

Occasional white spots on belly.
Obesity may be associated with nonproductivity.
Poor breeders, but good parents. Go nonproductive quite often. Must monitor birth
dates to identify non-productives. Only on a
5-month breeding rotation.
CAST/EiJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000928

n/a
Castaneus Eicher (Changed: 15-DEC-04)
Wild-derived inbred strain (species: M.m. castaneus, Thailand)
H2 haplotype:
n/a
Genes/alleles:
n/a
Development:
Founders were trapped in a grain warehouse in Thonburi, Thailand, by Dr. Joseph T. Marshall.
Mice were sent to Dr. Vernon Chapman and Dr. Frank Ruddle at Yale University, and from
there, to Dr. Eva Eicher and Dr. Thomas Roderick at The Jackson Laboratory in 1971. Dr.
Eichers colony was maintained by inbreeding to generate CAST/Ei; Dr. Rodericks colony was
maintained by inbreeding to generate CASA/Rk and CASB/Rk (Chapman and Ruddle, 1972).
Characteristics
and uses:
Technician
notes:
Research applications: genetics (evolution

and systematics, gene mapping [numerous
polymorphisms])
These mice are very difficult to handle.
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000655

Generation: F164+3 (30-APR-08)
n/a
CBA/CaH-T(14;16)6Ca (Changed: 15-DEC-04)
CBA/CaH-T(14;16)6CaJ (Changed: 15-DEC-04)
CBA/CaH-T6/J (Changed: 15-DEC-04)
Mutant strain, radiation induced mutation, chromosome aberration (translocation)

H2 haplotype:
Genes/alleles:
T(14;15)6Ca: reciprocal translocation, Chr 14 and 15, Carter 6
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
A substrain of CBA/CaH. Lyon, Harwell, from crosses of translocation T(14;15)6Ca to

CBA/Ca for 13 generations.
Harwell to MC Green (1963), to JAX Foundation Stocks (1968).
Histocompatible with CBA/CaJ.
Does not have Pdebrd1.
Homozygous for the marker translocation
T(14;15)6Ca; results in nondisjunction at a
rate of 4.4% in males, 22.2% in females.
Used in tandem with the CBA/H strain in

foreign body tumorigenesis studies in
which the T6 chromosome was used as a
marker to distinguish donor cells from host.
Research applications: cancer, tissue/cell
markers.
Somewhat jumpy.
Clean mice.
May have hair loss.
CBA/CaHN-Btkxid/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001011

n/a
CBA/NJ (Changed: 15-DEC-04)
Inbred strain, mutant
H2 haplotype:
Genes/alleles:
Btkxid, Bruton agammaglobulinemia tyrosine kinase; X linked immune deficiency

common name: xid
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Strong (1920) from cross of Bagg albino female to DBA male. Sent from Little to Haldane and
Grunebaerg (1932), to Carter (1947), to Harwell (1954). CBA/CaH from Harwell to NIH
(1966). Derived from a subline of CBA/CaH bearing foam cell reticulosis (fm).
NIH to CL Sidman at JAX (1983) at F513 to JAX (1983).
Carries a mutation in the Brutons tyrosine
kinase gene (Btk); is a model of human Xlinked immunodeficiency.
B-lymphocyte-specific defect results in an
inability to launch an antibody response to
thymus-independent type II antigens,
although they do produce normal amounts of
antibody in response to some protein
antigens.
Low serum IgM and IgG3 and a reduced
number of B-cells. Moreover, B-cells that are
present have reduced surface IgMIgD ratio,
which suggests a disorder in B-cell
maturation.
The Btkxid mutation, a recessive X-linked

B-cell defect, which, in hemizygous males
and homozygous females, prevents the
mice from making antibody response to
type III pneumococcal polysaccharide and
other thymic-independent antigens, was
discovered in the non-fm substrain at NIH.
inflammation.
Jumpy; startled by loud noise.

Coat color may appear lighter agouti than
normal.
Poor breeders.
Medium litter size.
CBA/CaJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000654

CBA Carter J;
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Rmcf s: resistance to MCF virus; MCF sensitive
Strain origin:
Source:
Strong (1920) from cross of Bagg albino female x DBA male. To Little at JAX.
From Little to Haldane and Gruneberg, University College, London (1932), to Royal Cancer
Hospital (1933), to JG Carr and TC Carter, Institute of Animal Genetics, Edinburgh (1947), to
MC Green (1950), to JAX Foundation Stocks by hysterectomy derivation and fostering on
C57BL/6J (1966 and 1967).
Characteristics
and uses:
Histocompatible with CBA/H-T6J.

Low spontaneous incidence of leukemia but
relatively high inducibility of myeloid
leukemia in response to benzene and
radiation exposure.
Carries viral proteins Mtv8, Mtv9, and
Mtv14.
Males develop a mild adult onset diabetesobesity syndrome characterized by
hyperglycemia, hyperinsulinemia, and
insulin resistance. Pancreatic beta cells do
not degenerate, and circulating insulin levels
remain high throughout life.
Carries a Chr Y of Type 2 Asian M.m.

musculus origin (Tucker et al., 1992).
Does not have retinal degeneration
(Pde6brd1).
Not histocompatible with the CBA/J
substrain, although H2 locus is the same in
both substrains (Green and Kaufer, 1965).
cancer, diabetes and obesity, reproductive
biology.
Technician
notes:
Very jumpy, especially when disturbed.

Hyperactive.
Occasional silvery coat colors in wean only.
Barbering common.
Clean mice.
Good parents; wean almost all pups born;
very few missing.
CBA/J
Common name:
Former name:
Strain type:
Appearance:
Stock No 000656
CBA Jackson
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Strong (1920) from cross of a Bagg albino female x DBA male. To Andervont about 1940.
Andervont to JAX (1948) at F67. Reintroduced to Foundation Stocks by hysterectomy
derivation; fostered on DBA/2J (1975).
Some hepatomas.
Only CBA substrain that carries the
Pde6brd1 retinal degeneration allele
(Sidman and Green 1965), resulting in
blindness by weaning age.
Fairly high mammary tumor frequency in
breeding females at less than 1 year
(Smith et al., 1973).
Develop a mild hearing loss late in life,
with most of the hearing loss occurring in
the higher frequencies (Sweet et al.,
1988).
Susceptible to chronic whole body
irradiation.
Renal tubulointerstitial lesions at a high

frequency (Rudofsky, 1978).
Some CBA/J mice spontaneously develop
exocrine pancreatic insufficiency syndrome
(Eppig and Leiter, 1977; Leiter et al., 1977).
Relatively resistant to diet-induced
atherosclerosis.
Used to study granulomatous experimental
autoimmune thyroiditis (G-EAT).
cardiovascular, immunology and inflammation,
internal/organ, metabolism, sensorineural.
Older breeders prone to seizures.

Hair loss sometimes seen in breeders after 56
months of age.
Occasional rectal prolapse.
Cages may become quickly soiled due to urine.
Hyperactive mice. Jumpy, nervous.

Ring tail.
Missing fur.
Weanlings may have silver gray coats.
Entire litters may be missing at weaning.
Good parents.
CByJ.RBF-Rb(8.12)5Bnr/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001802

n/a
CBy.RBF-Rb(8.12)5Bnr/J (Changed: 15-DEC-04)
Rb5Bnr (Changed: 15-DEC-04)
Congenic, mutant strain, chromosome aberration (Robertsonian)

Albino; related genotype: Tyrp1b/Tyrp1b Tyrc /Tyrc
H2 haplotype:
n/a
Genes/alleles:
Rb(8.12)5Bnr: Robertsonian translocation, Chr 8 and 11, Unversitat Bonn/Rhein 5
Development:
Created by backcrossing the Robertsonian chromosome Rb(8.12)5Bnr on the BALB/cByJ

genetic background; by Dr. Muriel Davisson at The Jackson Laboratory. Donor strain:
RBF/DnJ.
Characteristics
and uses:
Technician
notes:
Strain created to facilitate selection of

immunoglobulin-competent hybridomas
(Taggert, 1983).
Research applications: cancer.
n/a
CE/J
Stock No. 000657
Common name:
Former name:
Strain type:
Appearance:
Extreme Dilution
n/a
Inbred strain, spontaneous mutation
Greyish white; related genotype: Aw/Aw Tyrc-e /Tyrc-e
H2 haplotype:
Genes/alleles:

0
Hc : hemolytic complement; deficient
C5-, C5-d, C5-def, C5-deficient, hco
Tyrc-e: tyrosinase; extreme dilution
common names: cd
Strain origin:
Source:
Knight (1920) from a mouse trapped in Illinois. Detlefsen studied genetics of the color type.
Inbred by Eaton at least 15 generations; some sent to Woolley, Sloan-Kettering.
Woolley to Speirs (1946); Speirs (2 gen. from Woolley) to Woolley and JAX (1948).
Characteristics
and uses:

hearing loss 1 mutation; onset prior after 10
months of age.
Resistant to amyloid induction and
development of amyloidosis.
Low mammary tumor frequency; 33% ovarian
tumors in old age.
Some sarcomas, wide range of tumor types;
high adrenal cortical carcinoma frequency
when gonadectomized at birth.

cancer, metabolism, neurobiology,
sensorineural, immunology and
inflammation.
Technician
notes:
Very, very jumpy mice. Hyperactive. Nervous,

shy; easily frightened. Handle gently.
Occasional kinky tails.
Fair breeders.
Usually chew ears of young mice.
Get fat as they age.
CZECHII/EiJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001144

n/a
Wild-derived inbred strain (species: M.m. musculus, Czechoslovakia)

H2 haplotype:
n/a
Genes/alleles:
n/a
Strain origin:
n/a
Source:
n/a
Characteristics
and uses:
Technician
notes:
Generation: F16+62 (21-NOV-06)
CZECHII/Ei (changed: 15-DEC-04)
Research applications: genetics research

(evolution and systematics, gene mapping
(numerous polymorphisms)
DBA/1J
Stock No. 000670
Common name:
D1;
Former name:
n/a
Strain type:
Appearance:
Inbred strain
Dilute brown; related genotype: a/a Tyrp1b/Tyrp1b Myo5a d/Myo5ad
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
The DBA strains are the oldest inbred strains. The name comes from the three coat color genes
for which the DBA strains are fixed: dilute Myo5ad, brown Tyrpb, nonagouti a. Little began
inbreeding in 1909 from a mouse colony segregating for coat color. During 1929 and 1930
crosses were made among substrains; several new substrains, including DBA/1 and DBA/2,
were established. DBA/1 and DBA/2 differ at a large number of loci (including the MHC H2
histocompatibility locus), which most likely results from residual heterozygosity in the strain
when the substrains were separated.
Fekete (1936) to JAX to Hummell (1947), Hummel to JAX (1948).
months of age.
Model of rheumatoid arthritis:
immunization with type II collagen leads to
the development of severe polyarthritis
mediated by an autoimmune response.
Intermediate susceptibility to development
of atherosclerotic aortic lesions on an
atherogenic diet.
In response to challenge, develop immunemediated nephritis (Xie et al., 2004).
Resistant to most DBA/2 transplantable
tumors.
Mammary tumors in about 75% of breeding

females over 1 year of age and in some
virgins after 18 months (Hoag, 1963).
Extremely susceptible to audiogenic
seizures.
Calcareous heart deposits in almost all
retired breeders.
Susceptible to inoculated TB.
Extreme intolerance to alcohol, morphine
and related opioids.
immunology and inflammation, arthritis,
neurobiology, sensorineural, dermatology.
Mice jumpy; can be difficult to handle.

Mice squeal when picked up.
Young mice can be very jumpy;
hyperactive at 23 weeks old. Weanlings
make a lot of noise when picked up.
Weanling coat color sometimes appears
silver gray.
Sometimes get diarrhea.
Females are sexually mature sometimes as

early as 25 days of age.
Good breeders. Lots of missing and born
dead pups.
At wean age, large number of pups have
short tails.
Some litters appear runted.
DBA/1LacJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001140

D1Lac;
n/a
Inbred strain
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
DBA/1LcJ, DBA/1J, and DBA/2J have a common origin. JAX to Laboratory Animal Center
(Lac), Carshalton, UK (1955). Recovered from Laboratory Animal Center, Carshalton, UK
Frozen Embryo Bank (1981) to Les at JAX.
To Mider and Wooley at Sloan-Kettering (1938), Mider to Heston at NCI, Heston to JAX
(1948) at F26. Les to JAX by hysterectomy derivation and fostering on C57BL/6J.
months of age.
Genetic monitoring at JAX of 11
genetic markers indicates no
difference between DBA/1J and
DAB/1LacJ (Les, 1990).
Low susceptibility to development of
atherosclerotic aortic lesions when on
an atherogenic diet.
Analysis of 35 additional loci of DBA/1LacJ

mice reported in the literature also indicate that
DBA/1J and DAB/1LacJ do not differ.
Immunization with type II collagen (CII)
induces an autoimmune arthritis in susceptible
DABG/1LacJH and DBA/1J mice (Joosten et
al., 1994; Walter et al., 1996).
immunology and inflammation, arthritis,
Jumpy, particularly at 34 weeks of

age; curious when young.
Diarrhea in the pups at wean age.
Good parents.
Urine burn on breeders occasionally.
DBA/2J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000671

Generation: F223p (03-JAN-08)
D2; D2J;
n/a
Inbred strain
H2 haplotype:
Genes/alleles:
Cdh23ahl: cadherin 23 (otocadherin); age related hearing loss 1;

GpnmbR150X: glycoprotein (transmembrane) nmb; iris pigment dispersion;
common names: GPnmbipd
Tyrp1isa: tyrosinase-related protein 1; iris stromal atrophy
common names: isa
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
DBA/1J and DBA/2J have a common origin (see DBA/1J).

To Mider and Wooley at Sloan-Kettering (1938), Mider to Heston at NCI, Heston to JAX
(1948) at F26.
hearing loss 1 mutation; severe by 3 months
of age.
Low susceptibility to development of
atherosclerotic aortic lesions when on an
atherogenic diet.
Aging mice develop progressive eye
abnormalities that closely mimic human
hereditary glaucoma.
Resistant to most DBA/1 tumors.
Tumor S91 grows in both strains.
A few mammary tumors in old breeding
females; frequency has decreased since
1955.
C5 deficient, unlike DBA/1J.
Audiogenic seizures: 100% of mice at 35
days; 5% after 55 days.
High mortality in males exposed to

chloroform fumes.
High incidence of calcareous heart deposits.
Extreme intolerance to alcohol, morphine
and related opioids (Phillips et al., 1994),
morphine (Berrettini et al., 1994; Belknap et
al., 1995).
Characteristics often contrasted with
C57BL/6J because of their genetic disparity.
Research areas: general purpose,
neurobiology, sensorineural, immunology
and inflammation, dermatology.
Jumpy; easily frightened by loud noises.

Squeal when picked up.
Wean coat color sometimes appears silver
gray.
Difficult to sex at weaning.
Females are sexually mature very early

(approximately 25 days).
Some litters may appear runted.
Very dirty; diarrhea more common in this
strain.
FVB/NJ
Common name:
Former name:
Strain type:
Appearance:
H2 haplotype:
Genes/alleles::
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Stock No. 001800

FVB; Friend Virus B NIH Jackson;

n/a
Inbred strain
Albino; related genotype: A/A Tyrc/Tyrc
q

Fv1b, Friend virus susceptibility 1; susceptibility
common names: Fv-1, Rv-1, Rv1
NIH to Taketo (1987) to Mobraaten (1988). Outbred Swiss mice N:NIH established in the early
1940s. In 1966 mice selected from this colony for histamine resistance (HSFR/N). Homozygous
Fv1b mice from the HSFS/N line were inbred as strain FVB without further selection (Taketo et
al., 1991).
Mobraaten to JAX (1990).
Homozygous for the retinal degeneration
allele Pde6brd1.
Has not been found to develop
spontaneous tumors, but is highly
susceptible to chemically-induced
squamous cell carcinomas with a high rate
of malignant conversion from papilloma
to carcinoma.
Resistant to collagen-induced arthritis.
Higher than average activity, anxiety, and
basal body temperature, and low stressinduced hyperthermia.
Prone to allergen induced, asthma-like,

bronchial hyperresponsiveness.
Pronuclei of zygotes are large and easily
identified, thus facilitating efficient production
of transgenics (Taketo et al., 1991).
FVB/N mice are good breeders; have
consistently large litters with a mean of 9.5
pups/litter.
Sex ratio: 53% females, 47% males.
sensorineural, immunology and inflammation.
Aggressive males; we wean males 10 per

weaning cage. Retired breeder males housed 1
per box (or they will fight).
Calm, clean mice.

Big eaters.
Good mothers.
Large litters.
HRS/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000673

n/a
Inbred strain, mutant strain, spontaneous mutation
Unpigmented, without hair; related genotype: Tyrp1b/Tyrp1b Tyrc/Tyrc Myo5ad/Myo5ad
Hrhr/Hrhr
Albino, unaffected; related genotype: Tyrp1b/Tyrp1b Tyrc/Tyrc Myo5ad/Myo5ad Hrhr/+
H2 haplotype:
Genes/alleles:
Hrhr: hairless; hairless

common name: hr
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Generation: F93 (date unknown)
Hairless
Developed by FAE Crew (Crew et al., 1931) from a pair of mice received from Mr. HC
Brooke, a well-known British fancier, captured in an aviary in London (Brooke, 1926). Chase
to EL Green (1952), to Les (1956), to MC Green (1959), to Lane.
Lane to JAX (1964) at F24.
Albino strain carrying hairless (hr) gene.
The hairless mutation was caused by a
naturally occurring provirus integration
(Stoye et al., 1988).
Homozygous hairless start to lose their
hair at about 10 days. Eventually hair
loss is total. Some hr/+ females have
significant hair loss after 4 months of
age.
Carries a Type 1B M.m. musculus Chr Y
Leukemia frequency (C-type MuLV) related to

mutant gene dose: 1% in +/+ HRS/J, 20% in
heterozygotes, 45% in hairless by 810 months,
virtually all by 28 months (Meier et al., 1969;
Heiniger et al., 1976).
Strain maintained by breeding haired (hr/+)
female x hairless (hr/hr) male.
dermatology, immunology and inflammation,
dermatology.
Can be jumpy.
Weanlings squeak a lot when handled.
Mice not real dirty but not overly clean.
Big eaters.
Hair flies when changing litters at 23 weeks of
age.
I/LnJ
Stock No. 000674
Common name
Former name
Strain type
Appearance
I Lyon;
n/a
Inbred strain
Pink-eyed dilute brown, piebald (spotted); related genotype: a/a Tyrp1b/Tyrp1b Oca2p/Oca2p
Myo5ad/Myo5ad Ednrbs/Ednrbs
H2 haplotype
Genes/alleles
Ednrbs: endothelin receptor type B; piebald

common name: s
Strain origin
Source
Characteristics
and uses
Technician
notes
Strong (1926) from unpedigreed mice (Strong, 1942).

Fenton, Brown University to JB Lyon, Emory University (1954), to ES Russell at JAX (1969).
Carries the Oca2p allele at the Phk locus.
Phosphorylase kinase activity virtually
absent in muscle and reduced in the brain,
kidney, and heart.
Spontaneous occurrence of absent corpus
callosum (Livy and Wahlsten, 1991;
Gruber et al., 1991).
Carries the allele for long incubation period at

the Prn-i (Sinc) locus, determining incubation
period of the scrapie agent.
reproductive biology, sensorineural,
dermatology, developmental biology,
Very docile.
Poor breeders.
JF1/Ms
Common name:
Former name:
Strain type:
Appearance:
Stock No. 003720

JF1/Msf (changed: 26-OCT-05)
Wild-derived inbred strain (species: M.m. molossinus, Japan)
Black-spotted white coat, black eyes; related genotype: a/a Ednrbs/Ednrbs
H2 haplotype:
n/a
Genes/alleles:
n/a
Development
Characteristics
and uses:
Technician
notes:
Generation: F26+6+18 (24-MAY-08)
Japanese Fancy Mouse 1
Mice of a stock identified as a Japanese Fancy Mouse were purchased from a market in
Denmark in 1987 and maintained by sibling inbreeding at the National Institute of Genetics,
Mishima, Japan. In 1993, at generation F20, the established inbred strain was named JF1
(Japanese Fancy Mouse 1). Genetic analysis of multiple markers led to the conclusion that JF1
is of the species Mus musculus molossinus (Koide et al., 1998). Mice of this strain were
imported by JAX in May 2000 from Dr. Toshihiko Shiroishi.
Research applications: genetics research
(evolution and systematics, gene mapping
[numerous polymorphisms]).
KK/HlJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 002106

Generation: F107+7 (24-MAY-08)
Kasukabe
n/a
Inbred strain
H2 haplotype:
Genes/alleles:

Development:
The KK inbred strain was inbred by K Kondo in 1944. Many of the KK stock carry the yellow
(Ay) allele. The KK/HlJ substrain, wild-type for the agouti gene, was provided by Dr.
Leiselotte Herberg, Diabetes Research Institute, Dusseldorf, Germany.
Characteristics
and uses:
Technician
notes:
Males exhibit diabetic symptoms that

include hyperglycemia, hyperinsulinemia,
insulin resistance.
Reports indicate that the KK strain is
hemolytic complement deficient (Hc0);
however our strains have not been tested
to confirm this allele (Cinader et al.,
1964).
Serves as a model of noninsulin-dependent,

type 2 diabetes.
n/a
LP/J
Stock No. 000676
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain
White-bellied agouti, piebald; related genotype: Aw/Aw Ednrbs/Ednrbs
H2 haplotype:
bc (Fischer Lindahl K 1997)
Genes/alleles:

Ednrbs; endothelin receptor type B; piebald
common name: s
Strain origin:
Source:
Dunn (1928) from a chinchilla stock from Castle and some coat color stocks from English
fanciers. To Scott at JAX, to Dickie at JAX (1947) at F30.
Dickie to JAX (1949) at F33.
Characteristics
and uses:

hearing loss 1 mutation; onset after 10 months
of age.
Fairly high incidence of tumors that develop
later in life, including mammary tumors,
lymphoma, lung and soft-tissue sarcomas.
Varied types of late occurring tumors; very
long lived.
Develops bony lesions that are grossly

and histologically similar to the lesions of
human otosclerosis.
neurobiology, sensorineural, dermatology,
developmental biology.
Technician
notes:
Active mice. Nervous. Crawly. Dont like to

stay in uncovered cages. Jumpy.
Poor breeders. Poor mothers; like to kill first
litter.
Active nest builders. We use Nestlets.

Pile up shavings under water bottle,
resulting in wet boxes.
MA/MyJ
Common
name:
Former name:
Strain type:
Appearance:
Stock No. 000677

Generation: F180+18 (23-JAN-08)
Marsh Murray
n/a
Inbred strain
Albino; related genotype: Tyrc/Tyrc
H2 haplotype:
Genes/alleles:

hf : hepatic fusion; hepatic fusion
Strain origin:
Source:
Marsh from Lathrop-Loeb colony (19031915). (MA = Marshs albino). Murray and Warner
separated this strain from MA after 37 generations.
Warner to JAX (1948) at F24.
Characteristics
and uses:

months of age.
Spontaneous mutation of hf results in
varying degrees of fusion in the hepatic
lobes.
Very low spontaneous mammary tumor
frequency.
Diabetes-resistant strain (Leiter, 1989).
Polyuria and polydipsia marked in breeding
females over 6 months (Bernstein, 1966).
Carries a Type 4 Chr Y of U.S. M.m.

domesticus origin (Tucker et al., 1992).
Cysts in neural and intermediate lobes of
pituitary in over 50% of the mice.
Susceptible to skin lesions.
High systolic blood pressure (128 mm Hg).
Short breeding life.
sensorineural.
Technician
notes:
Easy mice to work with.

Poor breeders; may not have first litter until
2 months after mating.
Chewed tails occasionally.

Small litter size; missing litters frequent.
MOLF/EiJ
Stock No. 000550
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Generation: ?+F2 (21-NOV-06)
Wild-derived inbred strain (species: M.m. molossinus; Fukuoka, Kyushu, Japan)

H2 haplotype:
n/a
Genes/alleles:
Pde6brd1: phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide; retinal degeneration 1;
Development:
MOLC, MOLD, and MOLF were all independently inbred from single pairings of related
M.m. molossinus mice held by M Potter at NIH. Sent to TH Roderick and EM Eicher at JAX
in 1969.
Characteristics
and uses:
Technician
notes:

allele Pde6brd1.
Research applications: sensorineural,

genetics (evolution and systematics, gene
mapping [numerous polymorphisms]).
MRL/MpJ
Stock No. 000486
Common name:
n/a
Former name:
n/a
Strain type:
Inbred strain
H2 haplotype:
Albino, unaffected; related genotype: a/a Tyrc /Tyrc Fas+/Fas+

k
Genes/alleles:
n/a
Appearance:
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Murphy at JAX from a series of crosses involving strains C57BL/6J, C3H/HeDi, AKR/J and
LG/J, followed by inbreeding. Faslpr (lymphoproliferation ) mutation found at F12.
Murphy to barrier facility at JAX (1980) by hysterectomy derivation; fostered on C57BL/6J at
F37.
Homozygous for the normal allele of Faslpr;
this strain serves as a homozygous normal
control for MRL/MpJ-Faslpr/J (000485).
Estimated to have derived 75% of genome
from LG/J.
Necrotizing arteritis is common.
Antinuclear antibodies appear at 10 months
in most mice.
Females die at 73 weeks, males at 93 weeks,
with chronic glomerulonephritis.
One sixth of mice autopsied have reticulum
cell neoplasia.
Females heal faster and more completely

than males (Blankenhorn et al., 2003).
Used as animal model for rheumatoid
arthritis (Axford et al., 1994; Hackshaw et
al., 1994), Sjogrens Syndrome (Sato and
Sullivan, 1994; Hayashi et al., 1995) and
systemic lupus erythematosis (SLE)
(Granholm and Cavallo, 1994; Green et al.,
1995).
inflammation, internal/organ,
Large body size. Docile.
Large litter size.
MSM/Ms
Common name:
Former name:
Stock No. 003719

Generation: F67+16 (24-MAY-08)
M.MOL-MSM
n/a
H2 haplotype:
Wild-derived inbred strain (species: M. m. molossinus; Mishima City, Shizuoka Prefecture,

Japan)
n/a
Genes/alleles:
n/a
Development:
The MSM inbred strain was derived from M. m. molossinus mice trapped in Mishima
Prefecture, Japan, April 1978, and maintained by Dr. Kazuo Moriwaki (Okumoto et al., 1995).
Mice were imported to JAX May 2000 from Dr Moriwakis colleague, Professor Toshihiko
Shiroishi.
Strain type:
Appearance:
Characteristics
and uses:
Technician
notes:
Resistant to development of lymphoma,

due to at least 2 loci identified in crosses
involving strain SL/Kh (Pataer et al.,
1996).
C3HxMSM F1 hybrids treated with MNU
develop squamous cell carcinomas
of the forestomach, with about 20% and 15%

having mutation in H-ras and p53 genes,
respectively (Masui et al., 1997).
Research applications: cancer, genetics
(evolution and systematics; gene mapping
[numerous polymorphisms])
NOD.CB17-Prkdcscid/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001303

Generation: N10F62 (03-JAN-08)
NOD SCID; NOD scid

n/a
Mutant strain, spontaneous mutation
H2 haplotype:
g7
Genes/alleles:
Prkdcscid : protein kinase, DNA activated, catalytic polypeptide; severe combined

immunodeficiency
common name: scid
0
Hc : hemolytic complement; deficient
Strain origin:
Characteristics
and uses:
Technician
notes:
Prkdcscid occurred spontaneously in a colony of BALB/c-Igh b (C.B-17) mice maintained at the

Institute for Cancer Research in Philadelphia, PA. The Prkdcscid mutation was backcrossed onto
the NOD/ShiLt background as follows: an NOD/ShiLt female was bred to a C.B-17-Prkdcscid
male; male Prkdcscid/+ offspring of the F1/N1 and subsequent generations were mated to
NOD/ShiLt females for a total of 10 crosses to NOD/ShiLt. At generation N10, Prkdcscid was
made homozygous by sisterbrother inbreeding.
Severe combined immunodeficiency; must
be maintained in SPF conditions.
Development of serum antibody,
leakiness, is lower on the NOD genetic
background than on other genetic
backgrounds.
Under SPF conditions, have a high incidence
of thymic lymphomas, which limits the
lifespan to about 8.5 months.
Low NK cell activity.
Hypogammaglobulinemia (no detectable
IgM, IgG1, IgG2a, IgG2b, IgG3, or IGA).
No hemolytic complement activity.

Insulitis- and diabetes-free throughout life;
serves as diabetes-free control for
NOD/ShiLtJ mice (001976).
Excellent hosts for xenografts; may be
useful for delineation of the role of T cell
subsets in autoimmune diabetes; can serve
as a source for NOD insulitis-free islets.
Research applications: cancer, diabetes and
obesity, immunology and inflammation,
internal/organ, virology.
Very active; wean are jumpy.

Sometimes mice have tails that are
abnormalkinky, set to one side, higher
than normal.
Pair mating is recommended.
Breed very well; large litters.

Strain-related illness sets in as mice reach
retiring age; often die just before retiring.
NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 005557
NOD scid gamma; NSG;

NOD-scid IL2Rgammanull; NOD-scid IL2Rgnull;
Generation: N8F?+4pF2 (03-JAN-08)
n/a
Congenic, mutant strain, spontaneous mutation, targeted mutation
H2 haplotype:
g7
Genes/alleles:
Il2rgtm1Wjl: interleukin 2 receptor, gamma chain; targeted mutation 1, Warren J Leonard

common names: [KO]gammac, CD132-, gammac-, IL2Rgammanull
Prkdcscid : protein kinase, DNA activated, catalytic polypeptide; severe combined
immunodeficiency
common names: scid
Development:
These double mutant mice were produced by breeding female NOD.CB17-Prkdcscid/J (001303)
mice with male mice bearing the X-linked B6.129S4-Il2rgtm1Wjl/J allele (003174). The
resulting male mice, heterozygous for the Prkdcscid allele and hemizygous for the Il2rgtm1Wjl
allele, were crossed to female NOD.CB17-Prkdcscid/J (001303) mice for 8 generations.
Heterozygotes were interbred to produce mice homozygous for the Prkdcscid allele and
homozygous (females) or hemizygous (males) for the Il2rgtm1Wjl allele. Donating investigator:
Leonard Shultz (JAX).
Characteristics
and uses:
Technician
notes:
Superior human hematopoietic

engraftment.
Significant human lymphoid expansion.
Significantly diminished NK activity;
improves quality and duration of
xenografts.
Lacks mature lymphocytes (B and T
cells) without leakiness.
Newborn recipients do not require IL-7
for thymopoiesis.
Does not produce detectable serum
immunoglobulin.
Resistance to lymphoma leads to longer

lifespan (>16 months) than that of NOD.CgPrkdcscid mice.
Supports adoptive transfer of diabetic T cells
without irradiation.
Superior for HIV and other infectious disease
research because of improved lymphoid
expansion.
Research applications: cancer, immunology and
inflammation, internal/organ, virology.
Because of severe immunodeficiency,

mice shold be handled with smoothtipped forceps that have been soaked in a
disenfectant solution.
Handlers should dip gloved hands into
disinfectant between touching the
outside of the cage and handling the
mice.
Even with severe immunodeficiency,
mice often survive past 910 months in
SPF colonies.
Great breeders; rarely lose litters.

Improved productivity when mice are first bred
at 56 weeks.
Change in food or environment can have
pronounced effects on productivity.
Mice love to burrow and nest; we supply
nesting material as environmental enrichment.
510% of breeders die before 7 months.
NOD/ShiLtJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001976

Non-obese Diabetic
NOD/LtJ (changed: 23-FEB-07)
Inbred strain
H2 haplotype:
g7
Genes/alleles:

Hc0: hemolytic complement; deficient;
Development:
NOD inbred mice originated early in the inbreeding of the Cataract Shionogi (CTS) strain.
Originally, the mice were outbred Jcl:ICR mice. At F6, the progenitors of the future NOD/Shi
mice were inbred on the basis of an elevated fasting blood glucose level in cataract-free mice.
At F13, the NOD progenitors were separated from what is now the NON/Shi strain. High
fasting blood glucose levels continued to be the basis for selection of the latter strain, while the
NOD progenitors at F13 and later were selected on the basis of normal fasting blood glucose
level. In 1974, at F20, a female in the normoglycemic line spontaneously developed overt
insulin-dependent diabetes mellitus with insulitis (IDDM). Selective breeding of the progeny
of this diabetic female produced the nonobese diabetic (NOD) strain. Originally restricted to
distribution in Japan, NOD substrains were distributed during the early 1980s to Australia and
the United States. NOD and NON strains were imported from a colony in Kyoto, Japan, by Dr.
M. Hattori to the Joslin Diabetes Center in Boston in 1984. Breeder pairs from Joslin Diabetes
Center were sent to Dr. E. Leiter at JAX and are the source of the production strains
NOD/ShiLtJ and NON/ShiLtJ (002423).
Characteristics
and uses:
Polygenic model for type 1 diabetes,

characterized by insulitis, a leukocytic
infiltration of the pancreatic islets. Marked
decreases in pancreatic insulin content
occur in females at about 12 weeks of age;
in males, several weeks later.
Consequently, plasma glucose levels
increase to greater than 250 mg/dl.
Females develop diabetes at an incidence of
90100% by 30 weeks of age; males at 40
60% by 3040 weeks.
Exhibit pancreatic beta cell destruction.
Major component of diabetes susceptibility
in NOD mice is the unique MHC haplotype
(H2g7 = Kd, Aad, Abg7, Enull, Db).
Homozygous for Cdh23ah1, the age-related
hearing loss 1 mutation; mice are deaf by 3
months of age.
Aberrant immunophenotypes include

defective antigen-presenting cell functions,
defects in regulation of the T lymphocyte
repertoire, defective NK cell function,
defective cytokine production from
macrophages, impaired wound healing, C5
complement deficiency.
Susceptibility to diabetes influenced by
environmental factors, including housing
conditions, health status, microbiologic
status of the colony, and diet.
Research applications: developmental
biology, diabetes, immunology and
inflammation, internal/organ, neurobiology,
sensorineural.
Technician
notes:
Mice are hyperactive, jumpy, nervous at 4

weeks and older. Forceps and noise seem to
make it worse.
Mice may be aggressive toward humans.
Mice are large and have large litters; pair
mating is recommended.
Have strong odor when they turn positive

for diabetes.
Mice are injected with Complete Freunds
Adjuvant (FAC) and delayed mated. They
turn positive for diabetes less often, so a
normal rotation has been made possible for
the most part.
NON/ShiLtJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 002423

Non-obese Non-diabetic
NON/LtJ (changed: 23-FEB-07)
Inbred strain
H2 haplotype:
nb1
Genes/alleles:
Strain origin:
The NON inbred strain arose out of a colony originally developed by selection for high fasting
blood glucose early in the inbreeding of the Cataract Shionogi (CTS) strain. These mice were
originally outbred Jc1:ICR mice A cataract-free substrain was initiated at F6, with selection
made on the basis of a high fasting blood glucose. This line was separated from the future
NOD/Shi line at F13, and originally designated NON for nonobese, nondiabetic.
Characteristics
and uses:
Technician
notes:

allele Pde6brd1.
Although closely related to NOD mice,
NON mice contain a diabetes resistant
MHC haplotype (H2nb1 = Kb, Anb1, Ek,
Db).
Name derived from Non-Obese Nondiabetic; however, NON/ShiLtJ mice
should not be considered normal.
Although ALS/Lt males share the impaired
glucose tolerance phenotype of NON/ShiLt
males, the ALS/Lt males differ in
developing progressive hyperinsulinemia
as they gain weight, whereas NON/ShiLt
males fail to hypersecrete insulin as they
gain weight as adults, suggesting a
potential beta cell response defect.
Maintains low plasma insulin level, which
may account in part why certain loci from
NON/ShiLt can enhance development of
autoimmune type 1 diabetes in segregating
hybrid mice following outcross to
NOD/ShiLtJ.
NON strain-characteristic immunologic

abnormalities include
perivascular/periductular leukocyte
infiltration into the pancreas and
submandibular salivary glands, and T
lymphocytopenia evident by 20 weeks of
age in spleen.
NON/ShiLt mice clearly harbor genes
predisposing to type 2 diabetes, as
evidenced by early impaired glucose
tolerance in males and females,
development of moderate mature-onset
obesity in the presence of low plasma
insulin levels, and development of
glomerulosclerotic kidney lesions.
sensorineural.
Aggressive.
Tend to be non-productive.
Play with their food; seem to pull it down

but not eat it, but rather leave a lot at the
bottom of the cage
NONcNZO10/LtJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 004456

Generation: N1F11+8 (16-NOV-05)
RCS-10
RC-10 (Changed: 15-DEC-04)
Recombinant congenic strain
H2 haplotype:
nb1
Genes/alleles:
n/a
Development:
A recombinant congenic developed by introgressing 6 known diabesity QTLs from the type 2
diabetes-prone and obese NZO/HlLt inbred strain into the nominally nonobese and diabetesresistant NON/ShiLt strain background. NZO-derived QTLs include those marked by
D1Mit411, D5Mit7, D11Mit261/D11Mit41, D12Mit231 and D15Mit159. Donating
investigator: Edward Leiter (JAX).
Characteristics
and uses:
Technician
notes:
Polygenic model of human metabolic

syndrome and type 2 diabetes.
Type 2 diabetes in males results from
polygenic interactions, producing a moderate
obesity rather than the massive obesity
elicited by the single locus diabesity mutant
models, such as the BKS.V- Lepob/J
(000696) and the BKS.Cg-m +/+ Leprdb/J
(000642) strains.
Progressively increasing plasma glucose
(280600 mg/dl) with age.
Moderately increased serum and leptin.
Elevated serum triglycerides.
Unlike mice with monogenic obesity

syndromes, males do not exhibit
hypercorticism, are not hyperphagic, and
show no obvious thermoregulatory defects.
Males weaned onto chow with 1011% fat
(wt/wt) develop visceral obesity, maturityonset hyperglycemia, dyslipidemia,
moderate liver steatosis, and pancreatic islet
atrophy.
Differentially sensitive to adverse hepatic
side effects of thiazolidinediones; may be
useful for pharmacogenetic analysis.
Research applications: diabetes and obesity.
n/a
NZB/BlNJ
Common name:
Former name:
Strain type:
Stock No. 000684

New Zealand Black

n/a
Inbred strain
Appearance:
H2 haplotype:
d2 (Fischer Lindahl K, 1997)
Genes/alleles:
Hc0: hemolytic complement; deficient;

PctpR120H: phosphatidylcholine transfer protein; R120H
Strain origin:
Source:
Outbred mice from Imperial Cancer Research Fund, London, to University of Otago Medical
School, New Zealand (1930). Inbred by Bielschowsky (1948).
NIH to ES Russell to JAX (1969).
Characteristics
and uses:
Displays a number of autoimmune

abnormalities, including hemolytic anemia,
elevated levels of immunoglobulin, antiDNA antibodies, anti-thymocyte
antibodies, and circulating immune
complexes causing glomerulonephritis.
Develops autoimmune hemolytic anemia
of the Coombs positive type and a
nephropathy (Bielschowsky et al., 1959).
Carries a Type 1 B M.m. musculus origin
NZB/BlNJ mice fed an atherogenic diet
fail to develop atherosclerotic aortic
lesions.
Poor reproductive performance.

High frequency of chronic gastroduodenal
ulceration.
F1 hybrids of NZB/BlNJ and NZW/LacJ
(NZBWF1/J [100008]) are widely used as a
model for autoimmune disease resembling
human systemic lupus erythematosus.
In hybrids with C57BL there is lateappearing positive direct systemic lupus
erythematosis (Hayes and Greiner, 1992).
Research applications: cardiovascular,
developmental biology, hematological,
Technician
notes:
Appear dumb.
Aggressive with each other. For males, we
house only littermates together.
Barbering in breeders and weanlings.
Older breeders have a brownish tint to coat
color.
Many missing litters.

High incidence of non-productive.
Females get chubby with age.
Build nests under water bottle, resulting in
wet nests.
We use Nestlets for breeders.
NZW/LacJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001058

New Zealand White

n/a
Inbred strain
Albino; related genotype: Tyrp1b/Tyrp1b Oca2p Tyrc/Oca2p Tyrc
H2 haplotype:
Genes/alleles:
PctpR120H: phosphatidylcholine transfer protein; R120H
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
From same outbred stock as NZB but inbred and selected for white color by Hall (1952).
Recovered from Laboratory Animal Center, Carshalton, UK Frozen Embryo Bank (1981) to S
Bernstein at JAX, to JAX by hysterectomy derivation and fostering on C57BL/6J.
Normal lifespan, but develop anti-DNA
antibodies, high serum levels of retroviral
gp70 antigen, and nephritis later in life.
Express glomerulonephritis beginning at 13
months.
High frequency of exencephaly,
predominantly in female mice (Vogelweid et
al., 1993).
F1 hybrids of NZB/BlNJ and NZW/LacJ

(NZBWF1/J [100008]) are widely used as a
human systemic lupus erythematosus.
Research applications: hematological,
Calm. Curious.
Small litters.
Fair to good breeders. Good parents.
P/J
Stock No. 000679
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain
Pink-eyed fawn, short ear; related genotype: a/a, Tyrp1b/Tyrp1b, Oca2p/Oca2p,
Bmp5se Myo5ad/Bmp5se Myo5ad
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Snell, extracted following outcross of strain BDP, which was developed by Gates. Sent to
McNutt at Wisconsin at F35.
McNutt to JAX (1948) at F39.
months of age.
allele Pde6brd1 (Sidman and Green, 1965).
High incidence of lymphatic leukemia.
Carries an Asian M.m. musculus Chr Y
High resistance to chronic whole-body Xirradiation.
Highly susceptibility to audiogenic and

electroconvulsive seizures (Deckard et al.,
1976).
Susceptible to the induction of colon
carcinogenesis (Rosenberg and Liu, 1995).
dermatology, developmental biology,
Small litters; many born dead.
Occasional kinky tails.
PERA/EiJ
Stock No. 000930
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Wild-derived inbred strain (species: M.m. domesticus, Rimac Valley, Peru)

H2 haplotype:
Genes/alleles:
Lith9PERA/EiJ : lithogenic gene 9; PERA/EiJ
Development:
In 1961, founders were trapped for ME Wallace, University of Cambridge, by O Atteck in a

Peruvian yard that was used to dry maize cobs in Nana Village, Rimac Valley, Peru. These
mice were held in a small closed colony by Wallace. In 1971, at approximately F25, members
of this colony were sent to EM Eicher and TH Roderick at JAX, where inbreeding of mice
continued.
Characteristics
and uses:
Technician
notes:
Research applications: genetics (evolution

and systematics, gene mapping [numerous
polymorphisms]).
PL/J
Stock No. 000680
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain
H2 haplotype:
Genes/alleles:
Strain origin:
From noninbred Princeton stock started in 1922 from 200 mice purchased from a dealer.
Inbred by Lynch, Rockefeller Institute, giving rise to a high leukemia strain (PL) and a second
strain (PLA) with lower frequency.
Source:
Characteristics
and uses:
Technician
notes:
Lynch to JAX (1951) at F22.

allele Pde6brd1 (Sidman and Green, 1965).
Develops clinical and histological
experimental allergic encephalomyelitis
(EAE) (Zamvil et al., 1987), with high
mortality.
Reports of leukemia incidence vary from
50% in females and 19% in males to 80
90%.
Low percentage of mammary tumors.
Carries a Type 4 U.S. M.m. domesticus
origin Chr Y (Tucker et al., 1992).
In addition to low threshold to

electroconvulsive seizures, mice are
susceptible to handling and rhythmic
tossing-induced seizures (Kitami T et al.,
2004).
Abnormal diploid/binucleated sperm cells
found in this strain (Burkhart and Malling,
1989).
Gentle but active mice.

Eyes sometimes different sizes.
Fair breeders.
Older breeders may have seizures.

Most weanlings have bent tails.
Weanlings often spin.
PWK/PhJ
Stock No. 003715
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Generation: F69+3+16 (24-MAY-08)
Wild-derived inbred strain (species: M.m. musculus, Prague; Lhotka, Czech Republic)
H2 haplotype:
n/a
Genes/alleles:
n/a
Development:
PWK/Ph is descended by sibling mating from a single pair of mice of the subspecies Mus m.
musculus caught in 1974 in Lhotka, Czech Republic (Von Deimling et al., 1988). The strain
was imported into JAX in May 2000 by Dr. Jiri Forejt, Institute of Molecular Genetics, Prague.
Characteristics
and uses:
Technician
notes:
Research areas: reproductive biology,

genetics (evolution and systematics; gene
RBF/DnJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000726

POSF
n/a
Inbred strain, chromosomal aberration (Robertsonian, translocation)
Albino; related genotype: Tyrc/Tyrc Mc1rE-tob/Mc1rE-tob
H2 haplotype:
n/a
Genes/alleles:
Mc1rE-tob: melanocortin 1 receptor; tobacco darkening

common name: Etob
Rd3rd3: retinal degeneration 3
Rb(9.14)6Bnr, Robertsonian translocation, Chr 9 and 14; Chr 14; Universitat Bonn/Rein 6
Rb(1.3)1Bnr, Robertsonian translocation, Chr 1 and 3; Chr 1; Universitat Bonn/Rhein 1
Rb(8.12)5Bnr, Robertsonian translocation, Chr 8 and 12; Chr 12; Universitat Bonn/Rein 5
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
RBF strain originated with inbred sisterbrother from F1 hybrids between wild-derived Mus
musculus poschiavinus (domesticus) mice, captured in Valle de Poschiavo in S.E. Switzerland,
and Swiss NMRI/Han (by A. Gropp, Lubck, Germany.
Gropp to Roderick (1969), to Davisson (1981), to barrier facility at JAX (1984) via
hysterectomy derivation and fostering on C57BL/6J.
Homozygous for Robertsonian
translocations Rb(1.3)1Bnr, Rb(8.12)5Bnr,
and Rb(9.14)6Bnr.
Homozygous for the Mc1rE-tob locus as well
as albino.
Homozygous for retinal degeneration 3,
Rd3, (Chang et al., 1993).
Used to facilitate selection of

immunoglobulin-competent hybridomas
(Taggert, 1983).
sensorineural, endocrine deficiency,
genetics.
Active.
Weanlings are especially active.
Chubby; clean and white coats.

Poor breeders.
RF/J
Stock No. 000682
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Inbred strain
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Furth (1928) from unknown stock at Rockefeller Institute. Stock transferred to Oak Ridge.
From Upton at Oak Ridge to JAX (1954) at F14 (since stocks arrival at Oak Ridge).
Expresses about 40% frequency of
leukemia (Buchberg et al., 1986), and
approximately 50% reticulum cell
sarcomas.
Carries a Type 5 Chr Y of U.S. M.m.
domesticus origin (Tucker et al., 1992).
High incidence of spontaneous glomerular

hyalinisation and glomerulosclerosis
developing between 820 months.
neurobiology, sensorineural, immunology
and inflammation.
Poor breeders.
Average litter size.
Breeders get fat with age.
RIIIS/J
Common name:
Former name:
Strain type:
Appearance:
Stock No. 000683

RIII/2J
Inbred strain
H2 haplotype:
Genes/alleles:
n/a
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
R3;
Derived from RIII and SEC/1Re. RIII from Dobrovolskaia-Zavadskaia, Paris (1928). To Wood,
Curtis and Dunning, Columbia University. Wood to Eisen to JAX (1948) (RIII/J). Curtis and
Dunning to Andervont, NCI, to JAX (1953) at F23 (RIII/AnJ). SEC/1ReJ from SEC/1Gn
derived by Green from cross of NB x BALB/c (1941).
In 1967 RIIIS/J was derived from RIII/AnJ x SEC/1ReJF1 backcrossed to RIII/AnJ, then
crossed to RIII/J. Originally called RIII/2J, corrected to RIIIS/J in 1979 (Mobraaten). 1/8 of
RIIIS/J genes can be expected to be derived from SEC/1ReJ. RIIIS/J mice are a model for von
Willebrand disease (Sweeney et al., 1990); the disease is caused by a defect outside of von
Willebrand factor gene (Nichols et al., 1994).
Prolonged bleeding times with normal
platelet activity and low levels of factor
VIII:C and plasma von Willebrand factor
antigen, making it a good animal model for
human von Willebrand disease.
Low antibody response to several bacterial
polysaccharide antigens; reported to be
resistant to collagen induced arthritis.
Despite a B cell immunodeficiency,
develops severe experimental autoimmune
myasthenia gravis (EAMG) (Tzn et al.,
2004).
Carries no detectable endogenous ecotropic
MuLV DNA sequences (Jenkins et al.,
1982).
Largest known deletion of the T cell
receptor V beta genes13 of 21 known V
beta genes (Haqqi et al., 1989).
Carries a Type 1A Asian origin M.m.
musculus Chr Y (Tucker et al., 1992).
High incidence of mammary tumors and

ovarian tumors.
Carries Mtv8, and Mtv14, but high incidence
of tumors has not been reported. In fact,
some studies indicate a resistance to
chemically induced tumors. RIIIS/J mice
have been reported to develop far fewer lung
tumors than A/J or SWR/J mice subsequent
to urethane treatment. BALB/c x RIII F1
males are also highly resistant to
diethylstilbesterol-cholesterol induced
testicular tumors even though BALB/c is
highly susceptible.
Carries a spontaneous mutation, Hsf4ldis1,
that leads to a partial or complete disruption
of the lens and cataracts (Jablonski M, et al.,
2004).
Research applications: cancer, hematological,
sensorineural.
Poor breeders.
Litters often born dead or missing.
SEA/GnJ
Common name
Former name
Strain type
Appearance
Stock No. 000644

Generation: F194+22 (10-DEC-07)
sea Green
n/a
Inbred strain
Light brown agouti, short ears;

related genotype: A/A Tyrp1b/Tyrp1b Bmp5se Myo5ad/Bmp5se Myo5ad
Light brown agouti, normal ears;
related genotype: A/A Tyrp1b/Tyrp1b Bmp5se Myo5ad/+ Myo5ad
H2 haplotype
Genes/Alleles
Bmp5se: bone morphogenetic protein 5; short ear

common name: seGnJ
Myo5ad: myosin Va; dilute
common names: d, dv, maltese dilution
Strain origin
n/a
Source
n/a
Characteristics
and uses
Technician
Notes
Research applications: dermatology,

development biology, metabolism.
n/a
SJL/J
Stock No. 000686
Common name:
Former name:
Strain type:
Appearance:
Swiss Jim Lambert;

n/a
Inbred strain
Albino; related genotype: Oca2p Tyrc /Oca2p Tyrc
H2 haplotype:
s2 (Fischer Lindahl K ,1997; Shen et al., 1982)
Genes/alleles:
Dysf im: dysferlin; inflammatory myopathy

common names: SJL-Dysf
Strain origin:
Source:
Developed by James Lambert at JAX (1955) from Swiss Webster stock from 3 sources
imported between 1938 and 1943 (SJL = Swiss Jim Lambert). Pen bred until 1955, when
inbreeding started in Foundation Stocks.
Reintroduced to Foundation Stocks by hysterectomy derivation and fostering on C57BL/6J
(1974) at F69.
Characteristics
and uses:

allele Pde6brd1 (Caffee et al., 1993),
resulting in blindness after 2 weeks of age.
Develops multicellular reticulum cell
sarcomas resembling Hodgkins disease in
91% of virgin females at 13.3 months, 91%
of males at 12.5 months (Murphy, 1963,
1969).
Predominant tumor type is pre-B-cell
lymphoma (Mucenski et al., 1988).
Carries a Type 3 Chr Y of Western
European M.m. domesticus origin (Tucker
et al., 1992).
Develops a spontaneous myopathy
resulting from a splice-site mutation in the
Dysferlin gene. This Dysfim allele has been
shown to result in decreased levels of
dysferlin protein in SJL/J mice and makes
this strain a good model for limb girdle
muscular dystrophy 2B (Bittner et al.,
1999).
Susceptible to experimental autoimmune

encephalomyelitis (EAE), making mice
useful for multiple sclerosis research.
Increased rate of muscle regeneration after
injury when compared to BALB/c mice.
Fed an atherogenic diet, fails to develop
atherosclerotic aortic lesions.
Useful as a control strain for studying
immune defects in NOD/ShiLtJ mice
(001976), a model for type 1 diabetes
(IDDM). Both NOD and SJL/J are derived
from Swiss mice; SJL are immunocompetent
but have elevated levels of circulating T
cells.
cardiovascular, diabetes and obesity,
Technician
notes:
Dirty; smelly.
Males are very aggressive; get mad easy
and fast; fight a lot; may kill cage mates.
High level of infant mortality due to male
aggression. Do not handle litters until pups
are at least 6 days old.
Females are extremely aggressive, too.
Fair breeders.
Weanlings are small in size.

Weanlings and female breeders have bite
wounds. Pups easily frightened when in with
the breeders. Wean have missing fur from
bites, mostly on the head.
Provide nesting material. Remove male
breeder the week before pups are born.
SM/J
Stock No. 000687
Common name:
Former name:
Strain type:
Appearance:
small;
n/a
Inbred strain
White-bellied agouti: related genotype: Aw/a
Black: related genotype, a/a
H2 haplotype:
Genes/Alleles:
Neu1a: neuraminidase 1; a variant

common name: Neu-1s
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
MacArthur (1939) crossed 7 stocks (including DBA) selected for small body size in a
genetically heterogeneous population. Transferred to Runner at JAX (1948).
Runner to JAX (1954) at F14.
Low tumor frequency.
Both sexes live for 570600 days.
Hyperresponsiveness to B cell mitogens
(Clark et al., 1981; Engel et al., 1981).
Point mutation in Neu1 is responsible for
partial deficiency of lysosomal
neuraminadase; may explain altered
immune response (Rottier et al., 1998).
Small in size at birth through weaning, but
attain a normal body weight as they age.
Carries a number of rare polymorphic

alleles; often matched to LG/J (000675),
A/J (000646) or NZB/BlNJ (000684) for
quantitative trait locus (QTL) analysis.
Susceptible to diet-induced atherosclerosis
(Nishina et al., 1993) and cholelithiasis
(gallstones); carries the atherosclerosis 8,
Ath8, gene (Paigen, 1995).
Research applications: general purpose as
well as cardiovascular, developmental
biology, diabetes and obesity, immunology
and inflammation.
Calm. Easy to work with.

Small body size.
Delicate appearing.
Good parents; produce consistently.
SPRET/EiJ
Stock No. 001146
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Wild-derived inbred strain (species: M. spretus; Puerto Real, Cadiz Province, Spain)
H2 haplotype:
n/a
Genes/alleles:
n/a
Strain origin:
n/a
Source:
n/a
Characteristics
and uses:
Technician
notes:
Resistant to high doses of tumor necrosis

factor alpha (TNFa) (Staelens et al., 2002).
Mice from a C57BL/6J x SPRET/Ei F1
cross were protected from TNFa-induced
arthritis and partially protected against
induced allergic asthma (Staelens et al.,
2004).
Often used in crosses with common inbred

strains to create highly polymorphic panels
for genetic mapping.
inflammation, reproductive biology,
genetics (evolution and systematics, gene
ST/bJ
Stock No. 000688
Common name:
n/a
Former name:
n/a
Strain type:
Appearance:
Generation: F164p
Inbred strain
H2 haplotype:
Genes/alleles:

Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
From a closed colony of Danish white mice from a Mrs. Street (1932) to Engelbreth-Holm,
Copenhagen (1940), to Heston, NCI at F23 (1947).
Homozygous for the retinal
degeneration allele Pde6brd1.
12% leukemia, including some plasma
cell leukemias; about 3% other tumors,
principally pulmonary adenomas and
mammary carcinomas; some
polydypsia and polyuria; high
resistance to chronic whole-body Xirradiation.
Resistant to the induction of
experimental allergic encephalomyelitis
(Levine and Sowinski, 1973).
Of 19 inbred strains assessed for nicotineinduced seizure sensitivity, ST/bJ mice were
the most sensitive to i.v. and i.p. injection of
nicotine (Miner and Collins, 1989).
Research applications: sensorineural,
Poor breeders.
Small litter size (23 pups).
Breeders get fat with age.
SWR/J
Common name:
Former name:
Strain type:
Appearance:
H2 haplotype:
Stock No. 000689

swiss; SW
n/a
Inbred strain
q2 (Fischer Lindahl K, 1997; Shen et al., 1982)
Genes/alleles:

Strain origin:
Swiss mice from A de Coulon of Lausanne, inbred by Clara Lynch, Rockefeller Institute; to R
Parker, University of Toronto.
Parker to JAX (1947) at F28+.
Source:
Characteristics
and uses:

allele Pde6brd1.
Aging mice exhibit high incidence of lung
and mammary gland tumors; also develop
extreme polydipsia and polyuria
(nephrogenic diabetes insipidus) with
increasing age.
Females develop polydipsia at 610
months (Kutscher and Miller 1974).
Highly susceptible to experimental allergic
encephalomyelitis (EAE).
Germline deletion of about 50% of T-cell
receptor V beta-chain gene segments and a
T-cell receptor V alpha polymorphism are
responsible for resistance to collagen type
II-induced arthritis.
Intermediate susceptibility to developing
atherosclerotic aortic lesions on
atherogenic diet.
Recommended for generation and
propagation of transgenic mice because
they are high responders to exogenous
hormones, have large and prominent
pronuclei with good resistance to lysis
following microinjection, and are
genetically well defined.
Appear to be the only inbred strain
carrying the allele Soaa (Taster),
characterized by avoidance of sucrose
octaacetate solutions at low concentrations
(< 10-3M).
Highest blood pressure of 19 JAX mice

tested (Schlager and Weibust, 1967).
Spontaneous ovarian granulose cell tumors
(Beamer et al., 1985; 1993).
About half have primary lung tumors
(Mirvish and Kaufman, 1970).
Arteriosclerosis common (Russell and
Meier, 1966).
Low frequency of mammary tumors in
breeders and virgins.
High mortality in males exposed to ethylene
oxide oxidation products.
May be used for comparison to the
autoimmune diabetic NOD/ShiLtJ mice
(001976), especially for experiments
examining the aberrant immune functions of
NOD/ShiLtJ mice. Both NOD and SWR/J
mice are derived from Swiss mice. SWR/J
are in some cases more suitable than random
bred Swiss ICR mice because of their
genetic uniformity. Unlike NOD/ShiLtJ
mice they are not immunocompromised, and
they are genetically very different from
NOD.
Research applications: general purpose as
well as cancer, cardiovascular,
developmental biology, diabetes and
obesity, immunology and inflammation,
sensorineural.
Technician
notes:
Wide variation in reports from technicians

on behavior and breeding.
Cages appear dirty.
Jumpy. Quiet mice; easy to handle.
Aggressive toward people. Good idea to

have same tech changing this strain.
Breeding performance may be variable.
Poor to good breeders; good parents.
WSB/EiJ
Common name:
Former name:
Strain type:
Appearance:
Stock No. 001145

n/a
Wild-derived inbred strain
Agouti with head blaze, grayish coat; related genotype: A/A
Note: This strain is homozygous for a recessive pigment mutation that contributes a signature
head blaze (very high penetrance) and variable belly spotting. In addition, slight coat
dilution gives the illusion of the mouse being Aw (white bellied agouti). The pigment
mutation is being tested for allellism with recessive spotting, rs.
H2 haplotype:
n/a
Genes/alleles:
n/a
Strain origin:
Source:
Characteristics
and uses:
Technician
notes:
Generation: ?+F1 (05-DEC-07)
Watkin Star line B
Geographic origin: Centreville, Queen Anne City, Eastern Shore, Maryland

n/a
Research areas: dermatology, genetics
(evolution and systematics, genetics
[gene mapping])
These mice are very difficult to
handle.
4.B. Reproductive performance

Table 4.1 contains breeding data collected in the production colonies (pedigreed expansion
stocks) from which JAX Mice are shipped. Keep in mind that all mouse colonies, even within
a facility, are different and that breeding performance can vary among them. Thus, the values in
Table 4.1 should be used as guidelines to indicate the breeding potential of the strain and to help
identify potential breeding problems. Values do not represent absolute performance standards.
Table 4.1. Reproductive performance for selected strains of JAX Mice.
Strain of JAX Mice

(stock number)
129P3/J
Number Number
Number of pups
of
of
weaned litters
breedper
per
ing
female female*
pairs
(mean) (mean)
Maternal age
(days)
At
pairing
(range)
Litter size
(pups)
Birth
Percent Percent
of first
At
At
litter
birth wean wean: females
(mean) (mean) (mean) born weaned
Maternal age
(months)
when last
litter weaned
(mean, range)
Dates of
data generation
(mo/yr)
(000690)
48
13.4
3.2
18-30
80
4.6
4.2
86
50
6.1
(2.9-10.5)
12/065/08
129S1/SvImJ
(002448)
47
22.5
4.6
17-30
67
5.3
4.9
89
51
7.4
(3.8-11.3)
12/052/08
50
20.7
4.5
19-50
77
5.1
4.6
89
49
7.4
(3.2-9.8)
1/062/08
50
21.4
4.3
17-35
74
5.3
5.0
88
51
7.3
(5.2-9.2)
12/051/07
49
18.6
3.4
20-33
65
5.5
5.4
96
47
5.7
(3.6-7.6)
12/0511/07
19
21.6
3.4
29-62
70
6.6
6.3
92
50
6.3
(2.9-8.9)
6/076/08
50
17.3
3.9
25-31
74
5.2
4.5
83
48
7.2
(5.0-9.5)
12/058/07
50
19.8
3.8
18-62
84
5.4
5.2
96
57
7.8
(5.4-10.3)
12/059/07
50
21.1
4.1
18-26
92
5.5
5.4
98
50
7.7
(5.9-9.1)
3/067/07
50
17.3
3.5
18-41
73
5.2
5.0
92
47
5.9
(3.7-7.2)
12/056/07
C3H/HeOuJ
(000635)
50
20.1
4.3
19-25
72
5.0
4.7
93
46
6.1
(2.6-7.7)
12/057/07
C3HeB/FeJ
(000658)
34
34.1
5.3
17-26
65
6.6
6.4
96
49
7.2
(4.6-9.3)
12/055/08
C57BL/10J
(000665)
50
18.3
3.9
24-33
78
5.1
4.7
91
54
7.2
(4.6-9.8)
1//063/08
50
29.5
5.4
24-31
67
5.9
5.5
92
51
8.3
(5.7-11.2)
12/057/07
45
14.6
3.1
21-35
83
5.3
4.7
86
47
7.2
(3.4-9.7)
12/056/08
42
16.5
3.5
25-31
88
4.9
4.7
90
44
7.7
(3.2-11.4)
12/053/08
49
13.8
3.7
23-38
109
4.4
3.7
81
51
7.9
(4.8-9.9)
5/074/08
49
22.7
4.2
17-33
71
5.7
5.5
96
49
6.6
(3.9-8.2)
12/051/08
129X1/SvJ
(000691)
A/J
(000646)
AKR/J
(000648)
B6(Cg)-Tyrc-2J/J
(000058)
B6.129P2Apoetm1Unc/J
(002052)
BALB/cByJ
(001026)
BALB/cJ
(000651)
C3H/HeJ
(000659)
C57BL/6J
(000664)
C57BLKS/J
(000662)
C57L/J
(000668)
CAST/EiJ
(000928)
CBA/CaJ
(000654)
Table continued on next page.
Table 4.1. Reproductive performance for selected strains of JAX Mice. (continued)
Maternal age
Litter size
Number Number
(days)
(pups)
Number of pups
of
Maternal age
(months)
when last
litter weaned
(mean, range)
Dates of
data generation
(mo/yr)
51
7.5
(6.2-9.0)
12/057/07
89
44
7.6
(5.3-9.4)
1/0612/07
4.4
84
50
7.6
(4.4-9.3)
1/061/08
4.8
4.6
92
50
6.9
(5.9-9.6)
12/058/07
68
7.4
7.3
98
51
7.1
(5.6-11.5)
1/069/07
25-31
72
5.5
4.7
83
52
6.0
(2.1-8.1)
12/0510/06
3.9
18-29
85
4.0
3.3
77
55
7.2
(3.9-8.9)
12/054/08
18.0
3.4
19-27
72
5.6
5.4
95
51
6.4
(3.7-8.1)
12/052/08
50
23.7
4.1
18-32
81
6.1
5.8
94
51
6.1
(4.0-8.4)
1/068/07
NOD.Cg-Prkdcscid
Il2rgtm1Wjl/SzJ
(005557)
(pair-mated)
25
25.2
4.0
19-65
69
6.7
6.4
96
48
(trio-mated)
10 trios
20.4
3.2
21-65
77
6.5
6.6
98
53
NOD/ShiLtJ
(001976)
50
27.0
3.5
19-35
83
8.4
7.7
92
51
50
7.7
2.6
25-30
89
4.3
3.0
58
50
5.7
(3.6-8.5)
12/0511/07
50
15.8
3.9
21-31
76
4.8
4.0
81
45
6.4
(3.8-9.1)
12/0511/07
49
19.1
4.5
19-32
91
4.6
4.3
89
47
7.2
(3.9-10.7)
1/063/08
50
32.3
5.2
19-27
68
6.6
6.3
92
51
7.7
(4.5-9.7)
12/058/07
50
11.8
2.9
21-33
80
4.7
4.1
79
49
6.2
(3.6-9.5)
12/053/08
Strain of JAX Mice

(stock number)
CBA/J
(000656)
DBA/1J
(000670)
DBA/1LacJ
(001140)
DBA/2J
(000671)
FVB/NJ
(001800)
KK/HlJ
(002106)
LP/J
(000676)
MRL/MpJ
(000486)
NOD.CB17Prkdcscid/J
(001303)
NZB/BlNJ
(000684)
NZW/LacJ
(001058)
PL/J
(000680)
SJL/J
(000686)
SM/J
(000687)
Birth
of first
At
At
Percent Percent
litter
birth wean wean: females
(mean) (mean) (mean) born weaned
of
breeding
pairs
weaned
per
female
(mean)
litters
per
female*
(mean)
At
pairing
(range)
49
21.7
5.4
18-26
79
4.3
4.0
90
50
20.3
5.2
19-30
71
4.1
3.9
49
22.8
5.2
19-28
68
4.9
50
24.8
5.3
18-47
73
50
35.5
4.9
19-29
25
14.9
3.2
50
12.7
50
6.1
(3.0-10.3)
6.7
(5.2-10.5)
6.0
(4.2-8.8)
6.2
50
21.8
3.3
18-27
77
6.8
6.6
98
49
(000689)
(3.1-10.1)
*The number of litters produced during the optimal breeding period (see below), not the total number of litters a breeding
pair can produce. (Includes litters for which no pups were weaned.)
Includes litters from which no pups survived (weaned litter size = 0) and litters with more pups weaned than born, which
occurred occasionally due to undercounting litter size at birth.
Excludes litters with more pups weaned than born to provide a more accurate estimate of neonatal mortality.
A breeding pair was retired when the caretaker judged that the period of optimal breeding performance had ended for that
breeding pair, based on experience and general guidelines for the strain.
SWR/J
10/0610/07
1/068/07
2/065/08
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149
Chapter 5: Choosing a Mouse Strain for

ResearchConsiderations and Resources
Joanne M. Currer, Barbara Witham, Carol Linder, Kevin Flurkey
The choice of mouse strain and controls influences both the potential and limitations of a
research program. This choice is complicated by the massive amounts of information and the
quantity of mouse strains available.
Our objective for this chapter is to help researchers with the selection process by providing 1)
lists of resources that can supply the detail necessary to help refine and finalize a strain choice
for specific research areas, and 2) some universal guidelines and words to the wise about
choosing a strain and controls.
5.A. General sources of information about mouse strains........................................ 150
5.A.1. Resources at The Jackson Laboratory website: www.jax.org ............ 150
5.A.2. An example of a strain characteristic comparison from the Mouse
Phenome Database (MPD): www.jax.org/phenome............................ 151
5.A.3. Other websites........................................................................................ 152
5.A.4. Books ...................................................................................................... 152
5.B. Seven considerations for selecting a mouse strain............................................ 153
5.C. Guidelines for selecting and planning for control mice ................................... 156
5.D. Guidelines for selecting a supplier of mice ....................................................... 158
5.E. Guidelines for alternatives to maintaining live mice ........................................ 158
5.F. Sources of information related to selected research areas................................ 159
5.G. References ........................................................................................................... 164
Acknowledgments: We would like to thank the Technical Information Services staff (Karen
Fancher, David Higgins, Peter Kelmenson, Tanya Lansley, Janice Pendola, Yan Yang, and Jim
Yeadon) as well as Bo Chang, Shaoguang Li, Leonard Shultz, and especially Ed Leiter for their
valuable input to this chapter.
5.A. General sources of information about mouse strains

Following is a list of resourcesat The Jackson Laboratory and elsewherethat are useful for a
strain search. We also provide an example of how one resource, the Mouse Phenome Database
(MPD) can help refine a search.
For the most widely-used strains of JAX Mice, detailed tabular information can be found
within this book in Chapter 4, Characteristics of Popular Strains of JAX Mice, Including
Reproductive Performance, and in Appendix D, Commonly-Used Inbred Strains and
Substrains of JAX MiceGenes and Research Applications.
5.A.1. Resources at The Jackson Laboratory website: www.jax.org

Besides providing details on more than 4,000 strains of JAX Mice, The Jackson Laboratory
website also provides access to several databases and other information related to research that
can help refine a choice of mouse strain. Table 5.1 will help you get started accessing our online
information. Because our site is updated on a regular basis, new resources will become
available; therefore, be sure to check www.jax.org frequently for new information.
Table 5.1. The Jackson Laboratory website (www.jax.org): information about mouse strains and research.
Resource
Web address
JAX Mice strain database:

Phenotypic and genotypic characteristics and husbandry
information for each strain of JAX Mice. Search on strain
name, stock number, gene, allele, research area, disease
term, etc.
JAX Mice strain lists, organized as follows:

Most popular
Strain type (categories such as inbred, congenic, etc.)
New JAX Mice strains
Strains under development
JAX Mice by research area (including mice used as
research tools, for example, with Cre-lox Systems and
fluorescent proteins)
www.jax.org/jaxmice/findmice/browse
Mouse Genome Informatics (MGI) website:

Data on the genetics, genomics, mutant phenotypes, and
biology of the laboratory mouse, including
Links to databases such as
Mouse Phenome Database (MPD)
Mouse Tumor Biology (MTB) database
International Mouse Strain Resource (IMSR) database
www.informatics.jax.org
Online books
Biology of the Laboratory Mouse. 1996. Green E.
Mouse Genetics. 1995. Silver, LM.
The Anatomy of the Laboratory Mouse. 1965. Cook MJ.
The Coat Colors of Mice. 1979. Silvers WK.
Origins of Inbred Mice. 1978. Morse, HC III.
www.jax.org/phenome
http://tumor.informatics.jax.org/mtbwi/index.do
www.informatics.jax.org/imsr
(More Resources menu option)
Assistance with locating or creating a novel mouse strain
www.jax.org/jaxservices/straincreation
Information about transgenic and targeted mutant mice
www.jax.org/imr
Table continued on next page
Chapter 5: Choosing a Mouse Strain for Research 151
Table 5.1. The Jackson Laboratory website (www.jax.org): information about mouse strains and research.
(continued)
Resource
Web address
Information about mice carrying spontaneous mutations
http://mousemutant.jax.org/index
Information about recombinant inbred (RI) and chromosome

substitution (CS) strains
www.jax.org/smsr
Research areas and faculty website:

Links to information about research being conducted at The
Jackson Laboratory
www.jax.org/research/faculty
Courses and education website
www.jax.org/courseseducation
Technical support and literature website:

Requests for JAX Mice Literature (including the JAX
Mice Catalog, resource manuals, mouse model lists, price
list, JAX NOTES)
Technical support on any research issues involving strains
of JAX Mice and related services
www.jax.org/jaxmice/support
Festings characteristics of inbred mice and rats
www.informatics.jax.org/external/festing/
search_form.cgi
5.A.2. An example of a strain characteristic comparison from the

Mouse Phenome Database (MPD): www.jax.org/phenome
The Mouse Phenome Database (MPD), which is maintained at The Jackson Laboratory, is an
international, collaborative initiative to establish a comprehensive collection of phenotypic data
for mouse strain comparisons. The MPD is a very powerful way to compare well-characterized
strains of laboratory mice. (For an overview of the MPD, see 6.C.2, Other databases.)
For our example, we searched for mouse models with which to study heart disease risk factors.
A search of the MPD for triglyceride data displayed a strain comparison of circulating
triglycerides (Svenson et al., 2007) (Figure 5.1). This strain comparison, comprising 42 strains,
allowed us to very quickly narrow our search to the strain subset with high values. Using
additional MPD functionality, we could have linked directly to additional information about the
strains. For strains of JAX Mice, we could have linked directly to the strain datasheet.
Figure 5.1. Example of Mouse Phenome Database (MPD) strain comparison for triglycerides.
5.A.3. Other websites

Table 5.2 provides a list of other websites that provide information related to mouse strains.
This list represents sites that our researchers and technical support personnel have found
particularly valuable.
Table 5.2. Other public websites: information about mouse strains.
Organization
Web address
National Institutes of Health (NIH)
www.nih.gov
Trans-NIH Mouse Initiatives

European mutant mouse pathology database
www.nih.gov/science/models/mouse/
www.pathbase.net
Organizations related to specific research areas, for example

National Cancer Institute
American Society of Hematology
www.cancer.gov
www.hematology.org
Literature search engines, for example, the PubMed service

provided by the National Library of Medicine and the
National Institutes of Health
Institute for Laboratory Animal Research (ILAR), U.S.
National Academy of Sciences
Deltagen Mouse Histology Atlas
www.pubmed.gov
Ensemble Genome Browser

University of California, Davis (UCDavis) Mouse Biology
Program
www.ensembl.org
http://mouse.ucdavis.edu
http://dels.nas.edu/ilar
www.deltagen.com/target/histologyatlas/
HistologyAtlas.html
5.A.4. Books
Biology of the Laboratory Mouse, Second Edition. 1966. Green E, ed.
Guide for the Care and Use of Laboratory Animals (often referred to simply as The Guide).
1996. National Research Council.
Inbred Strains in Biomedical Research. 1979. Festing MFW.
The Laboratory Mouse. 2001. Suckow, et al.
The Laboratory Mouse. (Handbook of Experimental Animals). 2004. Hedrich H, ed.
The Mouse in Biomedical Research, Second Edition. 2007. Fox JG, et al., eds.
NOD Mice and Related Strains: Research Applications in Diabetes, AIDS, Cancer, and Other
Diseases. In Medical Intelligence Unit. 1998. Leiter E, Atkinson M (eds.). RG Landes Co.
Austin TX.
5.B. Seven considerations for selecting a mouse strain

1. Confirm that the strain is appropriate for the study.
Strain characteristics that can affect a study include variations in anatomy, development,
behavior, survivability, reproduction, and onset and variability of disease. For all strains of
JAX Mice, comprehensive information is conveniently provided in the strain datasheet (see
sidebar). For the most popular JAX Mice, an overview is provided in Chapter 4,
Characteristics of Popular Strains of JAX Mice, Including Reproductive Performance; a
brief summary of genes and applications in a tabular format is provided in Appendix D,
Commonly-Used Inbred Strains and Substrains of JAX MiceGenes and Research
Applications. Following are a few examples of the types
of things to watch for:
The JAX Mice datasheet: the most up-do-date,
Mice from strains homozygous for the Pde6brd1 allele

detailed information for any strain of JAX Mice
(for example, C3H/HeJ [000659]) are blind by 45

Each strain of JAX Mice has an associated datasheet
that is updated on a regular basis. Information includes
weeks of age. These strains would be inappropriate for
Full description of the strain: full name and
behavioral studies that rely on vision.
nomenclature, stock number, common and former
A/J (000646) mice are homozygous for the progressive
names, genetic and allelic details, phenotypes, coat
prmd
color, H2 haplotype, mating scheme, current
muscle dystrophy allele of the dysferlin gene (Dysf
).
generation number
Thus, while they may be good models for the influence
Strain origin and history
of dysferlin on muscle maintenance, they could be poor
Related strains and control information
models for the study of general influences (such as
Husbandry information, including diet
exercise) on muscle development.
Links to health reports
AKR/J (000648) mice express the ecotropic retrovirus
Research applications, including links to references
AKV from birth in all tissues, leading to a high incidence
Price and availability
of thymic lymphoma beginning around 46 months of
Links to relevant databases, customer service, tech
age. Thus, while they might be appropriate for studies of

support, JAX Services, and other web-based
information.
normal function before the lymphoma develops, they
Access strain datasheets at www.jax.org/jaxmice/query.
would be inappropriate for studies of normal function in
mature adults.
2. Understand that the strain background may affect the phenotypic expression
of a mutation.
A phenotype in a mutant strain is the result of both the genetic mutation, spontaneous or
induced, and the strain background on which it is maintained. Even an allele that is named for
the phenotype it produces in one strain may not produce that phenotype on other genetic
backgrounds. Table 5.3 shows the effects of strain background on two diabetogenic mutations,
Leprdb and Lepob. The appropriate choice of model depends on which phenotype is of interest.
Table 5.3. Effects of strain background on the Lep
The combination of
this allele
Obese mutation
(Lepob)
Diabetes mutation
(Leprdb)
ob
db
and Lepr
mutations.
on this
background
creates
this strain
with this phenotype.
C57BL/6J (B6)
(000664)
B6.V- Lepob/J
(000632)
Transient hyperglycemia
with obesity
C57BLKS/J (BKS)
(000662)
BKS.V- Lepob/J
(000696)
Overt diabetes
with obesity
C57BL/6J (B6)
(000664)
B6.BKS(D)-Leprdb/J
(000697)
Transient hyperglycemia
with obesity
C57BLKS/J (BKS)
(000662)
BKS.Cg-m +/+ Leprdb/J

(000642)
Overt diabetes
with obesity
When transferring a mutation onto another background strain to create a congenic, we

recommend that the phenotype be evaluated at backcross generation N5 or N6. At this point
more than 95% of the genome typically is of the host genotype, and it is by this stage that
background effects will become noticeable. (See 3.C.2.a.1, Congenic strains.)
3. Do not assume that substrains have identical phenotypes because they have
the same strain of origin or a similar name.
Most substrains have been separated by at least 20 generationsoften many more, over a span
of many yearsand they are often further apart genetically than one might think. (See 3.B.1.a.2,
Substrains, and Appendix C, Origins and Relationships among Common Strains and
Substrains of Laboratory Mice.) Examples of substrain differences include the following:
C57BL/6J (000664) and C57BL/10J (000665). These substrains have been separated since the
mid 1930s, and they differ at approximately 140 loci (calculation based on formulas from
Bailey [1978]), including a minor histocompatibility locus (H9), an immunoglobulin heavy
chain locus (Igh2), and a locus that regulates heme metabolism (Lv).
A muscular dystrophy mutation (Dysf prmd) arose in A/J (000646) mice as a result of a
retrotransposon insertion in the dysferlin (Dysf) gene. Because evidence of the mutation was
not present in the AXB and BXA recombinant inbred (RI) lines, which were constructed in
1975, this mutation occurred and became fixed in The Jackson Laboratory A/J foundation
stock sometime after 1975. The mutation does not exist in the A/HeJ (000645) substrain,
which was separated from Strongs progenitor A strain in 1938. (Ho et al., 2004.)
4. Consider using strains that are
the founders of recombinant strain
panels.
Strains that have been used as founders for
recombinant strain panels offer a distinct
advantage. As an example, assume that you
investigate a phenotype in a founder strain,
find a difference from published values for
other strains (including the other founder
strain for a panel), and then determine that
the difference is reproducible in your own
lab. By evaluating that phenotype in the
strains of the recombinant panel, you can
readily study the genetic regulation of the
phenotype and its relationship to other
phenotypes without genotyping or further
phenotyping. Thus, studying just one
founder strain opens the door to the
powerful mapping opportunities provided
by the entire recombinant strain panel. An
additional benefit of studying a founder
strain is that the availability of information
on other characteristics for strains of the
panel provides the opportunity to look for
mechanistic relationships with the
phenotype you originally evaluated.
Strain panels as research models: A strategy to

combine genetic homogeneity with diversity
No single inbred strain represents laboratory mice any
more than a single person represents Homo sapiens.
Thus, to incorporate diversity into a study, one
research approach is to use a genetically mixed
population of mice. But individual genotypes in a
population of this type cannot be reliably reproduced.
An alternate approach is to use a panel of inbred
strains of mice. Strain panels combine genetic
diversity with all the advantages of inbred strains
including reproducibility.
An example: In The Jackson Aging Center, a 32strain panel of inbred mice was screened to study
genetic influences on patterns of aging and agerelated disease. Because these strains have already
been densely mapped (SNP markers), genetic
analysis of aging phenotypes can proceed without
genotyping any mice. For details, refer to our aging
center website at www.agingmice.org.
Another application of strain panels is for drug
studies. By treating a panel of well-characterized
inbred strains or a panel of their F1 hybrids,
pharmacology researchers may observe a range of
responses. This strategy avoids the generalization of
results based on an idiosyncratic response of a single
strain or F1 hybrid. In addition, the use of an inbred
strain panel can establish a foundation for studies on
the genetic basis of the response differences. The
common use of standard outbred mice for this type of
research is a poor substitute because outbred stocks
typically are incompletely inbred and genetically
uncharacterized.
One caveat in comparing a strain panel

founder to the derived strains of the panel
is that the founder strain genotype is not
completely reproduced in the strains of the
panel; genetic drift can influence the
genotypes in both. The example given above (Consideration 3) for substrain divergence also
illustrates this point. The dysferlin mutation in A/J (000646) is not present in any of the strains
in the AXB or BXA RI panels derived in the 1970s (Ho et al., 2004).
5. Ensure that your facilities can accommodate all the requirements for the strain
and the study.
Some disease models require special husbandry conditions and animal care such as isolator
caging, a specific pathogen free (SPF) environment, a warmer temperature, or special feeding
strategies. For example, immunodeficient mice need an SPF environment. Also, the health of
hypothyroid mice, such as the Snell dwarf strain (DW/J Mlphln Pou1f1dw/J [000643]), may be
compromised even at temperatures just below 22 C (72 F). (K. Flurkey, personal observation).
Some mice may require single housing. For example, SJL/J (00686) and BALB/cJ (000651)
males can usually be weaned in groups. Over time, however, they often become so aggressive
that they may kill cage mates.
Phenotypes may vary depending on the microbial environment of the mouse room. Ensure that
your colony conditions match the needs of your model and the phenotype you intend to study.
For example, almost all inbred strains have greater lifespans in SPF colonies than in
conventional colonies where pathogens are not controlled (Russell, 1966), indicating that old
mice are particularly sensitive to subclinical infections that are common in conventional
colonies. Therefore, SPF conditions are necessary to study normal aging without complication
from age-related sensitivity to infectious disease. For other strain-dependent phenotypes,
however, a very clean mouse room might result in the loss of a phenotype. As an example,
gallstone development in mice requires non-pathogenic bacteria Helicobacter in the
environment (Maurer et al., 2006). This issue has become increasingly relevant since the late
1990s, when numerous colony managers began testing for and eliminating Helicobacter.
6. For transplantation studies, be sure that histocompatibility and tissue
rejection do not interfere with the study requirements.
One major advantage of inbred mice is that, within individuals of a strain, tissues can be
transplanted from experimentally treated mice to normal hosts or vice versa to compare the
functions of that tissue in different internal environments. For example, by transplanting liver
from an old mouse to a young mouse, one can study whether age-related impairments in liver
are due to intrinsic aging or general aging of the individual. Recognize, however, that although
inbred strains are considered genetically homogeneous, one cannot be assured that they are
homozygous for all of the 100+ histocompatibility loci until they have been inbred for more
than 60 generations.
Non-inbred stocks in particular are inappropriate for use in tissue transplantation studies. Even
if only minor histocompatibility differences exist, the resulting gradual tissue rejection can
complicate interpretation of results of a transplantation study.
Also, keep in mind that, because of differences in innate immunity, F1 hybrids are not
completely histocompatible with their parental strains. This phenomenon, called hybrid
resistance, results from innate immunity rather than acquired immunity. This issue is especially
relevant for hematopoietic cells. Lethal irradiation (with hematopoietic reconstitution) and antiNK cell treatment may alleviate this problem. (For details, see 3.B.3, F1 and F2 hybrids.) For
tables listing histocompatibility genotypes, see Appendix F, Histocompatibility Haplotypes and
Loci.
It is not just the histocompatibility loci that affect tissue rejection. Antigenic differences are
important as well. For example, injecting syngeneic B lymphocytes into B6.129S2-Igh-6tm1Cgn/J
(002288) recipients leads to rejection because the mice have never seen mature B lymphocytes
and therefore are not tolerant to B cells.
7. Solicit input from animal caretakers and technicians about their experience
with specific strains.
When considering a new mouse strain, check to see if the caretakers and technicians in your
facility have had experience with it. Often, they possess a wealth of information about specific
models that is not reflected in the technical literature. This knowledge is particularly important
regarding characteristics that can vary among different animal facilities, such as breeding
performance, behavior (especially aggression), and health. Involving your caretakers and
technicians in the discussion of a mouse strain has an additional advantage: If they are aware of
the strain characteristics and phenotypes of interest in your mice, they are much more likely to
be attuned to anything unexpected that might appear when your program is in process.
5.C. Guidelines for selecting and planning for control mice

Sometimes, choosing the most appropriate control is a challenging component of a research
program. Several considerations and examples follow. For details on choosing controls for
specific of JAX Mice, refer to the strain datasheet, available at www.jax.org/jaxmice/query.
5.C.1. Selecting control mice

5.C.1.a. Controls for inbred strains
For an inbred strain model of a specific condition or disease (e.g., NOD/ShiLtJ [001976] for
diabetes research), if no condition-free or disease-free control with the same genetic
background exists, an appropriate control is a closely related strain or substrain that does not
exhibit the phenotype of interest. For example, for NOD/ShiLtJ (001976) mice, which get
type 1 diabetes, NOR/LtJ (002050) mice can be used as a control strain because they are
MHC identical and 88% of their genome is NOD. NOR/LtJ mice exhibit no insulitis and no
diabetes.
Another appropriate control for studies of basal measurements could be mice that have been
treated experimentally or genetically to prevent disease expression. For example,
NOD.CB17-Prkdcscid/J (001303) mice, which have no functional T cells and are both
insulitis- and diabetes-free throughout life, serve as a diabetes-free control for comparison to
NOD/ShiLtJ mice. NOD.CB17-Prkdcscid/J can be used as treatment controls to identify
effects of a treatment for diabetes that are independent of the effects on the disease. And, they
are ideal as donors of NOD islets that are free of diabetogenic T cells.
For an inbred strain being used to test the effect of an experimental condition, if possible,
always use littermate controls. The use of untreated littermate controls assures that all mice
have been subjected to the same maternal and environmental conditions except for those
produced by the experimental treatment. To avoid the confusion of litter effects with
treatment effects, do not assign all mice from one litter to the same treatment or control
group. Rather, randomly assign littermates to treatment and control groups.
5.C.1.b. Controls for mutant strains on an inbred background, including

segregating inbred strains, congenic and coisogenic strains
When possible, the best controls are gender-matched, unaffected littermates, which are
produced when the mutation is maintained heterozygously. If the mutation is dominant, one
parent must be a homozygous wild-type. If the mutation is recessive, one parent must be a
homozygous mutant. (With a recessive mutation, the symbol +/? identifies these controls,
indicating that genotyping has not been performed and that they may be either +/+ or
+/mutant.)
When littermates cannot be used as controlsfor example, when the mutation is maintained
homozygouslythe background inbred strain can be used as controls. Note that the degree of
similarity between the background inbred strain and the mutant strain depends on two
variables: 1) the amount of residual heterozygosity in the background strain when the
separation of the mutant strain occurred, and 2) the number of generations that separates the
strains. (For a detailed discussion on substrain divergence, refer to 3.B.1.a.2, Substrains.)
If the genetic difference between the background strain and the mutant strain is a concern, an
alternate strategy is to outcross the mutant with an inbred mouse of the desired genetic
background and intercross the F1 hybrids to produce F2 hybrids. In this F2 generation, the
phenotype will segregate to produce mutants and controls.
If the exact background strain is not available, select the most closely related substrain. But
keep in mind that, in some cases, substrains with dissimilar names are genetically closer than
those with more similar names. For example, for CBA/CaJ (000654) mice, CBA/CaHT(14:15)6Ca/J (000655) mice are more appropriate controls than CBA/J (000656) mice. (For
charts that show the relationship between many common substrains, see Appendix C,
Origins and Relationships among Common Strains and Substrains of Laboratory Mice.)
5.C.1.c. Controls for mutant strains on a mixed background

If a mutation is maintained heterozygously on a mixed background, unaffected littermates will
be available and can be used as controls. If the mutation is maintained homozygously on a
mixed background, you may need a breeding colony of approximate control mice. One example
is targeted gene knockouts that have been made in embryonic stem (ES) lines derived from a
129 strain. The mutated ES cells are usually injected into C57BL/6J (B6; 000664) blastocysts,
which results in chimeras that contain cells of B6 and 129 origin. Often, these chimeras are then
crossed with a B6 mouse. If the targeted mutation has gone germline, the progeny are hybrids of
B6 and 129 strains. These hybrids are then intercrossed to maintain the mutation. Approximate
physiological controls can be provided from a B6129F2 colony. Because of the allelic
segregation and assortment from F1 hybrid parents, the genetic background of the F2 generation
will vary in composition similarly to that of the targeted mutant. (The Jackson Laboratory offers
two F2 hybridsB6129PF2/J [100903] and B6129SF2/J [101045]). B6129F1 hybrids are a less
appropriate control because all mice of the F1 generation are genotypically identical.
5.C.2. Purchasing and housing control mice

To minimize variation due to substrain differences, obtain controls and research mice from the
same supplier. To minimize variation due to environment or health status, house treated mice
and controls in conditions as similar as possible. If treated and control mice can be
unequivocally distinguished, house them in the same cages. Otherwise, make every effort to
house them as close to each other as possible.
5.D. Guidelines for selecting a supplier of mice

Expect the following from a supplier of laboratory mice:
Animals of high genetic quality that are free from common infectious diseases and pathogens.
Quality control procedures to ensure genetic consistencyso that the mice of a strain they
ship three years from now will be as genetically identical as possible to those they ship this
year.
Publicly available health reports on the mice.
Trained technical support personnel who can assist with any issues you may encounter.
Unless absolutely necessary, avoid switching from one supplier to another during a research
program. Even though the strain names might be the same from one supplier to another, it is
likely that the mice are different enough genetically to confound research results.
5.E. Guidelines for alternatives to maintaining live mice

For some research it may be cost effective to use biological materials other than live mice.
Studies involving analysis of extracted DNA, RNA or protein; frozen tissues or organs; or
histology may not require live mice at your site. An option is to purchase this material
instead.
Some institutions may not have the specific facilities or expertise to house, breed, maintain,
or treat specific mouse models or to perform specific procedures for in vivo studies. One
option is to outsource specific tasks. Another option is to contract for someone else to run the
study.
To learn more about these alternatives, or for information about how these strategies might meet
the needs of your research program, call our technical information scientists at 1-800-422-6423
(North America) or 1-207-288-5845 (international). Also, refer to Chapter 18, JAX Services.
5.F. Sources of information related to selected research

areas
Tables 5.4 through 5.13 provide lists of resources for selected research areas. They supplement
the more general information provided in 5.A, General sources of information about mouse
strains.
Table 5.4. Information resources: aging.
Resource
Web address
The Jackson Laboratory:

Jackson Aging Center, including the Nathan Shock Center
www.agingmice.org
The Mouse Phenome Database (MPD)
www.jax.org/phenome
Information about our aging research
Lifespan data on some common strains of JAX Mice and

hybrids from those mice
www.jax.org/research/faculty/harrison/
ger1vi_Data2
National Institute on Aging (NIA)

Biology of Aging Program (BAP) of the NIA
www.nia.nih.gov
www.nia.nih.gov/ResearchInformation/
ExtramuralPrograms/BiologyOfAging/
BAPScientificPrograms
The Aging Program of The Ellison Medical Foundation
www.ellisonfoundation.org/adsp.jsp?
key=10aging_about
Table 5.5. Information resources: autoimmunity, including type 1 diabetes.

Resource
Web address

Type 1 Diabetes Resource and repository
http://type1diabetes.jax.org/index.html
Diabetes incidence studies for JAX Mice most commonly

used to study autoimmunity
www.jax.org/t1dr/gqc_incidence_studies
Lists of research models
www.jax.org/jaxmice/research/
diabetes/type1.html
Center on Immunological Tolerance in Type-1 Diabetes

(Harvard Medical School)
www.citdh.org/mock_new2_content.html
National Institute of Diabetes and Digestive and Kidney

Diseases (NIDDK)
www2.niddk.nih.gov
National Institute of Allergy and Infectious Diseases (NIAID

of the NIH
www3.niaid.nih.gov
Juvenile Diabetes Research Foundation International
www.jdrf.org
Table 5.6. Information resources: cancer.

Resource

The Jackson Laboratory Cancer Center website
Our cancer resource, with links to
lists of research models
the Cancer Research Manual
the cancer research databases (Mouse Tumor Biology
[MTB] and the Mouse Phenome Database [MPD])
Web address
www.jax.org/research/cancer
www.jax.org/jaxmice/research/cancer
Information about our cancer research
American Cancer Society (ACS)

Cancer statistics
www.cancer.org
www.cancer.org/docroot/stt/stt_0.asp
National Cancer Institute
www.cancer.gov
Cancer Models Database
https://cancermodels.nci.nih.gov/camod/
login.do
The Mouse Models of Human Cancers Consortium

(MMHCC)
http://emice.nci.nih.gov/emice
American Association of Cancer Research
www.aacr.org
Table 5.7. Information resources: cardiovascular biology.

Resource
Web address

Heart, Lung, Blood and Sleep Disorders Center website
www.jax.org/pga
Lists of research models
www.jax.org/jaxmice/research
Cardiovascular Research Manual
www.jax.org/jaxmice/manual
Information about our research
National Heart Lung and Blood Institute of the National

Institutes of Health
www.nhlbi.nih.gov
CardioGenomics, a program for genomic applications

sponsored by the National Heart, Lung & Blood Institute
(NHLBI)
http://cardiogenomics.med.harvard.edu/
American Heart Association
www.americanheart.org
Table 5.8. Information resources: hematology.

Resource
Web address

Hematological web resource, with links to
Mouse Heart, Lung, Blood and Sleep Disorders
(HLBS) Center website
information about our research
www.jax.org/jaxmice/research/hematology.html
National Heart Lung and Blood Institute of the National

www.nhlbi.nih.gov
Table 5.9. Information resources: immunology, immunodeficiency and infectious disease.

Resource
Web address

Immunology and inflammation web resource, with links
to
the immunodeficient poster
the Infectious Disease Resource Manual
www.jax.org/jaxmice/research/immunology
National Institute of Allergy and Infectious Diseases

(NIAID) of the NIH
www.niaid.nih.gov
Table 5.10. Information resources: metabolism.

Resource
Web address

Metabolism web resource, with links to
National Institute of General Medical Sciences (NIGMS)
of the National Institutes of Health
www.jax.org/jaxmice/research/metabolism
www.nigms.nih.gov
Table 5.11. Information resources: neurobiology, including neuromuscular and

sensorineural biology.
Resource
Web address

Alzheimers disease web resource, with links to
information about the Alzheimers Disease Mouse
Model Resource (ADMMR)
the Neurobiology Resource Manual
other relevant information
Cranofacial mutant web resource, with links to
Cytogenic models web resource, with links to
protocols
Neural tube mutant web resource, with links to
Neurobiology web resource, with links to
the Neurobiology Resource Manual
other websites related to neurobiology research
www.jax.org/jaxmice/research/neurobiology/
alzheimers
http://craniofacial.jax.org/index
www.jax.org/cyto
www.jax.org/ntd
www.jax.org/jaxmice/research/neurobiology
Table continued on next page
Table 5.11. Information resources: neurobiology, including neuromuscular and sensorineural biology
(continued).
Resource
Web address
Parkinsons disease web resource, with links to

www.jax.org/jaxmice/research/neurobiology/
parkinsons
Sensorineural web resource, with links to

a web resource about hereditary hearing impairment
in mice
www.jax.org/jaxmice/research/sensorineural
Neuromice
www.neuromice.org
The Mouse Brain Library
www.mbl.org
The Gene Expression Nervous System Atlas (GENSAT)

project
www.ncbi.nlm.nih.gov/projects/gensat
The Neuroscience Gateway
www.neuroscience-gateway.org
The Allen Institute for Brain Science
www.alleninstitute.org
The Allen Brain Atlas
www.brain-map.org
The Alzheimer Research Forum
www.alzforum.org
The ALS (amyotrophic lateral sclerosis) Association
www.alsa.org
The National Ataxia Foundation
www.ataxia.org
The National Institutes of Health:

National Institute of Alcohol Abuse and Alcoholism
www.niaaa.nih.gov
National Institute of Deafness and Other Communication

Disorders
www.nidcd.nih.gov
National Institute of Drug abuse
www.nida.nih.gov
National Eye Institute
www.nei.nih.gov
National Institute of Mental Health
www.nimh.nih.gov
National Institute of Neurological Disorders and Stroke
www.ninds.nih.gov
Table 5.12. Information resources: pharmacology.

Resource
Web address

Phenotyping and efficacy testing services (JAX
Services)
www.jax.org/jaxmice/services/
phenotyping-and-efficacy-testing
National Institute on Alcohol Abuse and Alcoholism

(NIAAA) of the National Institutes of Health
www.niaaa.nih.gov
National Institute on Drug Abuse (NIDA) of the National

www.nida.nih.gov
European Medicines Agency (EMEA)
www.emea.europa.eu
Table 5.13. Information resources: reproductive biology.

Resource
Web address

Reproductive Genomics: Mutant Mouse Models of Infertility

website, with links to
other information related to reproductive biology
http://reproductivegenomics.jax.org/
lists.html
National Institute of Child Health & Human Development

(NICHD), National Institutes of Health
http://nichd.nih.gov
GermOnline
www.germonline.org
Table 5.14. Information resources: type 2 diabetes, obesity, and metabolic syndrome.
Resource
Web address

Diet and obesity web resource, with links to
additional resources
the Type 2 Diabetes and Obesity Resource Manual
www.jax.org/jaxmice/research/diabetes/
type2.html
Diet-Induced Obesity (DIO) Services (JAX Services)
www.jax.org/jaxmice/services/dio
Genome-wide scan profiles for all 10 NONcNZO strains
www.jax.org/research/faculty/leiter/
type2_genomics
American Diabetes Association
www.diabetes.org
Animal Models of Diabetic Complications Consortium (AMDCC)
www.amdcc.org
Joslin Diabetes Center
www.joslinresearch.org
National Institute of Diabetes and Digestive and Kidney Diseases

(NIDDK)
www2.niddk.nih.gov
Diabetes Genome Anatomy Project (DGAP)
www.diabetesgenome.org
Obesity Gene Map Database
http://obesitygene.pbrc.edu
5.G. References
Press, NY. pp 197215.
Cook MJ. 1965. The Anatomy of the Laboratory Mouse. Academic Press. (Available online at
www.informatics.jax.org/cookbook)
Festing MFW. 1979. Inbred Strains in Biomedical Research. Macmillan Press, London. (Note:
Also available online at www.informatics.jax.org/external/festing/search_form.cgi)
Fox JG, Barthold SW, Davisson MT, Newcomer CE, Quimby FW, Smith AL, eds. 2007. The
Mouse in Biomedical Research, 2nd Edition. American College Laboratory Animal Medicine.
Academic Press.
Hedrich H (ed.). 2006. The Laboratory Mouse (Handbook of Experimental Animals). Elsevier,
San Diego CA.
Ho M, Post CM, Donahue LR, Lidov HGW, Bronson RT, Goolsby H, Watkins SC, Cox GA,
Brown RH Jr. 2004. Disruption of muscle membrane and phenotype divergence in two novel
mouse models of dysferlin deficiency. Hum Mol Genetics. 13:19992010.
Staff of The Jackson Laboratory. 1966. Biology of the Laboratory Mouse, 2nd Edition. Green E
(ed). Dover Publications, Inc. NY. (Available on line at www.informatics.jax.org/greenbook).
Leiter E, Atkinson M (eds). 1998. NOD Mice and Related Strains: Research Applications in
Diabetes, AIDS, Cancer, and Other Diseases. In Medical Intelligence Unit. RG Landes Co.
Austin TX.
Maurer KJ, Rogers AB, Ge Z, Wiese AJ, Carey MC, Fox JG. 2006. Helicobacter pylori and
cholesterol gallstone formation in C57L/J mice: a prospective study. Am J Physiol Gastrointest
Liver Physiol. 290:175182.
Morse HC III, editor. 1978. Origins of Inbred Mice. Academic Press. (Available online at
www.informatics.jax.org/morsebook)
Russell EJ. 1966. Lifespan and Aging Patterns, in Biology of the Laboratory Mouse, 2nd
Edition. Green E (ed) Dover Publications, Inc. NY.
Silver LM. 1995. Mouse Genetics: Concepts and Applications. Oxford University Press.
(Available online at www.informatics.jax.org/silverbook)
Silvers WK. 1979. The Coat Colors of Mice: A Model for Mammalian Gene Action and
Interaction. Springer Verlag. (Available online at www.informatics.jax.org/wksilvers)
Suckow MA, Danneman P, Brayton C. 2001. The Laboratory Mouse. CRC Press LLC, Boca
Raton FL.
Svenson KL, Von Smith R, Magnani PA, Suetin HR, Paigen B, Naggert JK, Li R, Churchill
GA, Peters LL. 2007. Multiple trait measurements in 43 inbred mouse strains capture the
phenotypic diversity characteristic of human populations. J Appl Physiol. 102:23692378.
165
Chapter 6: Bioinformatics Resources at Mouse

Genome Informatics (MGI) and The Jackson
Laboratory
Joanne M. Currrer
Throughout the history of The Jackson Laboratory, a consistent goal has been to enhance
biomedical research around the world. One way we do this is by freely sharing information.
Currently, with both public and private funding, and in collaboration with other institutions, our
staff provides investigators worldwide with access to the most up-to-date information about the
genetics of the laboratory mouse and available research models. Today, The Mouse Genome
Informatics (MGI) website and The Jackson Laboratory website are recognized as preeminent
repositories of public databases and resources related to laboratory mouse genetics.
Our objective for this chapter is to introduce the online resources available to the public from
MGI and The Jackson Laboratory and to show how to get started using them. The chapter is
organized as follows:
6.A. What is bioinformatics?........................................................................................166
6.B. Introduction to bioinformatics resources at the Mouse Genome
Informatics (MGI) website ...................................................................................166
6.B.1. How to access MGI and get help ..............................................................166
6.B.2. What you can do from the MGI website
(www.informatics.jax.org) ........................................................................167
6.B.2.a. Quick Search ...............................................................................167
6.B.2.b. Explore MGI ...............................................................................167
6.B.2.c. The menu bar ..............................................................................170
6.B.3. Examples: using MGI to find a mouse model associated with
a disease and to find phenotypic information for a gene.........................170
6.C. Reference information: bioinformatics resources at MGI and
The Jackson Laboratory........................................................................................171
6.C.1. Databases that are part of MGI .................................................................171
6.C.2. Other databases ..........................................................................................173
6.C.3. Online books available from MGI ............................................................174
6.C.4. Additional resources ..................................................................................174
6.D. Literature ...............................................................................................................174
6.D.1. Literature related to MGI ..........................................................................174
6.D.2. Literature related to other databases .........................................................175
Acknowledgments: We would like to thank Karen Fancher (Technical Information Services)

and Janan Eppig, David Shaw and Susan McClatchy (all from Mouse Genome Informatics) for
their valuable input to this chapter.
166 Section III: Bioinformatics
6.A. What is bioinformatics?

The term bioinformatics refers to computer access, integration, and analysis of collections of
biological data. Uses of bioinformatics can be as simple as a search for information about a
mouse gene in one database or as complex as the generation of a novel discovery through
analyses of multiple databases.
The rapid advancements in genetic research since the late 1970s would not have been possible
without bioinformatics. For example, suppose in 1986 that a researcher was searching for the
gene responsible for a mutant phenotype in a mouse. Even if the phenotype was mapped to a
1020 cM region, it might have taken several yearsand considerable luckto narrow the
search down to a few reasonable candidate genes. To actually identify the gene would have
taken several more years. Also, because so many genes had not yet been identified or annotated,
the candidate list would have been incomplete, and might not have included the gene. Today,
however, the mouse genome is sequenced and most of the genes are identified. Thus, within a
mapped region of the same size of 1020 cM, a researcher could conduct a similar search and
identify several candidate genes within minutes.
Taking full advantage of the power of bioinformatics presents several challenges: First is
locating and accessing the specific databases that can help resolve a research issue. Second is
finding ways to integrate relevantbut disparatedatabases to exploit the strengths of each.
Third is understanding the use of the computational tools that crunch and analyze the data.
MGI and The Jackson Laboratory assist researchers with these issues by maintaining several
databases accessible to the public, by providing links toand integration withdatabases
maintained by others, and by providing computational resources for analysis of this data.
6.B. Introduction to bioinformatics resources at the

Mouse Genome Informatics (MGI) website
The Mouse Genome Informatics (MGI) website offers seamless queries of multiple databases
from a single search interface, with integration of all results in one display, and links to other
databases and resources from search results.
6.B.1. How to access MGI and get

help
To access the MGI website, link to Mouse
Genome Informatics (MGI) in the Shortcuts for
researchers text box, which is displayed on The
Jackson Laboratory homepage (www.jax.org)
and on many other pages of The Jackson
Laboratory website. Alternately, go directly
www.informatics.jax.org.
For help using the MGI website, from the MGI homepage, choose the Tour the MGI website
button. Also look for frequently asked questions (FAQs) and links to context-sensitive help
information throughout the site.
For additional help, contact the MGI staff using one of the following methods:
In the menu bar on each MGI webpage, click the Contact Us link and complete the online
form.
Email [email protected].
Call 1-207-288-6445.
Fax 1-207-288-6132.
Chapter 6: Bioinformatics Resources at Mouse Genome Informatics (MGI) and The Jackson Laboratory 167
6.B.2. What you can do from the MGI website

(www.informatics.jax.org)
The MGI homepage has three basic functional areas:
Quick Search, for single searches on individual MGI ID numbers, gene symbols, or gene
names.
Explore MGI, for access to resources and help documents organized by functionality.
A menu bar, for quick central access to MGI features.
Following is an overview of these three functional areas.
6.B.2.a. Quick Search

The Quick Search area of the MGI website allows users to quickly conduct a search on an ID
number, gene symbol, or gene name directly from the upper right-hand corner of most MGI
webpages. (The ID number is the MGI accession number that is assigned sequentially to data
objects as they are added to the database. An example of an ID number is MGI:75909.)
To conduct a Quick Search, simply enter
the search argument and click the Quick
Search button.
6.B.2.b. Explore MGI

The Explore MGI area of the MGI website is organized in eight functional areas, identified by
title and icons.
Following is a task-based overview of each functional area. It is important to note that, because
these areas are organized by function, they generally do not represent a one-to-one relationship
with a specific database. Rather, some databases are accessible from multiple areas, as tasks
require. For reference information about the most commonly used databases, see 6.C,
Reference information: bioinformatics resources available at MGI and The Jackson
Laboratory, later in this chapter.
6.B.2.b. Explore MGI (continued)

Genes (Genes, Genome Features & Maps)
Search for
- genes and genome features by symbol,
name, location, gene ontology classification
or phenotype,
- sequences by mouse strain or biological
attribute,
- mouse genes and genome features using
nucleotide or protein sequences
(MouseBLAST).
Display
- genetic maps,
- specific regions of the mouse genome,
- nomenclature guidelines.
Download
- results of batch searches (multiple arguments),
- plain text files of any genes and markers query
result.
Submit a new gene or genome feature to receive
official nomenclature and an MGI accession
identifier.
Also find FAQs, information about collaborators,
and links to help text and other related sites.
Phenotypes (Phenotypes, Alleles & Disease Models)

Search for mutations or QTLs based on
- phenotype, allele, disease model,
- mammalian phenotype (MP) ontology terms,
- human disease (Online Mendelian Inheritance
in Man [OMIM]) terminology,
- mutation type,
- gene,
- genome location.
Display nomenclature guidelines for naming
alleles and mutations.
Download results of batch searches (multiple
arguments).
Submit
- a new allele, mutation or transgene to receive
official nomenclature and an MGI accession
identifier,
- a description of a spontaneous, induced or
genetically-engineered mutation that is
already registered in MGI.
Also find FAQs, information about collaborators,
and links to help documents and other related sites
Expression (Gene Expression Database [GXD])

Search for
- detailed gene expression assay results,
- references on gene expression during
development,
- genes expressed in some anatomical structures
and/or developmental stages but not in others,
- anatomical structures, including links to
associated expression results,
- anatomical terms and associated expression data
in the Edinburgh Mouse Atlas,
- expression information based on tissue or cellline origin of cDNAs.
Download a tool to manage your own

expression data and submit them.
Also find FAQs, information about collaborators
(such as the Mouse Gene Expression Information
Resource [GEIR]), the Gene Expression Database
(GXD), and links to help documents and other
relevant resources.
Function (Functional Annotation Using the Gene Ontology [GO])

Browse the Gene Ontology (GO) and mouse
annotations in MGI.
Search for genes using GO terms and other gene
attributes.
Access GO annotations for genes associated with
OMIM.
Download sets of IDs or symbols for use in GO tools.
Use GO annotations to discover what gene

sets might have in common.
Also find FAQs; information about GO
resources, annotation projects and literature;
and hints for interpreting annotations.
Pathways (Biochemical [metabolic] Pathways)

Search the MouseCyc database.
Compare metabolic pathways across species.
Browse the MouseCyc
- pathway ontology,
- all pathways, genes, proteins and compounds
represented in MouseCyc.
Download gene names for any pathway.
Overlay experimental data onto the Pathway

Tools Omics Viewer.
Generate a mouse metabolic map.
Also find FAQs, information about MouseCyc
and collaborators, and links to help documents
and other relevant websites.
Strains/SNPs (Strains, SNPs & Polymorphisms)

Search for
- SNPs by strain, attributes, genomic position or
associated genes,
- RFLP or PCR based on polymorphisms by
strain, locus symbol or map position,
Search through the listing of Inbred Strains of
Mice and Rats, by M. Festing and an MGI
report of official strain names
View
- a chart depicting the origins and relationships
of inbred mouse strains,
- nomenclature and naming guidelines.
Register a new strain and receive official

nomenclature and an MGI accession identifier.
Also find FAQs; information about strains, SNPS
and collaborators; and links to help documents, the
International Mouse Strain Resource (IMSR)
database, and other relevant websites.
Orthology (Mammalian Orthology)

Search for
- orthologs between 2 species using marker
symbol or name, accession ID, chromosomal
location, author or reference ID,
- gene family data using the Protein Information
Resource SuperFamily (PIRSF) browser.
Build a comparative map using the Linkage
Map tool.
View the mouse-human and mouse-rat orthology

maps.
Download a complete set of rat, human, dog or
chimpanzee orthologs for mouse genes.
Also find FAQs, information about orthology, and
links to help documents, other relevant websites, and
reports generated nightly by MGI.
Tumors (Mouse Tumor Biology [MTB] Database)

Link to the Mouse Tumor Biology (MTB)
database and
Search for
- tumor types,
- tumor incidence and latency,
- tumor pathology reports and images,
- genetic factors associated with tumors and
tumor development.
Compare cancer profiles of different strains of

mice.
Review the patterns of mutations in specific
cancers; identify genes commonly mutated across
a spectrum of cancers.
Also find information on, and links to, related online
resources.
6.B.2.c. The menu bar

The menu bar on the MGI website is available from almost every MGI webpage.
The menu bar includes the following functionality:

Search: Access to MGI search functionality from a single location.
Download: Access to MGI download functionality from a single location.
More Resources: Links to online resources such as research community email lists, online
books, nomenclature information, online databases, other relevant websites, and software
developer tools.
Submit Data: Links to web resources for submitting and registering gene, allele, and strain
names and for contributing data.
Find Mice (IMSR): Link to the International Mouse Strain Resource (IMSR) database.
Contact Us: Send an email message directly to the MGI staff.
6.B.3. Examples: using MGI to find a mouse model associated with

a disease and to find phenotypic information for a gene
Following are two examples of using MGI: How to find a mouse model associated with cystic
fibrosis, and how to find information about phenotypes related to the Cftr mouse gene.
Keep in mind that MGI functionality is very diverse and very flexible. Each example represents
just one way to complete a task. We encourage you to explore ways that might suit you better.
Table 6.1. Example: How to find mouse models associated with cystic fibrosis.
Action
Result
1. From the Explore MGI area of the MGI homepage,

select the Phenotypes option.
Phenotypes, Alleles & Disease Models page.
2. Select the Human Disease (OMIM) Browser link.
Human Disease Vocabulary Browser.
3. In the Search the vocabulary field, type cystic

fibrosis and click the Search button.
A list of OMIM IDs and descriptions with

numbers of available mouse models.
4. In the Human Disease column, select a cystic

fibrosis link that indicates a quantity of available
mouse models.
Human Disease and Mouse Model Detail

page.
5. In the Mouse Models section of the page, select the

mouse model with the allelic composition of interest.
Phenotypic Allele Detail page.
6. In the Allele details section of the page, select the link

to the International Mouse Strain Resource (IMSR) or
the Mouse Models of Human Diseases.
Information about mouse models.
Table 6.2. Example: How to find phenotypes associated with the Cftr (cystic fibrosis
transmembrane conductance regulator homolog) gene.
Action
Result
1. From the Explore MGI area of the MGI homepage,

select the Genes option.
Genes, Genome Features & Maps page.
2. Select the Genes and Markers Query link.
Genes and Markers Query Form.
3. In the Gene/Marker Symbol/Name field, type cftr

and click the Search button.
Genes and Markers, Query Results

Summary.
4. In the Symbol, Name column, select the Cftr

link.
Gene Detail page
5. In the Phenotypes section of the page, select the link

of interest.
Information about the gene with links to more

detailed information.
6.C. Reference information: bioinformatics resources at

MGI and The Jackson Laboratory
Following is reference information about the most commonly used online resources accessible
through the MGI and The Jackson Laboratory websites. Most often, you will access these
databases via links from other webpages or search interfaces. We provide the web addresses of
the databases, however, should you want to access them directly.
6.C.1. Databases that are part of MGI

The MGI database system comprises integrated databases that collectively provide access to
data on the genetics, genomics, and biology of the laboratory mouse. The databases listed below
are those that are accessed from the functional areas of the Explore MGI area and menu bar of
the MGI website (www.informatics.jax.org).
Mouse Genome Database (MGD)
Description:
Contents:
Functions:
Address:
The international community database for the laboratory mouse, providing a current,
integrated representation of mouse genetic, genomic, and biological information. The
MGD forms the core of MGI.
genes and genomic features
allelic variants
phenotype descriptions
orthologous gene
relationships and
comparative
sequence map
functional gene
classifications
molecular reagent data
SNP data
Search, download, and display data in a variety of tabular, graphical, and map
formats.
Link from mouse data to relevant related data in a variety of other data resources.
Gene Expression Database (GXD)

Description:
Contents:
A community resource of endogenous embryonic gene expression data for the

laboratory mouse; integrated with MGI and hosted by The Jackson Laboratory.
Integration of multiple types of expression data, including
RNA in situ hybridization
immunohistochemistry
Functions:
Address:
northern and western

blot
RT-PCR
RNAase protection
cDNA source data
Access data in formats appropriate for comprehensive analysis.

Integrate with the MGD for combined analysis of genotype, expression, and
phenotype information.
Interconnect with sequence databases, databases for other species, and other online resources.
www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml
6.C.1. Databases that are part of MGI (continued)

International Mouse Strain Resource (IMSR) database
Description:
An online database of mouse strains and stocksincluding inbred, mutant, and geneticallyengineeredavailable worldwide. The goal of the IMSR is to assist the international
scientific community in locating and obtaining mouse resources for research.
Contents:
holder of the strain
Functions:
Address:
state of the strain (e.g.,

live, frozen, etc.)
type of mutation (i.e.,

targeted or transgene)
Search for mice by strain, status, mutation, chromosome.

Link to information about specific strains, alleles, and the holder of the strain.
From MGI allele detail pages, automatically search the IMSR for relevant models.
www.informatics.jax.org/imsr
Mouse Tumor Biology (MTB) Database

Description:
Contents:
Functions:
Address:
A community resource for integrated information on tumor genetics and pathology in

genetically defined mice. The MTB allows cancer models to be evaluated as they apply to
humans, presents mutation patterns for specific mouse cancers, and allows comparison
across cancer models. The MTB is the most comprehensive database available on cancer
characteristics of different strains of mice.
Integration of multiple types of expression data, including
tumor types
tumor incidence and
latency data in various
mouse strains
tumor pathology reports

and images
genetic factors associated
with tumors and tumor
development
information on, and links to,

related online resources
Choose experimental
models
Compare the cancer
profiles of different
strains of mice
Review the patterns of

mutations in specific
cancers.
Identify genes that are
commonly mutated across
a spectrum of cancers.
Search for tumor

information based on
parameters such as mouse
strain, tumor type, gene
name, and organ name.
http://tumor.informatics.jax.org/mtbwi/index.do
MouseCyc Database
Description:
A genome database of metabolic pathways for the mouse that is integrated with MGIs
well-curated information on phenotypes, gene expression data, functional annotations, and
mammalian homology for mouse genes. Emphasis is on genes with direct human
counterparts.
Contents:
proteins
pathways
Functions:
Address:
reactions
compound genes
RNAs
Analyze mouse genetic and genomic data in the context of biochemical and metabolic
processes.
Compare human and mouse pathways based on curated orthologous genes and conserved
synteny relationships.
http://mousecyc.jax.org
6.C.2. Other databases

The Jackson Laboratory provides access to other databases that play an integral role in mouse
genetics. Following are descriptions of two of the most widely used. For access to other online
genetics resources, visit www.jax.org/research/resources.
Mouse Phenome Database (MPD)
Description:
Contents:
Database of information gathered by the Mouse Phenome Project, an international,

collaborative initiative to establish a comprehensive collection of phenotypic data for
mouse strain comparisons. The MPD also includes data generated from a focused effort
to comprehensively evaluate multiple phenotypes in a set of 36 priority strains under
uniform conditions. An objective of the MPD is to facilitate the study and use of
laboratory mice in researching human health issues. The MPD is maintained at The
Jackson Laboratory.
Information on mouse phenotypes, including
cancer susceptibility
neurological and
behavioral disorders
sensory function defects
atherosclerosis
gallstones
Functions:
Address:
blood disorders
infectious disease
susceptibility
lung function
hypertension
osteoporosis
obesity
body weight
blood chemistry values
images
Assists investigators in identifying mouse strains for experiments.

Makes phenotype-genotype association predictions.
Identifies and determines the function of genes that participate in normal and disease
pathways.
Graphically compares data acrossor betweenstrains.
www.jax.org/phenome
JAX Mice Database

Description:
Contents:
An online database providing direct access to comprehensive information about the

biology and genetics of mouse strains maintained at The Jackson Laboratory.
Strain-specific information, including
complete strain name,
common name and
nomenclature
strain description and
source
phenotypes and genotypes
Functions:
Address:
full and common

names of relevant
genes and alleles,
including haplotype
and coat color
links to references
husbandry conditions
(including room number
and diet)
animal care tips
Provides a complete picture of all strains of mice maintained or cryopreserved at The

Jackson Laboratory.
Provides search functionality on Mammalian Phenotype Ontology and human disease
(Online Mendelian Inheritance in Man [OMIM]) terminology.
Feeds current strain information to several databases at The Jackson Laboratory,
avoiding duplication and assuring accuracy.
6.C.3. Online books available from MGI

MGI provides public online access to five important books related to mouse genetics. The
Biology of the Laboratory Mouse is available in limited quantities (see sidebar for ordering
information). The other four books are out of print.
Biology of the Laboratory Mouse. 1968. Green EL (ed). Dover Publications, Inc., NY.
Mouse Genetics, Concepts and Applications.
1995. Silver L. Oxford University Press.
To order a copy of the Biology of the
Laboratory Mouse
The Anatomy of the Laboratory Mouse. Cook
1. Go to the online version of the book. (Use the
M. 1965. Academic Press. M.R.C. Laboratory
procedure below left or go directly to
Animals Centre, Carshalton, Surrey, England.
www.informatics.jax.org/greenbook.)
The Coat Colors of Mice, A Model for
2. At the bottom of the book cover webpage,
select the link to purchase the book from The
Mammalian Gene Action and Interaction.
Jackson Laboratory.
1979. Silvers WK. Springer Verlag.
Origins of Inbred Mice. 1978. Morse HC III
(ed). Academic Press. National Institute of Allergy and Infectious Diseases, National
Institutes of Health, Bethesda, Maryland.
To access an online book:
1. From the MGI menu bar, select More Resources.
2. From the More Resources drop down menu, select Online Books. Then, from the flyout
menu, select the book.
6.C.4. Additional resources

www.jax.org/jaxmice/support
Technical support and literature on JAX Mice, including the JAX Mice Catalog, resource
manuals, model lists, price list, JAX NOTES, the JAX Mice News newsletter
Appendix N: Sources of Information about Laboratory Mice
6.D. Literature
6.D.1. Literature related to MGI
Begley DA, Krupke DM, Vincent MJ, Sundberg JP, Bult CJ, Eppig JT. 2007. Mouse Tumor
Biology Database (MTB): status, update, and future directions. Nucleic Acids Res. 35:638642.
Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, Mouse Genome Database Group. 2008.
The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res.
36:724728.
Eppig JT, Blake JA, Bult CJ, Richardson JE, Kadin JA, Ringwald M, The MGI staff. 2007.
Mouse genome informatics (MGI) resources for pathology and toxicology. Toxicol Pathol.
35:456457.
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group. 2007.
The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids
Res. 35:630637.
Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, Mouse Genome Database Group. 2005.
The Mouse Genome Database (MGD): from genes to mice, a community resource for mouse
biology. Nucleic Acids Res. 33:471475.
Gene Ontology Consortium, Blake JA, Bult CJ, Eppig JT, Ringwald M. 2008. The Gene
Ontology project in 2008. Nucleic Acids Res. 36: D440444.
Krupke D, Nf D, Vincent M. Allio T, Mikaelian I, Sundberg J, Bult C, Eppig J. 2005. The

Mouse Tumor Biology Database: integrated access to mouse cancer biology data. Exp Lung
Res. 31:259270.
Smith CL, Goldsmith CA, Eppig JT. 2005. The Mammalian Phenotype Ontology as a tool for
annotating, analyzing and comparing phenotypic information. Genome Biol. 6:7.
6.D.2. Literature related to other databases

Grubb SC, Churchill GA, Bogue MA. 2004. A collaborative database of inbred mouse strain
characteristics. Bioinformatics. 20:28572859.
McKusick VA. 2007. Mendelian Inheritance in Man and Its Online Version, OMIM. Am J Hum
Genet. 80:588604.
177
Section IV: Colony Management

Colony management in its broadest sense involves your animals, your facility, your staff, and
your administration. Colony management issues range in scope from simple tasks performed
day after day (checking water bottles and changing cages) to complex tasks that you hope you
never have to perform (recovering from microbial contamination or a natural disaster). Colony
management has one purpose: to produce and maintain healthy, genetically consistent animals,
suitable for biomedical research.
In this section, we will address issues that almost every colony manager and institution must
address. Our objective is to present guidelines and choices, anticipate questions you might have,
and explain where to get more information. Well also explain what we do at The Jackson
Laboratory. This information is especially relevant because it details the conditions under which
JAX Mice are bred and housed.
This section is organized as follows:
Chapter 7: Animal HealthPreventing, Identifying, and Eradicating Microbial
Contamination..................................................................................................179
Chapter 8: Genetic Quality ControlPreventing Genetic Contamination and
Minimizing Genetic Drift................................................................................191
Chapter 9: Animal Husbandry (including physical aspects of a mouse room,
routine tasks and issues)..................................................................................201
Chapter 10: Food and WaterNutritional and Health Implications ................................217
Chapter 11: Recordkeeping and Identification of Mice ....................................................229
Chapter 12: Introduction of New Mice into a Colony (including acclimating mice
to a colony) ......................................................................................................237
Chapter 13: Breeding Strategies and Techniques (including breeding characteristics
and optimal conditions for breeding, reproductive techniques,
troubleshooting breeding problems)...............................................................241
Chapter 14: Emergency Planning........................................................................................255
Chapter 15: Human Health ConcernsMouse Allergies, Bites, Zoonotic Disease........259
Chapter 16: Vivarium Staff Development and Contribution (including training and
development of staff, facilitating communication, maximizing job
contribution and satisfaction)..........................................................................265
179
Chapter 7: Animal HealthPreventing, Identifying,

and Eradicating Microbial Contamination
Peggy Danneman, Dorcas Corrow, Joanne M. Currer, Kevin Flurkey
If you manage a production or research colony, maintaining animal health is one of your most
critical responsibilities. This issue includes preventing and identifying microbial contamination
as well as ridding your colony of a contamination, should one occur. Whether you purchase
mice or acquire them from other research colonies, your concern also includes the possibility of
introducing contaminated animals into your colony.
The objective of this chapter is to describe considerations for developing an animal health plan
and managing a microbial contamination. We also provide an overview of our animal health
plans at The Jackson Laboratory.
7.A. Developing an animal health plan..............................................................................180
your colonies....................................................................................................180
7.A.2. Preventive measures to keep unacceptable agents out of your colonies ......181
7.A.3. Monitoring procedures to identify the presence of unacceptable agents .....182
7.A.4. Containment and eradication procedures to prevent the spread of an
infection and to eliminate it from your colony ..............................................184
7.B. Our animal health plan at The Jackson Laboratory ..................................................184
7.B.1. Our exclusion list.............................................................................................184
7.B.2. Our preventive measures.................................................................................185
7.B.3. Our monitoring procedures .............................................................................186
7.B.4. Our containment and eradication procedures ................................................188
7.B.5. Routine health reports .....................................................................................189
7.C. References ...................................................................................................................189
180 Section IV: Colony Management
7.A. Developing an animal health plan

There is no universal agreement on the desired health status of mice used in research. Individual
scientists must avoid microbial contaminants that could impair the performance of mice in their
research programs, either directly, by causing clinical disease, or indirectly, by causing physical
or physiological changes that could alter or confound data. Facility managers and veterinarians
would prefer to exclude any microorganism that could have a negative impact on any of the
animals or research projects in their facility. Thus, there is widespread, if not universal, interest
in excluding pathogenic murine viruses from research facilities. However, there is no consensus
on the importance of excluding organisms such as pinworms, Helicobacter, Pneumocystis
murina, Staphylococcus, and Pseudomonas. The strict barrier operations needed to maintain
mouse colonies free from these organisms are costly and labor intensive, and researchers often
find that working under the restrictions imposed by these operations is cumbersome. If these
costs are perceived as being out of proportion to any potential negative impact of a particular
microorganism, there may be little enthusiasm for attempting to exclude it.
In fact, in some situations, microorganisms that are viewed as unacceptable by some are actually
considered desirable by others. There are many examples where the desired phenotype of a
valued mouse model was lost following rederivation and transfer to an ultra-clean barrier
environment. For example, in most mouse models of inflammatory bowel disease (IBD), a
complex enteric flora is required to produce gut pathology. Accordingly, 100% of IL-10
knockouts (e.g., B6.129P2-Il10tm1Cgn/J [002251]) maintained under conventional conditions will
develop enterocolitis by three months of age, whereas most rederived knockouts housed under
specific pathogen free (SPF) conditions show no signs of enterocolitis by 12 months, and
germfree knockouts never develop enterocolitis (Kuhn et al., 1993; Kullberg et al., 1998; Sellon
et al., 1998). In some cases, multi-level SPF facilities within an institution may be necessary to
accommodate different research applications and requirements.
Thus, it is up to you and your institution to set suitable standards for your environment and
develop an animal health program to meet those standards. Most programs comprise four
components:
The exclusion list
Preventive measures
Monitoring procedures
Containment and eradication procedures
Notification procedures, in the event of a break, are critical for commercial suppliers and should
be considered for any institution that distributes mice to collaborators or other researchers.

your colonies
Realistically, you cannot exclude all agents that might cause disease or interfere with research in
your mouse colonies. Only you can decide which agents you can and cannot live with based on
the needs of your research program or institution.
When determining your exclusion list, consider the ability or willingness of your institution to
exclude an organism and to eradicate if it is found. Unless you can and will implement
appropriate measures to exclude and eradicate an agent, there is no point in including it on your
list. Considerations include the following: What are the potential consequences of the presence
of the agent on animal health? Can your institution live with the agent in all colonies? Some
colonies? How disruptive will an infection be to research? Can the agent affect your technicians
adversely? How costly would an infection be in terms of lost animals or compromised research?
Chapter 7: Animal HealthPreventing, Identifying, and Eradicating Microbial Contamination 181
For an example of the organisms you might want to consider excluding, refer to Table 7.1,
Infectious agents monitored at The Jackson Laboratory, later in this chapter. This table lists
the organisms on our exclusion list at The Jackson Laboratory. This list is quite comprehensive,
and it may not be practical or economically feasible to exclude all of these organisms from your
animal colonies. Also, note that not all organisms are excluded from all animal colonies at The
Jackson Laboratory; some opportunistic organisms (Helicobacter spp. and Pasteurella
pneumotropica) are currently tolerated in some research colonies, and as noted above, are
essential for pathology development in IBD models. These opportunistic organisms are not
tolerated in our production colonies.
7.A.2. Preventive measures to keep unacceptable agents out of

your colonies
Your pathogen protection goals are to keep undesirable agents out of your facility, your mouse
rooms, and your cages. The best protection is provided by the use of multiple strategies,
including the following:
Set up physical barriers to prevent pathogens
from entering your facility. Define strict
procedures for anything and anyone entering
a barrier facility. Develop detailed
procedures for any animal work conducted
within a room. Thoroughly document all
procedures and requirements, distribute the
procedures to all personnel who enter the
rooms, train personnel in the procedures, and
post the procedures in the rooms.
Can a colony be completely germ free? Would

this be a good idea?
It is possible to have completely germ free
axeniccolonies, but the extreme effort required
is warranted only for very specific purposes, such
as microbiological studies involving reconstruction
of gut bacteria populations with single organisms.
For most research, however, axenic colonies are
undesirable. Some bacteria, such as those in the
gastrointestinal tract, are necessary for normal,
biological processes. Ridding colony animals of
these agents may result in animals inappropriate
for most research.
For equipment and supplies, set up traffic

routes so that contact between clean,
incoming material and dirty, outgoing
material is eliminated or minimized. For employees, set up procedures to minimize movement
from one colony to another.
Develop detailed procedures for introducing mice into your facility.
Thoroughly disinfect the outside of shipping containers and check their integrity before
opening them. Briefly check each mouse as you unpack it.
Determine whether mice should go directly to the colony room, be quarantined, or be
rederived. The greatest risk is with the first option. However, if you limit this practice to
vendor mice from an SPF facility, the risk is comparatively low. Quarantine is more
expensive because it requires separate, dedicated space. A good quarantine program also
involves thorough follow-up testing. If necessary, animals in quarantine may be made
available to researchers if appropriate considerations are made to avoid the potential for
contamination. For example, mice that must be used in research soon after arrival may be
received into a separate quarantine area and manipulated using strict biocontainment
procedures. Rederivation is the safest optionand also the most expensive. It requires a
separate facility and technicians with expertise in assisted reproductive techniques (ARTs).
Also, all rederivation procedures require a source of highly-monitored SPF foster or
recipient mothers.
It is worth noting that any violation of quarantine and import procedures opens the colony
to a wide range of pathogens that can affect the health, performance and value of the mice.
Thus, it is essential to ensure full cooperation of all members of a research staff in adhering
strictly to institutional policies.
7.A.3. Monitoring procedures to identify the presence of

unacceptable agents
The goal of health monitoring is to find at least one animal that is infectedor was previously
infectedwith an agent on your exclusion list that has gained access to your colony. Of course,
you cannot test every animal. Thus, you must conduct routine monitoring at a stringency to
guarantee that you will meet or exceed the level of detection acceptable to your institution. If
you have a break or are recovering from one, more stringent monitoring will be necessary.
Following are considerations for effective health monitoring.
7.A.3.a. Sampling considerations

All monitoring programs are based on the concept of prevalencethe proportion of mice in the
colony that are infected. Many formulas for the calculation of the sample size needed to detect a
given prevalence are based on the simplifying assumption that any infection is randomly
distributed through the colony. For example, if the prevalence is 10%, the chance that any given
animal in the colony is infected is 10%. To find organisms that are present at lower prevalence,
more mice must be tested. If you are able to tolerate the presence of a contaminant until it is
present at a higher prevalence, you can test fewer mice.
Everyone should be on the monitoring team
Every person who works with your mice should be
vigilant for any overt sign of sick mice that could
indicate a breach in the pathogen barrier. Such
signs include unusual newborn mortality, diarrhea,
wasting, unresponsiveness to cage disturbance, or
unusual behavior.
Animal care technicians, who observe your mice on
a daily basis and who are familiar with their normal
characteristics, are valuable stewards of the health
of your animals. They, and anyone else who is in
regular contact with your mice, should be made
aware of symptoms of ill health and should be
encouraged to freely communicate any concerns
they might have.
Of course, to take full advantage of well-trained and
involved staff, researchers must be willing to submit
unanticipated sick mice to the veterinary health
monitoring program.
The assumption of random distribution of an infection

complicates the interpretation of results. In fact, infections are
rarely randomly distributed through a colony. Thus,
assignment of mice to be sampled should take into account a
number of non-random factors. For example, if several strains
of mice are present in the room, or if mice from several
different investigators are present in the room, it is desirable to
test mice from every strain and/or investigator. In general, test
animals of both sexes and various ages. Note also that
practices designed to prevent the spread of disease (i.e.,
microisolator caging and microisolator technique) will also
complicate health monitoring efforts, as these practices will
inhibit or prevent the random distribution of contaminants
within a colony. Once you control for variables such as these,
however, in the absence of some specific information that
would help pinpoint which animals are most likely to be
contaminated, the best approach is to test randomly selected
animals.
7.A.3.b. Frequency of monitoring

The frequency of monitoring for organisms on your exclusion list may vary for different agents
based on the likelihood of infection and the potential impact of the infection. See 7.B.3.a. for
information about the frequency of our monitoring at The Jackson Laboratory. In general, it is
advisable to monitor more frequently for organisms that are more prevalent in laboratory mice
or are more likely to cause disease or interfere with research (e.g., MPV or MHV). Costs can be
reduced by monitoring less frequently for organisms that are less likely to be present or to
interfere with research (e.g., K virus, Polyoma virus).
7.A.3.c. Choice of test animals

Appropriate test animals are those that are at least as likely as other members of the colony to
become infected with the organism(s) of interest, and if infected, to show a positive response on
the test being used to identify the infecting organism.
Choose colony animals or sentinels on the basis of your needs and availability of animals.
Colony animals are especially useful because they have the same genetic background and have
been treated the same (including experimental manipulations) as the rest of the colony. Sentinel
animals, which are brought into the colony specifically to detect contamination, are an option
when valuable colony animals cannot be sacrificed or for serologic monitoring of
immunodeficient animals or those that are prone to autoimmune disorders. (Immunodeficient
animals have impaired antibody response to pathogens. Autoimmune animals produce a high
level of antibodies that could interfere with a serologic test.)
Sentinels are of two types: Dirty bedding sentinels are routinely exposed to dirty bedding from
multiple cages of colony animals. Cage contact sentinels are housed in the same pen with
colony animals. Sentinels are less preferable than colony animals because they may have a
different genetic background and history. Furthermore, although dirty bedding sentinels in
theory permit you to survey a large portion of the colony, they have additional disadvantages.
They are notoriously poor indicators of colony infections by organisms that are not spread by
the fecal-oral route (e.g., Sendai virus). And, even with organisms that spread readily by the
fecal-oral route (e.g., MHV and MPV), spread to dirty bedding sentinels may be slow.
Therefore, exposure time of dirty bedding sentinels to potentially contaminated material should
be prolonged (a minimum of four weeks), which may be an issue when this approach is used to
monitor animals during quarantine. Also, if sentinels do not originate from a frequently
monitored colony of known high health status, they can actually introduce contaminants. This is
a particular concern with cage contact sentinels.
7.A.3.d. Types of tests

No single category of tests is sufficient. An effective monitoring strategy incorporates the
following:
Serology, for detection of antibodies that indicate exposure to viruses, mycoplasma, and some
bacteria. Note that false positives are more common with ELISA (enzyme-linked
immunosorbent assay) than with IFA (indirect fluorescent-antibody) assays, but may occur
with either.
Microbiologic culture, for specific, but more time-consuming, detection of most bacteria.
Parasitology (fecal flotation, direct microscopy, tape test, other).
Polymerase chain reaction (PCR), for direct identification of the DNA or RNA of viruses,
bacteria, fungi and parasites. Note that PCR can result in false positives or false negatives.
Histopathology and gross pathology.
General appearance, including fur loss, skin lesions, poor grooming, and emaciation, as well
as high neonatal mortality and runted weanlings.
7.A.3.e. Interpretation of monitoring results

It is worth noting that a monitoring program is designed only to detect the presence of an
organism, not its prevalence within the colony. It is also important to understand that no
monitoring program is foolproof. False positives and false negative results can occur, and even
if all results are accurate, there is always a potential for failing to detect infectious agents that
are present at low prevalence within the colony.
There is some art to interpreting test results. If you dont trust negative results, retest. If you
dont trust a positive result, retest using the same and different tests. (For example, if you tested
originally using ELISA, retest using ELISA plus an indirect fluorescent-antibody [IFA] test
and/or PCR.) If the result is reconfirmed, you may want to test more animals. Base your final
interpretation on all test results and your experiencewhether the results make sense to you.
When an initial positive result is confirmed and makes sense, it is time to implement your
containment and eradication plan.
7.A.4. Containment and eradication procedures to prevent the

spread of an infection and to eliminate it from your colony
Although your hope is to never need your containment and eradication plan, a wise strategy is to
assume that a break will happen. A comprehensive plan, developed by those who know your
mouse room operations the best, will ensure a swift, efficient, and effective response when the
break occurs.
Once you confirm an infection, your goal is to prevent further spreadboth within the room or
area of origin and to other animal roomswhile working to eradicate it. Strategies for
eradication include depopulation, rederivation, test and cull, and, perhaps, burnout (see
sidebar below right for important caveats regarding this often deceptively appealing alternative).
In most institutions, this means a significant deviation from business as usual. Thus, it is
important to identify decision makers and detailed proceduresand to get the endorsement of
administratorsbefore a break occurs.
Your plan should include written
documentation of the decision makers and
their areas of responsibility, the criteria for
implementation of the plan, the definition
of the containment and eradication
strategies, and criteria for resumption of
research in the affected area. Once your
plan is approved, you should rehearse it on
a regular basis to make sure that everyone
is familiar with their roles in the plan and to
identify modifications that may be required
as a result of changes in research, policies,
physical plant, etc.
A final note: As absolute insurance against
loss of an irreplaceable stock of animals
due to a contamination event, it is wise to
back up the stock via cryopreservation. For
details about cryopreservation and its use as
a backup strategy, refer to Appendix J,
Cryopreservation.
7.B. Our animal health

plan at The Jackson
Laboratory
Is burnout a reasonable option to handle

contamination in your colony?
Burnout refers to the strategy of letting the infection run
its course. Burnout may be an option when the
pathogen is one that spreads rapidly through a
susceptible population, causes only transitory infections,
and results in lifelong immunity (e.g., MHV). However, it
is risky, especially when dealing with immunodeficient
mice or genetically modified animals, which may
develop more prolonged infections and/or fail to produce
an effective immune response.
Researchers may pressure colony managers to use
burnout so they can complete long-term studies or for
economic reasons. But the agreement of all those
potentially affected (for example, researchers with
colonies in adjacent rooms) must be obtained before
proceeding with a burnout strategy.
If an infection is allowed to progress in one colony,
extreme measures must be taken to avoid spreading the
infection to other SPF colonies. For example, the flow of
supplies and mice, as well as caretaker and researcher
traffic, must be explicitly stated. It is critical to cease
introduction of new mice into a room during burnout; this
includes cessation of breeding. The affected room
should not be considered free of contamination until 1)
all animals in the room when the infection was identified
test positive for antibodies to the organism (indicating
that they have recovered from the infection), and 2) for
newly added mice, at least one mouse from every cage
tests negative for antibodies to the organism for at least
three consecutive months.
Following is a summary of the animal

health plan at The Jackson Laboratory. For
up-to-date details, including monitoring procedures and health status reports, visit our Animal
health & genetic quality website at www.jax.org/jaxmice/genetichealth.
7.B.1. Our exclusion list

At The Jackson Laboratory, we screen mice for a wide range of viruses, bacteria, fungi,
protozoa, and parasites. It should be noted that many of the organisms listed are unlikely to
cause overt disease. We include some, such as mouse parvovirus, primarily because of their
potential for interference with experimental results. We include others, such as Pneumocystis
murina, because they are opportunistic pathogens that seldom or never cause problems in
normal, healthy animals but may cause disease in severely immunodeficient or otherwise
compromised mice. We include trichomonads on the list because some users of JAX Mice
prefer to exclude these protozoa from their barrier mice even though they are nonpathogenic and
have never been shown to interfere with research.
Table 7.1 lists the agents we monitor as of the printing of this book. For a current list, visit
www.jax.org/jaxmice/health/agents_list.
Table 7.1. Infectious agents monitored at The Jackson Laboratory.
Viruses
Ectromelia virus (agent causing mouse pox)

GDVII (Theilers mouse encephalomyelitis) virus
Hantaan virus (Hantavirus)*
K virus
Lactic dehydrogenase elevating virus (LDV)
Lymphocytic choriomeningitis (LCMV)
Mouse minute virus (MMV)
Mouse adenovirus (MAV)
Mouse cytomegalovirus (MCMV)
Mouse hepatitis virus (MHV)

Mouse parvovirus (MPV)
Mouse norovirus (MNV)
Mouse thymic virus (MTV)
Pneumonia virus of mice (PVM)
Polyoma virus
Reovirus 3 (REO 3)
Rotavirus (Epizootic diarrhea of infant
mice [EDIM])
Sendai virus
Bacteria, mycoplasma, and fungi.
Bordetella bronchiseptica
CAR bacillus
Citrobacter rodentium (Citrobacter freundii 4280)
Clostridium piliforme
Cornebacterium kutsheri
Helicobacter spp.
Klebsiella spp.
Mycoplasma pulmonis
Pasteurella pneumotropica
Pneumocystis murina
Pseudomonas spp.
Salmonella spp.
Staphylococcus aureus
Streptobacillus moniliformis
Streptococcus spp.
Parasites and protozoa
Encephalitozoon cuniculi
Fleas, fur mites, lice
Follicle mites
Pinworms
Roundworms and other helminthes

Tapeworms
Opportunistic protozoa (e.g., Giardia,
Spironucleus)
Nonpathogenic protozoa (e.g.,
trichomonads)
* Neither wild nor laboratory mice of the genus Mus are natural hosts for hanta viruses, but they may
become infected if exposed.
Zoonotic agent that may cause disease in humans.
Pneumocystis murina monitoring is conducted in severely immunodeficient mice only.
7.B.2. Our preventive measures

Our health maintenance plan is based on physical barriers and strict adherence to barrier
procedures. Under no circumstances do we move mice from research colonies to production
colonies without rederivation. Everyone on our campus follows detailed standard operating
procedures (SOPs) for moving mice, supplies, and themselves into, out of, and around our
mouse colonies, and for activities within the animal room and operational support areas. New
staff members and new research technicians and students are fully briefed as to the required
measures for animal health protection to which they must fully subscribe.
7.B.2.a. Maintenance of mice

7.B.2.a.1. Barrier levels of our mouse rooms
We operate all of our animal rooms as barriers. The barrier level varies from low to maximum
depending on the location and use of the room. All levels have several characteristics in
common, including 100% fresh, HEPA-filtered air (under positive pressure in most areas), and
pre-defined traffic patterns that keep clean and dirty supplies from crossing paths. We rederive
all mice that come into The Jackson Laboratory from any outside source. For current
information about our barrier levels, visit www.jax.org/jaxmice/health.
7.B.2.a.2. Mouse room activities

We have detailed SOPs for entry into and exit from our mouse rooms, as well as for any tasks
that must be done within a room. SOPs cover a wide range of tasks, including how to remove a
mouse box from a shelf, how to add food and a new water bottle, and how to physically move
the mice from dirty to clean cages, as well as procedures and schedules for cleaning all parts of
the room.
7.B.2.b. Quarantine and importation

of mice
At The Jackson Laboratory, our quarantine and
importation facilities are located in a building
separate from research and production facilities.
All new stocks of mice arriving at our campus
must enter through the quarantine facility. This
facility is operated at negative pressure, as are
the isolators and individual ventilated caging
(IVC) systems used for quarantine housing. We
generally rederive strains via embryo transfer or
in vitro fertilization; however, we also use
hysterectomy derivation and, on rare occasions,
ovarian transplantation. (For details on these
procedures, see 13.E.2, Assisted reproductive
techniques [ARTs].) All material and
equipment leaving the quarantine facility are
autoclaved out.
What exactly do we mean by specific

pathogen free (SPF) colonies?
By definition a specific pathogen free (SPF)
colony is one from which specified pathogenic
microorganisms are excluded. Because the
excluded microbes can differ from colony to
colony, SPF colonies are not necessarily
microbiologically equivalent to each other. At The
Jackson Laboratory, the abbreviation SPF is also
used to denote animals with a defined aerobic
flora. Currently, JAX Mice from our SPF colony

harbor only the following aerobic bacteria:
Enterococcus spp., Lactobacillus spp., and
coagulase-negative Staphylococcus spp. These
mice are used as foster mothers for rederivation
of imported mice and for embryos recovered from
cryopreservation. They are also deployed as
sentinels in a few animal rooms in which we rely
in part on sentinels for health monitoring.
Our importation facility also includes an SPF barrier facility that contains several strains of mice
with an aerobically defined flora. We use females from this colony as foster mothers and as
recipients of ovarian and embryo transplants. All material that enters this maximum barrier
facility must be sterilized.
Importing and distributing new mutant mice: our
responsibilities as a publicly funded national
repository
Technicians who work in our quarantine and importation

facilities are not allowed to enter other mouse rooms on our
campus.
One of the most important roles The Jackson

Laboratory plays is to distribute mutant mice
developed by researchers throughout the world
including here at The Jackson Laboratory. We import
these mice via rederivation to assure their status as
pathogen-free mice. Currently, our repository staff
manages more than 2800 mutant strains. We import
new strains at the rate of about 600 per year.
Regardless of the technique used for rederivation, at weaning

we send all foster mothers and recipient females to our
diagnostic laboratory for health monitoring. We release litters
only if we receive negative results for all organisms other than
the allowed SPF flora.
We receive federal funding to provide this repository

service as well as to collect, summarize, and publish
information about these specialized mice.
7.B.3.a. Frequency and types of monitoring
7.B.3. Our monitoring procedures
At The Jackson Laboratory, we base our health monitoring on

the mouse room, not the mouse strain. We perform health
monitoring in all animal rooms at least quarterly. In some
special areas, such as those that house our foundation stocks,
pedigree expansion stocks, and foster mother colonies, we
monitor monthly. We screen for most organisms listed on the
health report at each monitoring interval. However, we make exceptions for some organisms
that are uncommonly found in modern laboratory mouse colonies: We screen semi-annually for
lymphocytic choriomeningitis virus, mouse thymic virus, and reovirus 3. We screen annually
for K virus, lactic dehydrogenase elevating virus, and polyoma virus. Current health reports are
available to the public at www.jax.org/jaxmice/health.
For further information about our repository and how

research scientists can take advantage of our
services, visit our Repository website at
www.jax.org/jaxmice/findmice/repository.
During daily welfare checks and as cages are changed, trained technicians search specifically
for mice with conditions abnormal for a specific strain. Animals with injuries or abnormalities
that are not clearly caused by disease or a genetic mutation are culled. Those showing
abnormalities that might be caused by an infectious agent are sent to the diagnostic laboratory.
If the abnormality is clearly not related to a microbial contamination, mice are set aside to see if
any researchers are interested in the phenotype. (See sidebar in 3.C.1.a.1 for information on our
deviant search program.) Some of the conditions that warrant diagnostic testing include
diarrhea, abnormal discharge from a body opening, visible masses on or under the skin,
abnormal swelling of a body part, poor physical condition, sores or other skin lesions with or
without loss of fur, head tilt or circling to one side, or runting of an entire litter.
7.B.3.b. Sample categories and sizes

When testing for pathogens at The Jackson Laboratory, we use colony or sentinel animals or a
combination of both, depending on the characteristics and use of the colony. When sentinels are
needed (e.g., for colonies of immunodeficient mice), we prefer to use SPF cage contact
sentinels. However, in some instances, we use dirty bedding sentinels as a supplement to colony
animals or cage contact sentinels.
The typical cage contact sentinel is a castrated male weanling
of a strain that can be readily infected with, and will mount a
strong immunological response to, a wide range of
microorganisms. We most often use BALB/cJ (000651) and
DBA/2J (000671) mice.
In our research facility, we test randomly-selected animals from
every animal room on a quarterly basis. If a particular room
houses animals owned by more than one investigator, all
investigators are asked to submit animals for monitoring. The
sample size for each mouse room is calculated based on a
prevalence of 18% for all organisms being monitored.
Weanling, young adult, and retired breeder mice are included in
the surveillance program.
The sick and injured animal program at The

Jackson Laboratory: technicians and
investigators partnering to maintain high
quality research
In our production colonies, any technician who
finds a sick or injured animal has the authority to
deal with it appropriately. But in a research colony,
an animal that looks or acts unusual may be
normal or valuable for the research. Thus, in our
research facilities, we have a formal program for
reporting sick and injured animals. Any technician
who observes an animal that is exhibiting an
abnormal phenotype that could indicate illness or
injury can initiate a process that, at a minimal level,
involves the investigator. If the investigator does
not respond within a specific time range
(depending on the observation, from 224 hours),
the technician has the authority to involve our
veterinary staff directly.
A different surveillance paradigm was developed for our

production colonies. In this system, mice from randomly
This program serves several important purposes: It
selected sample cages are pooled 10 to a cage for a total of 60
engages the technicians with the animals at a level
mice in six cages. The pooled mice are co-housed for six
above routine husbandry. It has a direct impact on
weeks, after which at least one mouse from every cage is sent
the well being of the animals. And, it has a direct
to our diagnostic laboratory for testing. If immunodeficient
effect on research, by providing a means of
mice are housed in the room, immunodeficient mice are pooled
identifying animals that might be inappropriate for
study, and by identifying unanticipated side effects
with immunocompetent mice. Only immunocompetent mice
of a treatment that researchers might initially miss.
are tested for viruses and other organisms that are detected
Our sick and injured animal program provides an
serologically, and only immunodeficient mice are tested for
effective example of how to utilize the unique
Pneumocystis murina. Both immunocompetent and
knowledge and experience of technicians to both
immunodeficient mice may be tested for all other organisms
improve the welfare of the mice and the quality of
(bacteria, parasites, and protozoa). At least one mouse from
the research.
each strain housed in the room is incorporated into the pooled
monitoring sample for that room at least twice per year
(quarterly in most cases). In addition to the pooled mice, we test 15 retired breeders for
serologic evidence of viral infection; this is done at every monitoring interval (quarterly or
monthly, depending on the room). Fecal samples are collected quarterly from animals in
approximately 10% of the cages in each of our maximum barrier rooms; these samples are
tested for excluded fecal bacteria, e.g., Pseudomonas, Proteus, or Klebsiella.
7.B.4. Our containment and eradication procedures

7.B.4.a. Our plan
Our containment and eradication plan is intended to prevent the further spread of a microbial
contaminant, eradicate the contaminant, and notify the public about the contamination. The plan
outlines the organization, facilities, and procedures used to protect employees, the public, and
the mice in the event of a microbial contamination. Specifically, the plan
describes actions to be taken in response to an outbreak,
establishes lines of authority for direction and coordination of activities during an outbreak,
and,
defines facilities, equipment, and communication pathways to be used during an outbreak.
The plan has four phases:
Phase 1, Confirmation: confirmation that a break has occurred, which requires confirmed
positive tests for the organism in question in at least two animals.
Phase 2, Lockdown: the initiation of containment, which involves
severe restrictions on the movement of animals, people, and materials within the institution,
special procedures to prevent the possible spread of the contaminant by air or water,
special procedures for personnel entry/exit, and
special procedures for handling of animals and materials within the room and after leaving
the room.
Notification of customers and other interested parties occurs early during the lockdown phase
and continues at frequent intervals until the contaminant is eliminated and shipping of
affected stocks resumes.
Phase 3, Elimination: ridding the contaminant from quarantined areas, either by depopulation
or test and cull. We select the method based on the organism in question and the degree of
spread within the room. Off-site housing is considered when valuable animals must be
relocated for completion of experiments or rederivation. Once mice are moved off-site, we
never return them to our campus.
Phase 4, Room redeployment: sanitization, disinfection, and monitoring, to assure elimination
of the contaminant from the room environment prior to restocking of the room or resumption
of shipping.
We hold at least four training exercises and drills every year. We update procedures when
necessary.
7.B.4.b. Additional details on containment and notification procedures

Actions taken upon confirmation of a contamination depend on the organism found, and in
some cases, on the location where it is found.
Many organisms are rigorously excluded from all facilities at The Jackson Laboratory and, if
found, would dictate immediate cessation of shipping and immediate notification of
customers. Specific actions taken upon confirmation of the contamination include the
following:
Immediately suspend shipment of mice involved in the contamination.
Implement the containment and eradication plan outlined above.
Update the ordering status for new orders to on hold.
Within two business days, send first class mail or a fax to institutions on the general JAX
Mice mailing list; post notification of the contamination on the health report for the
affected room on www.jax.org/jaxmice/health (and retain the posting for six months from
the date of notice).
Send additional information to our purchasing department, which will contact any
institution that received mice from this area within past three months.
Other organisms are rigorously excluded from only our production colonies. If any of these
organisms is found in a production colony, shipping would be stopped and customers notified
as described above.
Detection of these organisms in a research mouse room would trigger an investigation to find
and eliminate all infected animals. The findings would be noted on the health report for the
room, but research collaborations would not be stopped. It is the responsibility of the
individual researcher to notify collaborators of contamination in a research mouse room.
However, collaborators may request to be notified when a particular contaminant(s) is found
in a room from which they have received (or are scheduled to receive) mice. Researchers who
are interested in this option should contact Customer Service at 1-800-422-6423 (North
America) or 1-207-288-5845 (International). Or email us at [email protected].
Still other organisms are viewed as undesirable in most, but not all, facilities at The Jackson
Laboratory. If found in a room from which they are excluded, an investigation would be
undertaken to find and eliminate all infected animals. The findings would be noted on the
health report for the room, but shipping would not be stopped. If found in a room in which
they are currently tolerated, the finding would be noted on the health report for the room, but
no additional effort would be made to identify or eliminate infected animals and shipping
would not be stopped. Although we do not routinely notify customers of such contaminants, a
customer may request to be notified as described above.
For lists of specific organisms that correspond to the categories described above, visit our
website at www.jax.org/jaxmice/health.
7.B.5. Routine health reports

We update all health monitoring reports quarterly for all animal housing areas at The Jackson
Laboratory. When we ship JAX Mice, we include a printed copy of the health report from the
area of origin of the mice. The most current reports can be viewed at
www.jax.org/jaxmice/health.
7.C. References
Kuhn R, Lohler J, Rennick D, Rajewsky K, Muller W. 1993. Interleukin-10-deficient mice
develop chronic enterocolitis. Cell. 75:263274.
Kullberg MC, Ward JM, Gorelick PL, Caspar P, Hieny S, Cheever A, Jankovic D, Sher A.
1998. Helicobacter hepaticus triggers colitis in specific-pathogen-free interleukin-10 (IL-10)deficient mice through an IL-12- and gamma interferon-dependent mechanism. Infect Immun.
66:51275166.
Sellon RK, Tonkonogy S, Schultz M, Dieleman LA, Grenther W, Balish E, Rennick DM, Sartor
RB. 1998. Resident enteric bacteria are necessary for development of spontaneous colitis and
immune system activation in interleukin-10-deficient mice. Infect Immun. 66:52245231.
191
Chapter 8: Genetic Quality ControlPreventing

Genetic Contamination and Minimizing Genetic
Drift
Joanne M. Currer, Ray Vonder Haar, Dorcas Corrow, Kevin Flurkey
Whether you are a colony manager or researcher, you must be aware of the possibilities of
genetic contamination and genetic drift whenever you breed mice. How you manage each
concern has a direct effect on the genetic integrity of your mice and the reliability of your data.
In this chapter we highlight issues related to genetic contamination and genetic drift and explain
strategies we use at The Jackson Laboratory to prevent genetic contamination, minimize genetic
drift, and manage both.
8.A. Genetic contamination and genetic drift: what they are and how to manage them ... 192
8.A.1. Genetic contamination........................................................................................ 192
8.A.2. Genetic drift ........................................................................................................ 193
8.A.3. Identifying and managing events of genetic contamination and
genetic drift ......................................................................................................... 194
8.B. What we do at The Jackson Laboratory ....................................................................... 195
8.B.1. Our mouse colony structure: how it helps us maintain genetic quality
control.................................................................................................................. 195
8.B.2. Our genetic integrity programs .......................................................................... 197
8.B.2.a. Our Genetic Quality Control Program ............................................... 197
8.B.2.b. Our Genetic Stability Program ........................................................... 199
8.B.2.c. Summary of our programs .................................................................. 199
8.C. References ...................................................................................................................... 200
Acknowledgments: We would like to thank Laura Frye, Cathy Lutz, Rachel Malcolm, and
Laura Trepanier for their valuable input to this chapter.
8.A. Genetic contamination and genetic drift: what they

are and how to manage them
8.A.1. Genetic contamination
Genetic contamination is the accidental introduction of alleles from one mouse strain into the
genome of a second strain. Genetic contamination occurs quickly. It is probably the greatest
source of uncontrolled genetic variation in a research colony. It is due mostly to human errors
such as inadvertent outcrossing or mislabling of animals. As serious as genetic contamination is,
however, with commitment to proper precautions and procedures, it is relatively straightforward
to minimize, detect, and quickly eradicate.
8.A.1.a. Examples of genetic contamination

Following are three examples that illustrate the consequences of genetic contamination:
The inadvertent outcrossing of C57BL/6J (000664) to DBA/2, and probably to BTBR,
resulted in the C57BLKS strain (Petkov et al., 2004b), which dramatically changed the
carbohydrate metabolism in the animals, making them more susceptible to induction of
diabetes (Naggert et al., 1995).
Multiple accidental outcrossings of the 129 strain has complicated ES cell research (Simpson
et al., 1997; Threadgill et al., 1997).
Genetic contamination (affecting several chromosomes) with either FVB or an FVB-like
strain in two NIA contract colonies of C57BL/6 mice required destruction of the colonies
(www.nia.nih.gov/ResearchInformation/ScientificResources, 4/5, 2002; National Institute on
Aging, National Institutes of Health, 7201 Wisconsin Ave., GW 2C231, Bethesda, MD
20892; 301-496-0181).
8.A.1.b. Preventing genetic contamination

The most effective way to prevent genetic contamination is for all technicians and researchers to
be observant and diligent with their recordkeeping and animal care, and to develop breeding
strategies that minimize the possibility of errors that could lead to the mating of incorrect
animals. Precautions include the following:
If you must house multiple strains within a colony, ensure that strains housed adjacently are
as phenotypically and genotypically different as possible, to increase the probability that
contamination can be readily detected.
Adopt breeding strategies that make it easy to identify a desirable or undesirable genotype via
an observable phenotype such as coat color.
Maintain diligent breeding records; use complete, established nomenclature; vary the color of
cage cards among strains.
Practice animal handling techniques that reduce the chances of an escaped mouse. For
example, whenever lifting a cage top, check for mice that might be clinging to it. Return the
mice immediately to the cage. Never have two cages open at the same time on the same table.
This is especially critical with duplex caging.
Capture every escaped mouse as soon as possible. Mice can mate across a wire cage barrier
surprisingly easily, so you must prevent any escaped mouse from taking advantage of this
opportunity. When you capture an escaped mouse, euthanize it immediately.
Cryopreserve strains as a backup.
Chapter 8: Genetic Quality Control 193
8.A.2. Genetic drift

Genetic drift is caused by spontaneous mutations that become fixed in a line. Genetic drift
occurs slowly, subtly and surely. It is difficult to detect and control. If you breed mice, it will
occur. It is so relentless that after 10 generations, a strain of mice is likely to have undergone
some permanent genetic change. Genetic drift in isolated populations is a major cause of
inadvertent substrain creation. (For a discussion about genetic drift and the role it plays in
creation of substrains, see 3.B.1.d.2, Genetic drift.)
8.A.2.a. Examples of genetic drift

Following are examples of progressive genetic change that resulted from genetic drift:
At least 40 C57BL substrains developed between 1930 and 1970. Although some substrains
resulted from deliberate outcrossing, most originated as a result of genetic drift, because the
subcolonies were maintained separately from the originating
colony (Bailey, 1978).
Genetic drift and residual heterozygosity from
Histocompatibility variants have been discovered within
a quality control perspective
numerous inbred strain families: A, AKR, BALB/c, CBA,
When inbreeding to create an inbred strain
begins, the proportion of loci that are polymorphic
C3H, C57BL, C57L, DBA, and WG strains (Bailey, 1982).
(i.e., the residual heterozygosity) may be as high
A mutation of the nicotinamide nucleotide transhydrogenase
as 30% (Bailey, 1978). In inbred strains, this
gene (Nnt) was fixed in the C57BL/6J (000664) foundation
residual heterozygosity is a potential source of
genetic variation over time. It may take as many
stock sometime after 1975. The mutation is not found in
as 60 generations of sisterbrother mating before
C57BL/6 substrains that were separated from the C57BL/6J
one can be 99% certain that the level of residual
line before 1975 (Freeman et al., 2006). While this mutation
heterozygosity has diminished to the point where
may alter the initial !-cell secretion of insulin in response to
extinction of polymorphic alleles is balanced by
glucose, it does not influence the steady-state clearance of
the appearance of new alleles due to genetic drift
(i.e., to the point where heterozygosity in the
glucose (Berglund et al., 2008) or the development of
strain is at a minimal steady-state level).
impaired glucose tolerance in diet-induced obesity models
While colony managers normally do not concern

(JAX Services, 2008). Further details are given in the sidebar
themselves with residual heterozygosity in their
on the next page.
8.A.2.b. Minimizing the effect of genetic drift

The most effective way to minimize the impact of genetic drift is
to periodically replenish breeders with new breeding stock from
your supplier rather than breeding your own mice. This one
action virtually eliminates any divergence from the standardized
stock.
inbred mice, the strategy used to minimize effects

of genetic driftstrict sisterbrother matingalso
maximizes the rate at which residual
heterozygosity is eliminated. This breeding
strategy maximizes the rate of extinction and of
fixation of polymorphic alleles, whether they arose
spontaneously in a subline or were carried over
from the parental line. Other breeding strategies
will result not only in a slower elimination of
residual heterozygosity, but also in maintenance
of a greater, and potentially fluctuating, number of
heterozygous loci in the strain.
Keep in mind that no inbred strain is 100 percent homozygous:

A level of heterozygosity will always exist due to spontaneous
mutations. Although you can do nothing about the rate of the
occurrence of spontaneous mutations, you can affect the steady-state level of heterozygosity by
your choice of breeding strategies. To maximize the extinction rate of new mutations, use strict
sisterbrother mating in a single foundation lineage. (Note that sisterbrother mating also
maximizes the fixation rate of new mutations.) As a consequence, sisterbrother mating has
another effect: it minimizes the steady-state level of heterozygosity.
A recently developed strategy to minimize genetic drift itself is to cryopreserve a large stock of
embryos from the same generation and periodically replenish breeders from that frozen stock.
This approach, which greatly lengthens effective generation time, is the only breeding strategy
that actually retards genetic drift within an inbred strain. (For a specific example of how this
strategy is used at The Jackson Laboratory, see 8.B.2.b, Our Genetic Stability Program.)
8.A.3. Identifying and managing events of genetic contamination

and genetic drift
8.A.3.a. Identifying an event
Because genetic contamination involves large portions of multiple chromosomes, it is relatively
easy to directly identify. In contrast, identifying genetic drift is extremely difficult. Typically,
genetic drift is assumed to be the cause when a heritable deviant phenotype in an inbred strain
cannot be explained by contamination.
The most effective way to identify genetic
An example of the difficulty in positively
contamination is through a program of regular
confirming genetic drift.
genetic monitoring. Often, screening is done using
Confirmation of a specific instance of genetic drift
in C57BL/6J (B6J; 000664) mice illustrates the
markers for as few as half the chromosomes.
laborious process required to unambiguously
Intuitively, this may seem insufficient; however,
identify the genetic basis for a deviant phenotype
within the first few generations following a
that results from genetic drift.
contamination event, most chromosome pairs will
Cox and colleagues (Toye et al., 2005; Freeman
be affected. Therefore, discovery of just two or
et al., 2006), observed that B6J mice cleared
more aberrant chromosomes is sufficient evidence
injected glucose more slowly than mice of other
to indicate that a contamination event occurred.
standard laboratory strains. These researchers
used an F2 hybrid cross between B6J and
Subsequently, more complete genotyping for
C3H/HeH mice to map a locuson Chr 13that
selected mice should be carried out to confirm and
was associated with slower glucose clearance.
characterize the contamination.
They sequenced a candidate gene, nicotinamide
nucleotide transhydrogenase (Nnt), at that locus
An additional strategy is to monitor for observable
and identified a 5-exon deletion in the B6J Nnt
phenotypes that are not characteristic of a strain
gene.
and for any unexpected or idiosyncratic research
Analysis of the Nnt gene in other strains, including
results. Following observation of a deviant
closely related C57BL/6 substrains, indicated that
phenotype, determine if the phenotype has
the mutation exists only in the B6J strain, and that
appeared in other mice, particularly in mice that
it arose at The Jackson Laboratory sometime
are directly related to the deviant. In addition, set
after 1975. Because glucose tolerance in B6J
mice is within the normal range, as indicated by
up appropriate breeders to determine if the
hypoglycemic, euglycemic, and hyperglycemic
phenotype is heritable. Confirm any suspected
glucose clamp studies (Berglund et al., 2008), the
contamination by genotyping. For a heritable
altered phenotype is the relatively diminished
deviant phenotype that newly appears in an
glucose stimulation of early phase insulin
established inbred strain (filial generation > 60), if
secretion from pancreatic islets, and not impaired
glucose tolerance as claimed by Freeman et al.
genotyping does not indicate that contamination
(JAX Services, 2008).

occurred, it is probable that the phenotype is a
To unequivocally identify this mutation as the
result of genetic drift.
cause of the altered phenotype, Freeman et al.
Because the vast majority of genetic drift events
(2006) created a transgenic for a normal Nnt gene
will not be identified, a secondary tactic is to
on the B6J background. Clearance of injected
glucose in the B6J transgenic was comparable to
minimize the effect of genetic drift on
that of C3H/HeH mice, demonstrating that the Nnt
heterogeneity. This is done through strict
deletion in B6J mice could account entirely for the
adherence to sisterbrother mating.
altered phenotype. These results illustrate the
8.A.3.b. Managing an event
considerable effort necessary to identify genetic

drift as the cause of a new phenotype.
With either genetic contamination or genetic drift,

your goals are to identify the responsible breeders,
cull the colony to eradicate the contamination, and take action to prevent another occurrence.
Also, you must notify any users of the mice about the contamination.
8.B. What we do at The Jackson Laboratory

At The Jackson Laboratory, we ensure the genetic integrity of all JAX Mice at both our Maine
and California facilities with protocols that are the result of 75 years of experience in the areas
of mouse husbandry, mammalian genetics, and assay development. The success of our programs
relies on our rigorous standards as well as our skilled animal caretakers and technicians, who are
well trained in basic genetics and deviant recognition.
Following are overviews of the colony structure and genetic quality control processes we
employ at The Jackson Laboratory, including overviews of the two programs we have
developed to ensure the genetic integrity of JAX Miceour Genetic Quality Control Program
and Genetic Stability Program. We regularly upgrade our procedures to stay abreast of the latest
technologies and advances in mouse biology. For current program details, visit
www.jax.org/jaxmice/geneticquality.
8.B.1. Our mouse colony structure: how it helps us maintain

genetic quality control
At The Jackson Laboratory, we maintain more than 4,000 strains of inbred mice that we
distribute to researchers throughout the world. We have organized our mouse coloniesand the
procedures we use to manage themto meet the varying levels of demand for these mice while
adhering to strict genetic quality control guidelines. Figure 8.1 provides an overview of this
colony structure.
Figure 8.1. Our mouse colony structure at The Jackson Laboratory.
8.B.1.a. Our production colonies

The purpose of our production colonies at The Jackson Laboratory is to maintain pedigreed
stocks of our most popular inbred strains of JAX Mice and to efficiently breed large quantities
of these strains for distribution to researchers. To maximize genetic consistency while
minimizing effects of genetic drift, we maintain and expand these stocks using a three-tiered
structure of isolated coloniesfoundation stocks, pedigreed expansion stocks, and production
stocks (Figure 8.1). This structure allows us to track individual animals and their ancestral
relationships. It also enables our colony managers to unambiguously identify and remove from
the breeding pool any mice thought to carry a genetic change that could compromise the genetic
integrity of that inbred strain.
8.B.1.a.1. Foundation stocks (FSs)

Our foundation stocks (FSs) of JAX Mice are maintained by pedigreed sisterbrother breeding
pairs. Currently, we maintain foundation stocks for about 175 of our most popular strains.
Normally, we maintain just one family per strain of JAX Mice in an FS, with a single, parental,
sisterbrother breeding pair per generation. However, for strains with very high demand, we
may maintain two families. We never cross these families, however, and we maintain them so
that they are never more than 10 generations away from a single sisterbrother breeding pair.
This strategy prevents inadvertent development of substrains.
We cryopreserve embryos from foundation stocks to provide a source for rederivation should
the stock be lost due to a disaster.
8.B.1.a.2. Pedigreed expansion stocks (PESs)

Our pedigreed expansion stocks (PESs) include pedigreed sisterbrother breeding pairs from
our foundation stocks. The purpose of our PES colonies is to expand the foundation stock to
create breeders for the production stock. Sometimes, for more rapid expansion, we use sibling
trio mating (two sisters, one brother), which we define as PED expansion. To minimize genetic
drift, we ensure that mice in a PES are never more than five generations removed from their
founding FS breeding pair.
8.B.1.a.3. Production stocks (PSs)

Our production stocks (PSs) comprise breeding pairs from the PES colonies and their
offspringthe mice that we distribute to researchers throughout the world. We use either sister
brother breeding pairs from the PES or pooled breeders from a group of PES and PED litters.
(We call these mice our Pooled Production Stocks [PPSs].) Regardless of the expansion method,
we never exceed two generations in a PS. Thus, mice distributed from a PS are never more than
seven generations removed from a single FS sisterbrother breeding pair.
8.B.1.b. Our Repository

Most strains of JAX Mice are maintained in our live repository. These mice include standard
inbred strains that are in low demand, almost all of our mutant and genetically engineered mice,
and all new mice that have been recently imported into The Jackson Laboratory. We currently
manage more than 1,500 strains of JAX Mice in our live repository. For the past several years,
we have been introducing new strains of mice into this repository at a rate of 200300 per year.
We cryopreserve embryos for each strain of mice in the live repository.
All JAX Mice in our live repository are maintained as pedigreed foundation stocks. We
maintain each stock with strict sisterbrother mating and expand the stock for distribution on
demand. Any mice we ship will never be more than two generations removed from the
foundation stock.
We maintain stocks in our live repository unless demand is high enough to warrant a move to
the production colonies or low enough so that we maintain the stock only as cryopreserved ova,
sperm, or embryos in our cryopreservation storage facility.
8.B.1.c. Cryopreserved stocks: embryos, ova and sperm

We maintain supplies of frozen embryos, ova, and sperm in our cryopreservation facilities both
on and off campus (at a backup facility). This inventory has two main purposes: (1) as a
resource from which to recover any strain maintained by The Jackson Laboratory if, for some
reason, the live strain is lost; and, (2) as a way of preserving strains with a very low demand,
which are not maintained as live mice. From our cryopreservation repository, we ship frozen
material directly to researchers. Or, we recover frozen material and generate live mice for
shipment.
8.B.1.d. Research colonies

Research colonies are bred and maintained by individual faculty
members for their research programs. These mice are physically
and administratively separate from our production and
repository colonies. These mice are not JAX Mice and are
available to collaborators only through direct contact with the
faculty member who maintains them.
Mice from research colonies are subject to our lab-wide animal
health policies (see Chapter 7, Animal Health: Preventing,
Identifying, and Eradicating Microbial Contamination);
however, due to the nature of their maintenance and use, they
are not subject to the institutional policies for genetic quality
control that apply to JAX Mice.
From a quality control perspective, does it
really matter whether JAX Mice come from

our production or repository colonies?
The level of demand determines whether a strain
of JAX Mice is maintained and bred in

production colonies or repository colonies. In our
production facilities, we maintain and breed large
quantities of popular strains of mice. In our
repository colonies, we maintain a greater number
of strains with smaller demand. We move strains
from one type of colony to the other when
demand warrants a change in maintenance and
breeding strategies. Researchers can be assured
that, regardless of where a strain of JAX Mice is

maintained, our quality control standards and
practices are consistently stringent.
8.B.2. Our genetic integrity programs
For information on where a strain of JAX Mice is

maintained, please refer to its strain datasheet,
available at www.jax.org/jaxmice/query.
At The Jackson Laboratory, we have developed and documented

precise protocols for genetic quality controlour Genetic
Quality Control (GQC) Program and our Genetic Stability Program (GSP).
8.B.2.a. Our Genetic Quality Control (GQC) Program

At the core of our quality control effort is specific animal husbandry practices designed to
prevent genetic contamination and minimize the effects of genetic drift.
8.B.2.a.1. Preventing genetic contamination and minimizing genetic drift

At The Jackson Laboratory, we follow the procedures outlined in 8.A.1.b, Preventing genetic
contamination. In addition, because of the numbers of strains and mice we must accommodate,
our rigorous breeding protocols also include the following:
We isolate foundation, expansion, and production stocks from each other.
We keep thorough breeding records in accordance with our detailed pedigree numbering
SOPs (See 11.A.2.b, Our pedigree numbering system for JAX Mice.)
Wherever possible, we limit the number of generations attained in our expansion stocks so
that they are never more than seven generations from the main pedigree line.
8.B.2.a.2. Monitoring for genetic contamination

Regularly scheduled SNP genotyping
At The Jackson Laboratory we use single nucleotide polymorphisms (SNPs) as our major
genotyping tool. With a panel of just 27 SNPs, we can cover all 19 autosomes and Chr X
(Petkov et al., 2004a; 2004b) and differentiate most standard strains of JAX Mice from each
other. Through the use of this panel, when we identify a contamination event, we can usually
immediately determine the contaminating strain.
Production colonies:
The vast majority of the JAX Mice we distribute to researchers are bred in our production
colonies. Because of the scale of the expansion process and the exactness required, we have
developed and documented precise protocols for genetic quality control.
Currently, we conduct routine SNP genotyping in our colonies of JAX Mice on the following
schedule:
Pedigreed foundation stocks: We genotype every new breeder pair when we set them up.
Pedigreed expansion stocks: Every 6 months, we genotype six new breeders of our most
popular 100 strains. For all other PES stocks, we genotype four mice annually.
Production stocks: Every six months, we genotype six mice of our most popular 100 strains.
For all other production stocks, we genotype four mice annually. Additionally, for certain
mutant strains, we also monitor mice for the heritability and expression of the phenotype and,
when a genotype assay exists for the mutation, for the presence of the mutant allele.
Repository colonies:
Our repository colonies require a quality control strategy with a slightly different focus. Because
the majority of strains are specific mutant strains, we must validate that the mutation is
propagated and that it still produces the associated phenotype:
When new mice arrive in a repository colony, we characterize the genetic background of each
using the 27-SNP genotyping panel.
We characterize all new mutant or genetically engineered mice for the presence of the mutant
allele using a specific genotyping assay.
For each mutant strain in the live repository, we evaluate every sisterbrother breeding pair in
the foundation stock for the presence of the mutant allele. Similarly, we type mutant stocks
that we recover from the cryo repository for the presence of the mutant allele.
Once a year, we evaluate each strain for possible contamination using the 27-SNP genotyping
panel.
Periodically, we verify expected phenotypes in selected genetically engineered and mutant
mice.
Continual monitoring by technicians: all colonies
Our technicians are trained to be on high alert for any signs of genetic contamination.
Phenotypes of interest include any variation in coat color, body size, weight, skeletal structure,
behavior, reproductive performance, and occurrence of tumors. If technicians find unexpected
traits, they set the mice aside for further investigation.
Upon suspicion of contamination, we troubleshoot to identify the problem. We use SNPs to test
the animals to see if the deviant phenotype resulted from genetic contamination. If SNP markers
show that the deviant mouse has the correct genetic background profile, we mate it to determine
whether the phenotype is genetically transmitted. If the trait is heritable and is not a result of
contamination, we assume the deviant phenotype is a result of genetic drift.
8.B.2.a.3. Managing a genetic contamination event

If we confirm any genetic contamination, it is our strict policy to notify anyone who purchased
the mice as quickly as possible and to cull the colony as appropriate. Then we re-establish the
colony, genotyping new mice to ensure their genetic integrity.
8.B.2.b. Our Genetic Stability Program

We have initiated a Genetic Stability Program to minimize genetic drift in important foundation
stocks of JAX Mice by using cryopreservation. For each foundation stock in the program we
freeze enough embryos from a single generation to last 1025 years. Every five generations, we
re-establish foundation stocks from the frozen embryos.
Our program functionally extends the length of a single generation to between 10 and 25
years. The result is that, within a 100-year period, a foundation stock will advance no more than
410 generations. This is in contrast to even the best colony management production practices,
which result in about 3 generations per yearabout 300 generations over a 100-year period.
This effectively retards the rate of genetic drift by 20- to 50-fold.
We initiated our Genetic Stability Program with our most important strains of JAX Mice, and
we continue to add additional strains on a regular basis. To learn which strains are currently in
the program, visit www.jax.org/jaxmice/geneticquality/stability.
8.B.2.c. Summary of our programs

Figure 8.2 illustrates how our genetic integrity programs relate to our production breeding
colonies.
Figure 8.2. Steps we take to prevent genetic contamination and minimize genetic drift in
our production colonies at The Jackson Laboratory.
8.C. References
Bailey DW. 1982. How pure are inbred strains of mice? Immunol. Today. 3:210214.
Freeman HC, Hugill A, Dear NT, Ashcroft FM, Cox RD. 2006. Deletion of nicotinamide
nucleotide transhydrogenase: a new quantitative trait locus accounting for glucose intolerance in
C57BL/6J mice. Diabetes. 55:21532156.
JAX Services. 2008. Does a mutant NAD nucleotide transhydrogenase (Nnt) gene in
C57BL/6J impair responsiveness to diet-induced obesity? The Jackson Laboratory website:
www.jax.org/jaxmice/request/nntpaper (accessed October 2008).
Naggert JK, Mu JL, Frankel W, Bailey DW, Paigen B. 1995. Genomic analysis of the
C57BL/Ks mouse strain. Mamm Genome. 6:131133.
Petkov PM, Cassell MA, Sargent EE, Donnelly CJ, Robinson P, Crew V, Asquith S, Harr RV,
Wiles MV. 2004a. Development of a SNP genotyping panel for genetic monitoring of the
laboratory mouse. Genomics. 83:90211.
Johnson KA, Robinson P, et al. 2004b. An Efficient SNP System for Mouse Genome Scanning
and Elucidating Strain Relationships. Genome Res. 14:18061811.
16:1927.
Threadgill DW, Yee D, Matin A, Nadeau J, Magnuson T. 1997. Genealogy of the 129 inbred
strains: 129SvJ is a contaminated inbred strain. Mamm Genome. 8:390393.
Toye AA, Lippiat JD, Proks P, Shimomura K, Bentley L, Hugill A, Mijat V, Goldsworthy M,
Moir L, Haynes A, et al. 2005. A genetic and physiological study of impaired glucose
homeostasis control in C57BL/6J mice. Diabetologia. 48:675686.
201
Chapter 9: Animal Husbandry

Joanne M. Currer, Dorcas Corrow, Kevin Flurkey
Animal husbandry involves the physical setup of mouse colonies and the regular activities that
keep them running smoothly. Some requirements are federally mandated. Others are specific to
your institution and often represent the implementation of your animal health and genetic
quality control programs. Some husbandry tasks are simple and repetitive, but this does not
imply that they are easy to do well. They often involve adherence to meticulous standards under
demanding time constraints. Their objectives are clear: to provide a calm, comfortable
environment for your animals so they remain healthy and as free from stress as possible.
Our objective in this chapter is to provide guidelines related directly to the housing and daily
care of your animals. We also explain what we do at The Jackson Laboratory, which provides
you with critical information about the conditions under which your JAX Mice were raised.
It is important to note that, at The Jackson Laboratory, we continually evaluate our choices in
colony management and animal care by (1) adhering to current criteria specified by the National
Research Council (NRC), the Association for Assessment and Accreditation of Laboratory
Animal Care (AAALAC), and the American Association for Laboratory Animal Science
(AALAS); (2) maintaining our certification with AAALAC and AALAS; (3) monitoring
relevant research publications; and (4) listening to and working with our technicians, who
provide a pragmatic perspective on animal care.
9.A. Physical aspects of a mouse room..........................................................................202
9.A.1. Caging.......................................................................................................202
9.A.2. Water delivery .........................................................................................204
9.A.3. Room environment...................................................................................205
9.A.4. Cage bedding............................................................................................206
9.B. Day-to-day care .......................................................................................................207
9.B.1. Mouse room entry and exit procedures; traffic patterns within
and among mouse rooms .........................................................................207
9.B.2. Changing cages ........................................................................................208
9.B.3. Providing food and water ........................................................................209
9.B.4. Keeping mouse rooms clean....................................................................210
9.B.5. Minimizing genetic contamination .........................................................210
9.C. Other issues related to animal husbandry ..............................................................211
9.C.1. Providing environmental enrichment to alleviate stress........................211
9.C.2. Managing agression in a colony..............................................................212
9.C.3. Caring for wild-derived inbred mice ......................................................213
9.D. Sources of information regarding animal care ......................................................214
9.E. References ...............................................................................................................215
9.A. Physical aspects of a mouse room

9.A.1. Caging
Besides providing a method of mouse room organization and feeding and watering, caging
systems also protect the mice from pathogens and determine the ease of access to the mice for
technicians and researchers. The choice of caging system involves tradeoffs among cost,
convenience, and effectiveness.
9.A.1.a. Types of caging systems

Table 9.1 briefly describes the characteristics of three common types of caging systems, their
advantages, and their disadvantages.
Table 9.1. Summary of common types of mouse cages and shelving.
System and description
Advantages
Disadvantages
Conventional cages and shelving:

Boxes sit on, or fit into, open metal
shelves.
Boxes have wire lids that can contain
bins for food and water bottles; lids
may or may not have covers.
Air circulation in cages is determined
by room circulation and by air flow
caused by the thermal heat load of the
mice (Reeb et al., (1997).
Is least expensive.
Allows easy access to mice.
Allows cage changing and any
work with mice on open tables.
Even with filter covers, provides lowest

level of pathogen protection.
With filter covers, poor air circulation
can affect intra-cage temperature,
ammonia levels, humidity.
Requires more frequent cage changing
than other systems.
Microisolator cages and conventional

shelving:
Similar to conventional systems, except
individual boxes have covers
containing high efficiency particulate
air (HEPA) filters
Is a cost-effective, flexible way to

provide higher level of pathogen
protection than elsewhere in a
mouse room.
To maintain higher level of pathogen

protection, cage changing and any work
with mice must be done in HEPAfiltered hood.
Air circulation may be poor, usually
worse than conventional cages and
shelving.
May require more frequent cage
changing.
Ventilated, HEPA-filtered caging

systems, with heating, ventilation and
cooling (HVAC) functionality:
Boxes fit snugly into closed, forced
ventilated shelving system.
Provides highest possible pathogen

protection for the mice and
allergen protection for the
technicians.
Provides good air exchange.
Cages remain dry, which may
reduce cage change frequency and
labor expense.
Requires capital expense.

Cage changing and any work with mice
must be done in HEPA-filtered hoods.
Ventilation can result in drafts within
the cages, which might stress some
mice.
Portable ventilated caging systems:

Similar to stationary ventilated units,
but
- boxes fit into standalone units on
wheels, and
- incoming air is filtered room air;
exhaust is filtered back into the room.
Provides flexible solution for

pathogen protection.
Works well for light mouse loads.
Cages remain dry, which may
reduce cage change frequency and
labor expense.
Cages can be pushed together for
floor space economy without
inhibiting air circulation for
animals.
Numerous portable racks can increase

the heat load in the room. An option is
to modify rack ventilation so it is
exhausted outside the room.
Note: Caging made of polyphenyl-sulfone or other chemically resistant material is highly recommended if there is any
possibility of exposure to quaternary ammonium cleaners or other high pH agents (Koehler et al., 2003).
Chapter 9: Animal Husbandry 203
9.A.1.b. Cage space requirements for mice

The NRC height requirement for
laboratory mouse cages is 12.7 cm (5
inches). Table 9.2 provides the
specifications for floor space requirements
for mice of a specific weight. When caging
mice of different sizes, the floor space
requirements for the largest mouse is
assigned to all mice in the cage.
9.A.1.c. What we do at The

Jackson Laboratory
Throughout The Jackson Laboratory, we
use all four types of caging systems.
Table 9.2. Requirements for floor area for

laboratory mice; cage at least 5 inches high.
Weight (g) of the
heaviest mouse in
the cage
Floor area per mouse

(sq. cm)
(square in.)
< 10
38.7
1015
51.6
1525
77.4
> 25
> 96.75
12
> 15
National Research Council (1996), Guide for the Care

and Use of Laboratory Animals, p. 27.
In almost all of our production rooms, we use ventilated caging systems that provide heating,
ventilation, and cooling (HVAC) functionality, with 99.97% high efficiency particulate air
(HEPA) filtering, directly to the cages. Air circulation within each room is provided by a
separate, networked HVAC system. We conduct all cage changing and procedures within
HEPA-filtered changing stations.
In some of our production rooms, and in a majority of our research colonies, we use
conventional, double shoebox caging systems with polycarbonate or polyphthalate carbonate
boxes with overall dimensions of 28 cm x 27 cm x 13 cm deep; individual units (pens) are 28 x
13 x 13 cm. Weaning cages, which are used to house segregated groups of male and female
mice after weaning and before pairing, are 28 x 28 x 13 cm. Cage lids made of heavy wire
contain bins for food and water bottles. Cages are topped with a snug fitting filter hood made of
non-woven ramie fabric attached to a plastic frame. Air circulation within each room is
provided by a networked HVAC system.
In some research colonies in which we use standard caging systems, we also use microisolater
cages for mice that are immunologically compromised.
9.A.2. Water delivery

9.A.2.a. Types of water delivery systems
Two basic types of watering systems are commonly available for laboratory mouse cages:
automatic and bottle-based. A third type, less commonly used, incorporates plastic bags. Some
caging systems may require a specific type. Table 9.3 provides an overview of these systems.
Table 9.3. Summary of types of water delivery systems.
Advantages
Disadvantages
Automatic
Type of system
Individual cages will

never run low on water.
No sterilization of water
bottles and lids is required.
It requires a capital expense.

System must be maintained (per
manufacturers instructions) to prevent
buildup of mold and bacteria.
Some mice may need training to learn
how to use an automatic system.
It is difficult to determine water usage
for specific cages.
Leakage in some systems may cause
mice to drown if cages fill with water.
Cages must be checked daily for
evidence of water leakage.
Glass or plastic bottles in

following configurations:
Rubber stopper with sipper
tube.
Solid stopper or solid lid
with gasket; hole in bottle to
provide water.
Metal lid with gasket;
sipper hole in the middle
of the cap.
Water usage per cage can

be easily monitored.
Sterilization of bottles and
lids is very
straightforward; pathogen
protection is high.
Treatments can be easily
provided in the water on a
cage-specific basis.
Individual bottles and lids must go

through sterilization process.
Technicians must deal with individual
bottles when changing cages; if sipper
tubes are used, they must check for air
bubbles.
If lids or gaskets are broken or not
seated properly, water can leak. Even
small leaks can dampen bedding enough
to cause hypothermia.
Bottles must be checked daily for leaks
and to ensure adequate water supply.
Cages must be checked daily for
evidence of water leakage.
Plastic bags filled with water:

Plastic bag punctured with a
sipper stem and encased in a
mouse proof holder.
Water can be stored long

term, treated or untreated.
Disposable bags eliminate
labor and expense to wash
and process bottles.
Bags can be sterilized
separately and then filled
behind the barrier.
Viable option for
emergency planning.
It requires a capital expense for new

equipment, new technology.
Governmental or institutional policies
may require incineration of disposed
bags.
9.A.2.b. What we do at The Jackson Laboratory

At The Jackson Laboratory, we provide water to almost all mice in plastic water bottles capped
by metal lids with small sipper holes. We have found that leakage is less likely with these lids
compared to lids with sipper tubes and bottles with drip holes.
9.A.3. Room environment

Criteria for the room environmenttemperature, humidity, air flow, light and noise, for
exampleare specified by the National Research Council (NRC) and the American Association
for Laboratory Animal Science (AALAS). Table 9.4 highlights these requirements.
Table 9.4. Environmental parameters for mouse rooms (NRA or AALAS requirements);
what we do at The Jackson Laboratory.
Parameter
NRC or AALAS requirements

Requirement
Temperature
17.826.1 C
(6479 F)
Relative
humidity
3070%
Air flow
1015 room air

changes per hour
Light period
Comments
AALAS recommends 21.1

24.4 C (7076 F); optimal
temperatures are higher for
some mice (such as
hypothyroid mice).
What we do at The Jackson Laboratory

Requirement
Comments
18.921.1 C
(6670 F)
Measured in common air

exhaust duct as air exits
mouse room.
Monitored by alarm system.
45% 15%
(Engineering notified
when humidity
exceeds 70%.)
Measured in common air

exhaust duct as air exits
mouse room.
Monitored by alarm system.
AALAS has less specific

ventilation requirements that
are performance based rather
than quantitative (such as air
change per hour). They
consider air quality from the
perspective of both the
general room and cages.
Conventional
caging: 1518
room air changes
per hour
Fixed ventilated
systems: up to 60
cage air changes
per hour
Air is 100% HEPA-filtered.

For fixed ventilated caging
systems, because separate
systems provide cage and
room ventilation, sharing of
air by mice and caretakers is
minimized.
Rooms are positive
pressured.
Normal:12:12 L:D
Breeding: 14:10
L:D
AALAS specifications
Normal:14:10 L:D
Alternate: 12:12 L:D
A longer light cycle is used

because it may promote
breeding.
Light
intensity
130325 lux (cage

level)
AALAS specification
(Mice prefer low light
levels.)
! 323 lux (30 foot

candles), fluorescent
30 foot candles at 1 meter

above the floor is standard
for worker safety and
productivity. Otherwise,
AALAS requirements are
followed.
Noise
2540 decibels
acoustic (dBA)
AALAS specification;
recognized as relatively
quiet environment.
65 dBA
We strive to limit maximum

facility-related noise to no
more than 85 dBA. (Typical
noise levels in active animal
rooms are 65 dBA. )
Levels above 95 dBA may
induce seizures in certain
mice.
Our environmental monitoring systems are monitored 24 hours per day, 365 days per year by
The Jackson Laboratory security staff, which contacts the Facilities Operations staff, also on
call on the same schedule, whenever alarm limits are exceeded. All production and research
animal room systems are backed up by diesel-fired emergency/standby generators that turn on
automatically when they detect a power outage.
9.A.4. Cage bedding

9.A.4.a. Choices of bedding
Bedding has two obvious purposes: providing warmth and absorbing moisture. Bedding affects
the bacterial microenvironment and thus affects the rate at which bacteria break down urea to
produce ammonia in the cage. Bedding also provides environmental enrichment. Unfortunately,
no bedding material is perfect, so your choice depends on the needs of your specific mice and
colony. Table 9.6 provides advantages and disadvantages of the most used types of bedding.
Table 9.6. Advantages and disadvantages of common types of bedding for mice.
Type of bedding
Advantages
Disadvantages
Hardwood
shavings
Are cost effective.

Are physiologically inert; do
not elevate cytochrome p450
(Cunliffe-Beamer et al.,
1981; Weichbrod et al.,
1988).
May be dusty and irritating.

Is not as absorbent as other materials.
May be from an environment in which
chemicals were used.
Softwood shavings
(cedar, pine)
Are cost effective.
Same as for hardwood shavings, plus

Cedar and pine can be dusty and irritating.
Cedar, in particular, elevates expression of
hepatic p450 enzyme systems (Wade et al.,
1968).
Fractions or pellets
of corn cob
Are non-irritating.
Are physiologically inert; do
not elevate cytochrome p450
(Pick & Little, 1965).
Is moderately expensive.
Is not good for nesting; additional nesting
material may be required.
May be prone to mold.
Is less absorbent than other bedding.
Recycled paper,
cellulose chips
(alpha cellulose)
Provides superior absorbency

and ammonia control.
Is moderately expensive.
Can be dusty.
Fibers may be irritating to certain strains (e.g.,
nude or SKH-1) that have no eyelashes
(White, 2007).
Cotton-based
material
Is highly absorbent.
Is good for ammonia control
when shredded.
Is expensive.
Is effective against odors only if shredded
(some strains do not shred it.)
Fibers may entangle infant limbs and cut off
circulation.
9.A.4.b. What we do at The Jackson Laboratory

At The Jackson Laboratory, we use a dispenser to add autoclaved bedding to sanitized cages at a
depth of 1626 mm before cages are delivered to mouse rooms. We provide additional bedding
and non-woven cotton fiber (such as Nestlets) when necessaryfor breeding mice or when we
must single-house mice, for example. We use various types of bedding for our mice, and we
continually monitor research on bedding. For information about bedding used for specific
strains of JAX Mice, contact Customer Service at 1-800-422-6423 (North America) or 1-207288-5845 (International).
9.B. Day-to-day care

Day-to-day care for your animals involves several major efforts: to protect the animals from
pathogens, to keep them well fed and watered, and to maintain their genetic integrity.
Never forget that pathogen protection is only as effective as its weakest link. Thus, it is
mandatory that all activities related to animal care adhere to the pathogen protection standards
of your institution. (Details of setting up a pathogen protection plan are provided in Chapter 7,
Animal Health: Preventing, Identifying, and Eradicating Microbial Contamination.)
9.B.1. Mouse room entry and exit procedures; traffic patterns within
and among mouse rooms
9.B.1.a. Considerations
It is remarkably easy to introduce pathogens into a mouse
colony, even a colony that is fairly well protected. Although the
most common source of pathogen introduction is mice from
other colonies, pathogens also can enter a mouse room via the
air or other vectors such as humans, clothing, or supplies. They
can be easily spread by contamination of clean supplies with
dirty food, water bottles, bedding or cages.
9.B.1.b. What we do at The Jackson Laboratory
What about protection of humans from mouse

allergens?
Procedures that protect animals from human-borne
pathogens also protect technicians from animalborne allergens. In addition to following normal
SOPs in the mouse room, technicians susceptible
to allergies should wash their hands frequently,
keep their hands away from their faces and eyes,
handle mice within ventilated tables, and vacuum
floors rather than dry sweep. Showering after
leaving the mouse room is an additional option for
anyone suffering from allergy symptoms. For
further details, see Chapter 15, Human Health
ConcernsMouse Allergies, Bites, Zoonotic
Disease.
At The Jackson Laboratory, each production and research

mouse room has a materials lock and a personnel lock for entry
and exit of material and people. All sterilizable materials (such
as food, cages, water, supplies) are sterilized in a central area
and wrapped in plastic before delivery into the materials lock.
Before entry into the mouse room, material is unwrapped. Any
non-sterilizable material (such as electrical devices or laminated paper) is completely wiped
down with a solution of 70% ethanol before entry into the mouse room.
Once in the mouse room, all clean material is covered and kept separate from used cages,
bedding, food, and water. In all mouse rooms we have specific unidirectional traffic patterns for
clean and dirty supplies, and in some mouse rooms, we have clean and dirty doors.
All personnel that enter a mouse room must pass through a personnel lock. We have multiple
levels of barrier protection, depending on the mouse room. Our minimal level of pathogen
protection for technicians includes hand washing, either dedicated in-room shoes (that have
been autoclaved before being brought into the room) or disposable booties, and sterilized
garments with snap closures and long sleeves with rib-knit cuffs. In most production facilities,
we have 5-stage dressing locks, 2-piece scrub uniforms with knit cuffs at the ankle and wrists,
socks, dedicated shoes, face masks, hair (and beard) covers, and eye protection. For rooms that
house the most vulnerable and valuable mice, we have an additional level of protection: an air
shower or a wet shower for use upon both entry and exit.
We discourage movement of animals or people between mouse rooms. However, we know that
our employees must often visit more than one mouse room in a day, especially in our research
facility. Thus, we have a written policy: If technicians or researchers must visit multiple mouse
rooms in a single day, they must start in the room with the highest level of pathogen protection
and work their way down to the rooms with lower levels. The policy also includes a way to
handle emergency exceptions. An integral part of the policy is publication of a list of all mouse
rooms and their health statuses, which are evaluated quarterly. This information is available to
the public at www.jax.org/jaxmice/health.
9.B.2. Changing cages

Procedures for changing cages involve distribution of clean cages, food and water, removal of
used and dirty cages, cage contents, and equipment, all performed under requirements that meet
or exceed the level of pathogen protection for any single room. This means, for example, that if
you use special filter covers on your cages or ventilated system, technicians must change
cagesand researchers must handle micein a HEPA-filtered hood. If requirements do not
meet those standards, your pathogen barrier is not as strict as you might think, and pathogens
have an entryway into your colony.

Cage changing: a great opportunity to
monitor the health of your animals.
Animal caretakers see all the animals in all the
mouse rooms. We recommend training them to
watch for symptoms that might indicate illness in
the mice. These symptoms include diarrhea,
unusual fighting or marking, unusual levels of
scratching, and non-responsiveness to routine
cage disturbance.
At The Jackson Laboratory, we have standard operating

procedures (SOPs) that detail strict conditions and procedures for
changing cages. Within a room, any cage changing or work done
with the mice must be done in an environment that is at a
protection level at least equal to that of the cages. All mouse
room personnel are trained in these requirements and procedures.
When handling mice, technicians wear medical examination
gloves. Because of the identification of latex allergies over the
past several years, we now use non-latex gloves exclusively.
For cages in an open, conventional caging system, technicians transfer mice to clean cages
weekly. For ventilated caging racks, technicians change the cages bi-weekly (more often if
cages are excessively soiled). Cages with special requirements are changed more frequently.
Filter covers are changed when they are soiled and discarded when they are damaged.
When transferring mice, technicians use one of two procedures:
With a 10-inch dressing forceps, they grasp the mouse by the tail near its body, gently lift it
into the clean cage, and release it when its feet touch the bedding of the clean cage.
With gloved hands, they gently pick up the
mouse and place it in the clean cage.
Forceps are generally used for mice older than
15 days of age. Gloved hands are used for frail,
obese, or tailless mice. For mice between zero
and 15 days of age, often part of the nest is
scooped and moved to the clean cage in the same
approximate location.
Cage changing techniques that can minimize

escapes.
Escaped mice are costly. They disrupt the cage
changing procedures, and because of the
possibility of misidentification of an escapee, the
mouse can rarely be used, even if it is caught
quickly. To minimize escapes, whenever lifting a
cage top, check for mice that might be clinging to
it. Return those mice immediately to the cage.
Also, never have two cages open at the same
time. This is especially critical with duplex
caging.
Technicians take several steps to prevent spread

of pathogens from cage to cage. When they are
finished changing a cage, they soak the forceps
in an iodine disinfectant. (The usual procedure is
to have two forceps, one that is being used and
one that is being sanitized in the disinfectant.) They either change gloves or sanitize them using
70% ethanol. They wipe down changing tables and shelves per an SOP.
For immunocompromised mice and mice held in our highest level of pathogen protection,
technicians change cages in laminar flow cage changing units. When these mice are not within a
laminar flow system, technicians always protect them with a filter cover. All materials that
come into contact with these mice are sterilized prior to use.
Based on the needs of specific mice, we do make exceptions to the above procedures. For
example, when changing male mice, some technicians take a small lump of dirty shavings and
place this, with the mice, into the new cage. This familiar scent often prevents scuffling as the
males adjust to their new environment.
We segregate all dirty cages, cage covers, filter hoods, and water bottles in a dedicated spot in
each mouse room until we return them to our processing plant for cleaning, sterilizing, and
recycling. We never reuse dirty supplies.
Although it may seem obvious, we feel it is worth mentioning: Mice are master escape artists
that can squeeze through very small openings. Our technicians are trained to check for any
misalignment or misshaping of cage, cage top, food or water hopper wires. Sometimes, just a
small bend enlarges an opening enough for a mouse to escape. When technicians notice a
problem, either they reshape the wire or discard the piece of equipment.
9.B.3. Providing food and water

Care must be taken to ensure that food and water are not entry points for pathogens into the
mouse room. Food should be pasteurized, sterilized, or irradiated. If you have an automatic
watering system, you should follow daily or weekly maintenance routines recommended by the
manufacturer. If you use water bottles, water can be either prepared in the mouse room or
brought into the mouse room following the procedure set up for that room. Once water has been
sterilized, humans should not touch it before it is given to the mice.

At The Jackson Laboratory, we either 1) sanitize empty water bottles, fill them with treated
water, and cap them, or 2) fill them with treated water, cap them,
and then sanitize the filled bottles. We wrap all filled, sanitized
How much do normal mice eat and drink
bottles in plastic in a central area before distribution to mouse
each day?
rooms. We autoclave food bags received from the supplier and
According to AALAS (2006), per 10 g of body
wrap them in plastic. We introduce the filled water bottles and
weight, mice fed ad libitum consume
autoclaved bags of food to mouse rooms via the materials lock.
approximately 1.5 g of dry pelleted food per day
and drink 1.5 ml of water per day.
Exceptions are made for irradiated food, which is not autoclaved.
Rather, we thoroughly disinfect the outside of the bag and wrap it
in plastic before distributing it to the materials lock.
In the mouse room, technicians transfer the food to portable plastic containers for distribution.
To minimize contamination, they use a disinfected plastic scoop to transfer food from the
portable food container to the food bin in the cage. They never touch clean food with their bare
or gloved hands. Technicians top off food in the cage covers on a weekly basis or whenever
they notice that the food supply is low. They break up any clumped feed that may have resulted
from the autoclaving process.
Our mice drink from plastic water bottles with sipper holes in the caps. When changing cages,
technicians provide clean, full water bottles. We never refill empty or partially empty bottles.
To ensure that mice do not run out of water or suffer from wet cages due to a water bottle leak,
we assign specific technicians to check cages for both conditions once per day, following an
SOP. If the supply of water is low, technicians provide a clean, full bottle. If a cage is wet,
technicians change the cage and provide fresh water. If a bottle leaks for any reason other than a
mis-seated cap, it is sent to the Process Quality Control department for inspection.
In some of our research colonies, investigators use the water as a delivery system for treatments.
It is the responsibility of the investigator to prepare the treated water, using the water given
routinely to our mice as a base.
For immunocompromised mouse strains (such as mice with severe combined
immunodeficiency) that are vulnerable to pneumocystis, we treat the water with Sulfatrim, 2%
solution. We administer this treatment on a one-week-on, one-week-off schedule.
Note: For a discussion of nutrition and health as well as details about the mouse food and water
we use at The Jackson Laboratory, refer to Chapter 10, Food and WaterNutritional
and Health Implications.
9.B.4. Keeping mouse rooms clean

The main goal of room cleanliness is pathogen protection. All hard surfaces must be disinfected
regularly. Requirements must reflect the level of pathogen protection chosen for a specific
facility. A procedure with a lower level of protection lowers the level for the entire room.

On a strict schedule and according to detailed SOPs, we clean and disinfect rooms and
associated areas as follows:
At least daily, we disinfect changing tables, all work surfaces, floors, animal husbandry tools,
cleaning tools, floor drains, sinks.
Every week, we disinfect all work tables (including any associated filters and grain hoppers),
any plastic or glass surfaces, all vertical surfaces (including walls, doors, window frames,
etc.), mouse traps, and miscellaneous items (such as storage and trash containers, telephones
and electronic equipment, chairs, stepstools, and toilets), and wet and air shower areas.
Every month, we disinfect caging racks, wall filters, overhead vents and lights, and ceilings in
all mouse rooms, materials and personnel locks, and bathrooms.
9.B.5. Minimizing genetic contamination

To prevent the disaster of genetic contamination due to unintended breeding, techniciansand
anyone who works with the micemust be watchful on a routine basis for any indication of a
change in expected phenotypes. As an example, timely discovery of a mouse with a phenotype
that differs from the normal straina different coat color, for examplemay provide quick
identification of a breeding or genotyping error, which can lead to a quick response.

At The Jackson Laboratory, we have a stringent genetic quality control program to prevent
genetic contamination. (Details of our program are provided in 8.B.2.a, Our genetic quality
control [GQC] program, and at www.jax.org/jaxmice/geneticquality.) Highlights of our plan
We do our best to house separate strains in separate rooms. If we do house multiple strains in
the same room, we try to organize the colony so that the strains that share a room have
different coat colors. If this isnt possible, we at least try to avoid adjacent housing of strains
with the same coat color.
We keep meticulous records. (For details, see Chapter 11, Recordkeeping and Identification
of Mice.)
We educate our technicians to identify and report unusual physical characteristics or
behaviors that might indicate a mutation or cross-breeding.
Upon report of suspected genetic alteration, our colony managers immediately access
breeding records and establish the pedigree. We stop setting up new matingsexcept for test
matingsto determine if the altered phenotype is genetic.
9.C. Other issues related to animal husbandry

Following are some topics regarding husbandry and routine care that we are often asked about.
9.C.1. Providing environmental enrichment to alleviate stress

9.C.1.a. Implications of environmental deprivation
Environmental deprivation may be defined as a lack of species-appropriate environmental
stimuli that is sufficient to cause stress. Stressed animals do not breed well, and their
biochemistry (elevated glucocorticoid levels, for example) can confound research results. The
relevant issues are these: Just how do we identify environmental deprivation in a mouse? And
from the perspective of a mouse, exactly what enrichment reduces deprivation stress?
9.C.1.b. Identifying stress

Several behaviors may be indicators of stress, but none is definitive. Stressed mice may exhibit
stereotypic (repeated) behavior patterns, but some repeated behaviors may simply reflect
adaptation, to the cage environment, of a normal drive. For example, a mouse that repeatedly
jumps up and down in the corner of a cage may simply be expending energy, similar to running
on a wheel. Increased aggression may be a sign of stress, but normal murine social interaction,
such as barbering or dominance behavior, may be incorrectly interpreted by human observers as
signs of aggression. One of the more sensitive indicators of stress is reproductive performance.
However, many types of stresses can impair reproductive performance, and deprivation stress is
not considered a cause of diminished breeding. Thus, when mice exhibit signs of stress,
deprivation should be considered as just one possible source.
9.C.1.c. Identifying appropriate environmental enrichment

If we assume that animals have enriched lives in the wild, we can look at their natural
characteristics and behaviors for clues to the types of enrichment that may be most meaningful
to them in captivity. Mice have a strong sense of smell. They are territorial and they like to dig
and burrow. They generally prefer the edge of an area rather than the middleeven in their own
cages. (Interestingly, many strains of laboratory mice are blind and/or deaf by the time they are
eight months old, implying that visual and auditory stimuli are probably unnecessary.)
For strains that like to dig and build nests, one method of enrichment is to provide material for
nest buildingif the material is a type that mice of that strain like to use and if the material is
not harmful when eaten.
Some recommendations are to include toys in cages. But the toy must be appropriate for a
mouse. Dogs fetch and cats chase toy birds on strings because these activities mimic hunting
behavior. This implies that an effective mouse toy would encourage burrowing, climbing,
chewing, and running.
It seems that one of the most important features of successful enrichment is provision of the
mouse with some control over his environment, for example, by providing nest building
material and, in some ventilated caging systems, by providing a way to escape from drafts
(Baumans et al., 2002). This behavior also is strain dependent.
A few words about exercise wheels: Many people consider the relatively small cage
environment, as compared to mouse territories in the wild, as a source of stress due to spatial
limitations. One suggested remedy is the provision of running wheels. In fact, laboratory mice
do love to run. Flurkey (unpublished) has measured an average voluntary distance for a young
C57BL/6J (000664) mouse with only three days of training at six miles per day, every day.
However, chronic voluntary exercise has wide-ranging effects on the physiology of the mouse,
and the outcome is not necessarily positive. For example, Harrison (2008) found that group
housed mice given a running wheel from four months of age throughout their entire lives may
have a longer or a shorter lifespan or no difference in lifespan. The chronic exercise interacted
with sex and genotype to produce unpredictable effects.
Probably the greatest single source of enrichment to a mouse isanother mouse (National
Research Council. 1996). Cagemates provide a constantly changing, species-relevant source of
stimulationas well as a source of warmth. In fact, some consider single housing to be a type
of stress. Of course, concerns about aggression, especially with group-housed male mice of
certain strains, must be considered.
9.C.1.d. What we do at The Jackson Laboratory

At The Jackson Laboratory our Animal Care and Use Committee has developed a policy about
enrichment. In all colonies, our technicians are trained to watch for any behavior that is outside
the range of normal for the mice they tend, and, if they notice anything that might indicate
stress, they consider environmental deprivation as a possible cause.
We provide nesting material for all breeders. For group-housed mice that receive bedding that is
not conducive to burrowing or nest building, we provide supplemental, commercial nesting
material such as Nestlets. We do not provide any cardboard items such as empty paper towel
rolls because they may contain contaminants that could affect the health of our mice.
For mice housed singly for two weeks or less, we provide supplemental nesting material for
both warmth and enrichment. For mice housed singly for more than two weeks, we provide the
supplemental nesting material as well as a toy that promotes gnawing, climbing or hiding.
Approved objects include a short length of sterilized PVC pipe (with polished edges), a cage
card holder (without holes), a commercial plastic tunnel or igloo, a metal ring, or a Shepherd
Shack or refuge. We transfer durable toys with the mouse from a dirty to a clean cage. We
thoroughly sanitize any toy before giving it to a different mouse.
As with other issues related to animal care and health, we continually evaluate new research and
comments from our technicians to ensure the best care for all of our animals.
9.C.2. Managing aggression in a colony

Signs of aggression in mice range from patchy hair loss to death. Aggression appears to be more
common among males of specific strains (for example, SJL/J [000686] and most BALB/c
strains) and much more likely to occur among unrelated males who are first caged together after
they are sexually mature. However, even among male littermates, aggression may increase or
appear for the first time during adult maturation, even as late as 1518 months of age.
With male mice, it is important not to confuse signs of dominance with signs of aggression.
Often, submissive male mice back down following a show of dominance from another male
mouse. Fighting often ensues only when this balance is interfered with. Of course, sometimes
true aggression does occur, in which case intervention is required.
Managing aggression may seem more art than science. Here are a few suggestions:
Mice use scent, primarily from urine, to mark territories and establish dominance. Thus, when
group-housing males who have not previously lived together, use a clean cage, and try not to
transfer any scents from any of the used cages to the new one. On the other hand, when
moving all the mice from a dirty cage to a clean one, it sometimes helps to transfer some of
the old scent, by moving some of the dirty nesting material litter into the clean cage.
Sometimes, male aggression is heightened if a female is present. Be sure that a female hasnt
been placed in the cage inadvertently.
Depending on the strain, the addition of nesting material may help divert the energies and
activities of the animals.
Also, check references such as Ambrose & Morton, 2000; Emond et al., 2003; Hurst, 2005;
Singleton & Hay, 1982; Smith et al., 2004, 2005; National Research Council (1996). Also,
check current and back issues of JAX NOTES (www.jax.org/jaxmice/jaxnotes).
9.C.3. Caring for wild-derived inbred mice

Wild-derived inbred mice, which were trapped in the wild and inbred without domestication,
generally are more sensitive than common inbred strains to stresses associated with shipping,
new surroundings, and new handlers. A few extra precautions can make these miceand their
caretakersless stressed and more productive.
When you receive a shipment of wild-derived mice, take special precautions when removing
them from their shipping container. (For details, see 12.B.2, Special handling for newly
arrived, wild-derived inbred mice.)
Minimize activity and noise around wild-derived mice. Try to house them in a quiet room,
away from areas of heavy traffic and noise. Minimize rack and cage movement. It may help
to put wild mice labels on the cages as a reminder of their presence.
Handle wild-derived mice as little as possible, and always in a calm manner. Allow animal
caretakers adequate time to work slowly and patiently when changing cages, weaning, or
working with wild-derived mice. When being moved, some wild-derived mice might be less
stressed if forceps are used; others might be less stressed if gloved hands are used. If mice are
moved by gloved hand, either change or sanitize the disposable gloves between cages.
Regarding breeding, allow 812 weeks for a pair of wild-derived mice to settle down and
produce a litter. If a breeding pair does not produce pups after this time, place a different
female in the males cage. (If you swap males and females, it is preferable to keep the male in
his home cage.) Adding Nestlets or Kimwipes to cages can encourage nesting and
improve overall pup productivity.
Be prepared for aggressive male behavior, especially fighting that typically begins at 68
weeks of age. Aggression is particularly prevalent among mice of the CZECHII/Ei (001144)
strain and in progeny of any crosses involving Mus musculus castaneus. Try housing the
males singly or pairing them with females.
Keep a watchful eye on new mothers, who may abandon or cannibalize their litters. To
minimize these behaviors, avoid changing a cage if it contains a litter less than three days old.
If cages containing newborns must be changed, move the nest and pups as a unit using a
clean, gloved hand. (Human scent on pups may induce abandonment or cannibalizing.) If the
problem persists, consider fostering the pups to another female. (For details on pup fostering,
see 13.E.1.c, Fostering a litter.)
Make sure that anyone who works with wild-derived mice knows the special precautions
required for their care.
9.D. Sources of information regarding animal care

9.D.1. Organizations/agencies
Following is a list of organizations involved with animal care issues:
The National Research Council, a component of the National Academies: advises the federal
government on the broad community of science and technology.
(www.nationalacademies.org/nrc)
Institute for Laboratory Animal Research (ILAR), a component of the National Academies of
Science: evaluates and disseminates information on issues related to the scientific,
technological, and ethical use of animals and related biological resources in research, testing
and education (http://dels.nas.edu/ilar_n/ilarhome)
Office of Laboratory Animal Welfare (OLAW), a component of the National Institutes of
Health (NIH): provides regulations for organizations applying for NIH funding.
(http://grants.nih.gov/grants/olaw/olaw.htm)
The American Association for Laboratory Animal Science (AALAS): a nonprofit association
that promotes education and expertise in the care and use of laboratory animals
(www.aalas.org). AALAS is the organization that requires the formation of an Institutional
Animal Care and Use Committee (IACUC) at all research and instructional organizations
(www.iacuc.org). AALAS also provides certification programs for managers of animal
resources and animal care technicians.
The Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC)
International: a private, nonprofit organization that promotes the humane treatment of animals
in science. Institutional membership and assessments are voluntary, but are an important
indication of high quality animal care by institutions and technicians. (www.aaalac.org)
9.D.2. Publications
Following is a list of publications that provide detailed information about laboratory animal care
and use:
Guide for the Care and Use of Laboratory Animals (often referred to simply as The Guide.
1996. National Research Council. (The main resource used by AAALAC International.)
The Laboratory Mouse. 2001. Suckow MA, Danneman, P, Brayton C. CRC Press.
Laboratory Mouse Handbook. American Association for Laboratory Animal Science
(AALAS). 2006.
Journal of the American Association for Laboratory Animal Science (AALAS)
The Mouse in Biomedical Research, Volume 3, Normative Biology, Husbandry, and Models.
2007.(Fox JG et al. (eds). Academic Press.
9.E. References
Ambrose N, Morton DB. 2000. The use of cage enrichment to reduce male mouse aggression. J
Appl Anim Welfare Sci. 3:117125.
American Association for Laboratory Animal Science (AALAS). 2006. Laboratory Mouse
Handbook. Gografe SI (ed). Memphis, Tennessee.
Baumans V, Schlingmann F, Vonck M. van Lith HA. 2002. Individually ventilated cages:
beneficial for mice and men? Contemp Top Lab Anim Sci. 41:1319.
Cunliffe-Beamer TL, Freeman LC, Myers DD. 1981. Barbiturate sleeptime in mice exposed to
autoclaved or unautoclaved wood beddings. Lab Anim Sci. 31:672675.
Emond M, Faubert S, Perkins M. 2003. Social conflict reduction program for male mice.
Contemp Top Lab Anim Sci. 42:2426.
Harrison DE. 2008. Effects of exercise on lifespan in several strains of laboratory mice. The
Jackson Laboratory. http://research.jax.org/faculty/harrison/ger1vi_Exercise (accessed October,
2008).
Hurst J. 2005. Making sense of scents: reducing aggression and uncontrolled variation in
laboratory mice. NC3Rs. 2:18.
Koehler KE., Voigt RC, Thomas S, Lamb B, Urban C, Hassold T, Hunt PA. 2003. When
disaster strikes: rethinking caging materials. Lab Animal. 32:2427.
National Research Council. 1996. Guide for the Care and Use of Laboratory Animals.
Grossblatt N (ed). National Academy Press. Washington, DC.
Pick JR, Little JM. 1965. Effect of type of bedding material on thresholds of pentylenetetrazol
convulsions in mice. Lab Anim Care. 15:2933.
Reeb CK, Jones RB, Bearg DW, Bedigian H, Paigen B. 1997. Impact of room ventilation rates
on mouse cage ventilation and microenvironment. Comtemp Top Anim Sci. 36:7479.
Singleton GR, Hay DA. 1982. A genetic study of male social aggression in wild and laboratory
mice. Behav Genet. 12:435448.
Smith AL, Mabus SL, Stockwell JD, Muir C. 2004. Effects of housing density and cage floor
space on C57BL/6J mice. Comp Med. 54:656663.
Smith AL, Mabus SL, Muir C, Woo Y. 2005. Effects of housing density and cage floor space on
three strains of young adult inbred mice. Comp Med. 55:368376.
Wade AE, Holl JE, Hilliard CC, Molton E, Greene FE. 1968. Alteration of drug metabolism in
rate and mice by an environment of cedarwood. Pharmacology. 1:317328.
Weichbrod RH, Cisar CF, Miller JG, Simmonds RC, Alvares AP, Ueng TH. 1988. Effects of
cage beddings on microsomal oxidative enzymes in rat liver. Lab Anim Sci. 38:296298.
White, WJ. 2007. Management and Design: Breeding Facilities, in The Mouse in Biomedical
Research, Vol. III, Normative Biology, Husbandry, and Models. 2nd Edition. Fox JG et al.
(eds). American College of Laboratory Animal Medicine Series; Academic Press, Elsevier,
Burlington, MA.
217
Chapter 10: Food and WaterNutritional and

Health Implications
The National Research Council (NRC) has published guidelines for acceptable food and water
for laboratory mice. Details are provided in the Guide for the Care and Use of Laboratory
Animals (1996) and Nutrient Requirements of Laboratory Animals (1995). Within these
guidelines, colony managers must make a number of decisions that can directly impact the
health of their mice and the outcome of their research.
Reputable manufacturers of feed pride themselves in maintaining highand consistent
nutritional standards for their feed. But due to the nature of some ingredients, the manufacturing
and decontamination processes, and shipping and storage conditions, the feed that goes into the
food hopper has the potential to vary considerably from batch to batch in nutrient composition
and in levels of contaminationincluding both pathogens and toxins. Thus, if researchers or
colony managers observe anything unexpected in their animals, they should consider diet as a
possible etiologic factor.
In this chapter, we provide background information on manufacturing, decontamination, and
storage of feed, and discuss how nutrition is affected. We also explain the choices we make at
The Jackson Laboratory regarding mouse diet and water treatment.
Please note that this chapter provides information on the food and water itself. The ways in
which we provide both to the animals are discussed in Chapter 9, Animal Husbandry.
10.A. Choosing a diet and arranging for decontamination and storage of feed ............... 218
10.A.1. Types of diet................................................................................................ 218
10.A.2. Physical form of the feed............................................................................ 219
10.A.3. Decontamination of feed ............................................................................ 220
10.A.4. On-site storage of feed................................................................................ 222
10.A.5. Nutritional composition of feed and requirements for healthy mice ....... 222
10.A.6. Quality control............................................................................................. 225
10.A.7. What we do at The Jackson Laboratory .................................................... 226
10.B. Treating water ............................................................................................................ 226
10.B.1. Guidelines for safe water ............................................................................ 226
10.B.2. What we do at The Jackson Laboratory .................................................... 226
10.C. References .................................................................................................................. 227
Acknowledgments: We would like to thank David D. Myers for his valuable input to this
chapter.
10.A. Choosing a diet and arranging for decontamination

and storage of feed
When selecting a diet for your animals, you must consider several interrelated factors: the
various types and forms of the diets, the nutritional needs of the animals, decontamination
methods, and storage requirements.
10.A.1. Types of diet

Mouse diets are classified according to type of
ingredients (natural, purified, or chemically-defined), and
formula (open or closed).
10.A.1.a. Ingredient types

10.A.1.a.1. Natural
Natural ingredient diets, the most common diet type, contain agricultural products and byproducts such as whole grains, mill by-products, high-protein meals (animal and vegetable),
yeast, and mined or processed mineral sources (NRC, 1995).
10.A.1.a.2. Purified (semi-synthetic) and chemically-defined

Purified diets (also known as semi-synthetic diets) contain ingredients that represent single
nutrients: casein, starch, dextrins, sucrose, glucose, specific oils, cellulose, vitamins, and
minerals. Purified diets are more expensive than natural ingredient diets, but are useful when the
exact composition of a diet must be controlledas in nutritional studies, toxicological studies in
which results might be sensitive to low concentrations of contaminants, and immunological
studies in which animals may be influenced by antigens in the diet. But purified diets are not
recommended for long-term use. For example, survival rates in a lifelong treatment study were
lower in rats fed AIN-93M (American Institute of Nutrition, 1993, maintenance diet) compared
to a natural ingredient diet (Duffy et al., 2002).
A chemically defined diet is a type of purified diet in which individual amino acids are used in
place of a protein source, and specific fatty acids are used in place of oils. Chemically defined
diets are very expensive and are used mainly for studies of amino and fatty acid metabolism.
10.A.1.b. Formula types

10.A.1.b.1. Open and fixed
Open formula diets, which can be made of natural or purified ingredients, are fixed formula
diets, i.e., the macronutrient source is invariant. Manufacturers openly publish the exact
proportions of ingredients.
10.A.1.b.2. Closed and variable

Closed formula diets, which are always made of natural ingredients, are proprietary.
Manufacturers publish the ingredients, but not the specific formulations. Generally, the
information provided by the manufacturer includes at least the food sources that may have been
used and a proximate analysis of the concentrations of protein, fat, and ash.
In a closed formula diet, the concentrations of nutrients are specified, but the macronutrient
source may vary according to considerations such as market price. The source of dietary protein,
especially, is liable to vary in a closed formula diet. (For example, milk protein may be
substituted for fish meal). Manufacturers use variable formulations because considerable
variation in nutrient composition exists for the same raw foods from different locations and in
different seasons. Using proximate analysis, they can adjust proportions of raw foods in variable
formulations to achieve a highly consistent concentration of protein, fat, and ash in the diet.
Closed formula diets may vary in other nutrients that are not used for standardization, as the raw
food source varies. Knapka (1997) has argued that the varying ingredient inclusion rates in
Chapter 10: Food and WaterNutritional and Health Implications 219
variable formula diets poses a considerable risk of experimental variability. Researchers that are
concerned about the possible effects of varying dietary nutrients should use purified fixed
formula diets or have the relevant nutrients assayed independently by commercial laboratories.
As noted above, in variable formula diets, protein sources will vary. This can affect the biology
of the mouse. For example, simply varying the source of the protein, not the amount, could
double the inducible tumor incidence (Guo et al., 2004).
10.A.2. Physical form of the feed

10.A.2.a. Pellets and extrusions
The most common physical form of feed are pellets and extrusions (collets). Both
manufacturing processes start the same way: raw food material is ground, sifted, and mixed with
vitamin and mineral supplements into a meal.
10.A.2.a.1. Pellets
For pelleting, the meal is mixed with steam, which raises the temperature to 6580 C and
gelatinizes the starches, thus binding the diet ingredients together. The heat also reduces the
microbiological load by about two orders of magnitude. The meal is forced through a die and
cut at a specific length. Then, the resulting pellets are dried so that moisture content typically is
about 12%, a level at which free water content is too low to support growth of microorganisms.
As a result, pelletized food, when protected from moisture, can remain on a shelf for about six
months before loss of nutrient value becomes significant or growth of mold becomes a concern.
Purified diets require a manufacturing method slightly different than described above due to the
inclusion of casein (typically used as the protein source in purified diets) and simple
carbohydrates, both of which are particularly sensitive to heat. To minimize loss or alteration of
nutrients, meal is mixed with water, pelletized, and then dried at a low temperature (less than
60 C) in a vacuum. Purified diets generally have a shelf-life of about four months when
refrigerated or frozen.
10.A.2.a.2. Extrusions (collets)

For extrusion, meal is ground finer than for pelleting. Meal is mixed with steam and hot water,
brought to 8095 C, and extruded under pressure (about 35 atmospheres), allowing temperatures
of 150 C. Because steam is trapped within the food during extrusion, the extruded pellets
(collets) become honeycombed. The collets are dried by hot air to a moisture content of 812%.
Because of the higher temperatures used during extrusion, the loss of vitamins is greater during
preparation; however, because the higher temperatures also denature enzymes that break down
vitamins during storage and destroy mold and bacterial spores, extruded diets have longer shelf
lives than pelleted diets.
10.A.2.b. Other forms of food

10.A.2.b.1. Ground diets
Occasionally, ground diets are required. For example, some mice cannot eat pellets or collets
due to physical problems such as malocclusion or malformed, poorly developed, or broken
teeth. And sometimes researchers administer treatments through feed. Either purchase ground
feed or grind your own from pellets or collets. Note that grinding pellets or collets can reduce
vitamin stability, which reduces shelf life (Tobin et al., 2007).
Food cups can be used to serve ground food. It is perfectly acceptable, however, to simply place
the meal directly on the bedding in a dry area of the cage. While this may seem unsanitary, mice
are coprophagic, so placing feed on the cage bottom does not put the mice at risk as long as it
does not become moist and thus become a growth medium for bacteria or mold.
A word of caution about using ground diets: Because mouse incisors grow continuously, it may
be necessary to provide gnawing material when giving mice ground feed for more than several
weeks.
10.A.2.b.2. Gel diets

Gel diets are a special type of diet that combines food and water into one product. Gel diets are
useful for mice that either cannot access water from the standard water delivery system or
cannot eat normal food or both. Gel diets are also used during shipping. But gel diets are
expensive. They do not provide gnawing opportunities, and they require special precautions to
prevent spoilageboth during storage and in the cage (NRC, 1995).
10.A.3. Decontamination of feed

The risk of contamination by insects and microbiological organisms is unavoidable in food
manufacture, packaging, and shipping.
Historically, diets were sterilized or pasteurized primarily for use in specific pathogen free
(SPF) mouse colonies. Today, however, because of the recognition of infectious agents as a
source of uncontrolled variables as well as agents of overt disease, and because of the common
use of genetically modified mice, many with compromised immune systems, the elimination of
microorganisms from diets has become a standard practice.
Autoclaving and irradiation are processes used for sterilization and pasteurization. Sterilization
is defined as destruction of every living organism, including spores as well as vegetative forms.
Pasteurization eliminates vegetative bacteria and some spores. Pasteurization minimizes major
chemical alteration of the diet; however, it does not destroy bacterial spores.
10.A.3.a. Autoclaving
Autoclaving is the process of sterilizing or pasteurizing with steam at a specific temperature and
pressure for a specific length of time. Autoclaving is the most common method of sterilizing
mouse food. It is generally performed on site, typically in a double-door autoclave, after which
it is passed into a barrier animal facility. Because the process of autoclaving affects feed,
manufacturers produce feed specifically to be autoclaved and mark the feedbags accordingly.
Nutrients that are susceptible to damage by heat, moisture, and oxygen are especially affected
by autoclaving. Browning reactions among amino acids, especially methionine, cysteine, and
lysine, and between amino acids and carbohydrates, alters the structure of the amino acids and
can substantially diminish protein bioavailability. Milk proteins, such as casein, and simple
sugars, which are commonly used in purified diets, are particularly susceptible. Normally, feed
manufacturers counteract the diminished bioavailability of proteins due to autoclaving by
increasing the protein content of the autoclavable diet above minimal recommended levels or by
supplementing the diet with methionine, cysteine, and lysine.
Heat-labile vitamins (B1, B12, B6 and pantothenate) are particularly sensitive to autoclaving;
modest losses of vitamins A, D3, and folate also occur. Thus, manufacturers generally add
additional vitamins to diets that will be autoclaved. Because of this, toxicity can result if mice
are fed autoclavable feed that has not been autoclaved. (Also see 10.A.5.e, Essential amino
acids and vitamins.)
Autoclaving can affect the hardness of pellets. The degree of the effect varies with the specific
ingredients and formula of feed. Hardness tests on autoclaved food can identify any that is too
hard for mice to eat. Collets, which are made by extrusion and have a honeycombed structure,
are less susceptible to hardness problems.
Another issue with autoclaving is the clumping of food during the sterilizing process. Coatings
such as silica dioxide or calcium bentonite have been used in the past to minimize clumping.
Although these coatings are considered to be inert because they do not alter the normal
pathology of research animals, the potential exists for interference with specific end points in
research, and Tobin et al. (2007) recommend that coated diets be avoided.
10.A.3.b. Irradiation
Irradiation is the process of exposing feed to radiation for the purpose of destroying
microorganisms. The radioactivity damages the DNA and prevents replication. Although
irradiation is produced from a radioactive source, no radioactivity is transferred to the irradiated
feed. Irradiation is performed at specialized facilities rather than on-site.
Gamma irradiation is the most commonly used form of irradiation for diet decontamination.
Irradiation at doses less than 10 kGy (radicidation or radurization) is equivalent to
pasteurization. A minimum dose of 21 kGy is sufficient to kill most bacteria, molds and fungi,
and is considered a sterilizing dose, although killing Clostridium and Bacillus spores may
require doses above 30 kGy. Doses of at least 30 kGy may be necessary to inactivate some
viruses (Baldelli, 1967). The sensitivity of many pathogens to irradiation is provided by the
World Health Organization (WHO; 1999).
Because the radiation dose will vary throughout the product due to load pattern, density of the
product, and thickness of the load, the dose is usually stated as the minimum received by the
load (typically, at the center of the load). Often, a color indicator label is provided on each bag.
Colors may change somewhat with exposure to light and also vary among label manufacturers,
so labels and color keys should be checked carefully.
From the standpoint of nutrition, irradiation at doses typically used for rodent diets (2025 kGy
for barrier facilities) has no effect on protein bioavailability (Ford, 1979; Eggum, 1979) and
losses of most vitamins are less than 20 percent (Ford, 1979; Isler and Brubacher, 1999).
Because the effects of irradiation are transmitted by the production of free radicals, the main
concern for damage to the diet is the free radical-induced oxidation of fats, producing peroxides.
Ford (1979) reported a six- to eight-fold increase in peroxide values in a high fat diet irradiated
at 25 kGy; the increase was reduced to three- to four-fold by irradiating under a vacuum (in the
absence of oxygen). Peroxide levels continued to increase during storage.
Keep in mind that, although irradiated feed is free from pathogens, by the time the feed reaches
its destination, outside packaging might not be. Thus, standard operating procedures (SOPs) for
pathogen protection must be followed when bringing the food into mouse rooms (disinfecting
the outer bag, for example).
10.A.3.c. Comparison of decontamination methods

Each decontamination method has advantages and disadvantages. For larger operations, where
the expense of the autoclaving equipment and operating expertise is already assumed for other
needs, autoclaving will be the most cost effective. Autoclaving also may be necessary where
lipid peroxides in the diet may be a particular concern. And it has the additional advantage of
on-site decontamination, so that contamination during transport is of minimal concern.
Irradiated diets provide more consistent protein quality and levels of nutrients, and they are a
uniform hardness, but they are more expensive. Irradiated diets are typically preferred for small
barrier colonies or isolators where large autoclaves are unavailable. Pasteurization may be
preferred over sterilization when a more consistent dietary protein quality or vitamin level is
necessary, but neither pasteurization or sterilization by autoclaving provides the consistency of
irradiation (Tobin et al., 2007).
10.A.4. On-site storage of feed

The two most important factors affecting food during storage are temperature and humidity.
Natural-ingredient diets are typically stored at room temperature (22 C), and shelf lives are
calculated on that basis. Because the rate of biological processes typically doubles with each
temperature increase of 10 C, reducing the storage temperature to 12 C would reduce the rate of
vitamin destruction and the oxidation of fats by half, thus doubling the shelf life.
Because, compared to yeast or bacteria, mold starts growing at a lower relative humidity (about
80%), it will be the first microorganism to appear in stored food that is exposed to moisture.
Mold is a particular problem because of the production of mycotoxins, such as aflatoxins,
vomitoxin (deoxynivalenol [DON]), zearalenone, and fumonisin. Aflatoxins and DON are
especially dangerous for mice. For storage guidelines, the National Research Council (1996)
recommends a maximum exposure of 23 C and 70% relative humidity with a continuous
exposure of less than 21 C and 60% relative humidity.
It is important to heed storage conditions and the use by date recommended by the supplier.
Deviation from these guidelines can affect the nutritional value of the food.
10.A.5. Nutritional composition of feed and requirements for

healthy mice
To produce research results that are unambiguous regarding the health of the animals, any diet
you consider should be designed specifically for laboratory rodents. The Guide (NRC, 1995)
provides a comprehensive listing of nutritional requirements for mice, and Tobin et al. (2007)
provide a thorough review of nutrition.
Nutrients can be divided into five broad categories: protein, fat, available carbohydrates, fiber,
and essential nutrients. Essential nutrients, which include essential fatty acids, essential amino
acids, vitamins and minerals, are listed in Table 10.1.
Table 10.1. Essential nutrients for mice.
Essential amino acids:
Arginine (may not be essential
for adult mice)
Histidine
Isoleucine
Leucine
Valine
Threonine
Lysine
Methionine
Phenylalanine
Tryptophan
Essential fatty acids:
Linoleic
" linolenic
Macroelements:
Calcium
Phosphorus
Magnesium
Potassium
Sodium
Chloride
Sulfur
Trace elements:
Iron
Zinc
Manganese
Copper
Selenium
Iodine
Vitamins:
A (retinol)
Vitamin D3 (cholecalciferol)
Vitamin E (tocopherols)
Vitamin K3 (menadione)
Vitamin B1 (thiamine)
Vitamin B2 (riboflavin)
Available niacin
Vitamin B6 (pyridoxine)
Panthothenate
Vitamin B12 (cobalamin)
Available biotin
Folate
Choline
Ultratrace chemicals, which are not yet established as essential but may be required, include arsenic,
boron, chromium, cobalt, fluoride, lithium, molybdenum, nickel, silicon, tin, vanadium. Tabular
information compiled from Tobin et al., 2007.
10.A.5.a. Protein
Nutritional requirements for protein differ for the three classical physiological states:
reproduction (including lactation), growth, and maintenance.
10.A.5.a.1. Reproduction
The NRC (1995) states that natural ingredient diets containing 18
percent protein are appropriate for reproduction in mice. In fact,
diets with higher protein percentages (24%, for example), may be
sub-optimal (Knapka et al., 1977).
10.A.5.a.2. Growth
What percentage of protein in the diet is

most common?
In most mouse colonies in the United States,
commercial diets used for breeding, growth, and
maintenance are about 18% protein. In Europe,
maintenance diets are more typically 1416%
protein.
A maximal growth rate to mature body weight typically is

achieved on diets containing at least 1316% protein. Growth rate
immediately after weaning may be higher on 18% protein diets, compared to 14%, which may
reflect an interaction between the stress of weaning and dietary composition. Catch-up growth
occurs on the diets with 1416% protein, and subsequent growth to mature body weight
continues at the same rate with diets that range in protein composition from 1318% (reviewed
in Tobin et al., 2007). Though the NRC (1995) recommends 18% protein (or 20% casein in
purified diets because casein is about 88% protein), Tobin et al., (2007) state that optimal
growth rates can be maintained on diets of 1416% protein, assuming good-quality protein, i.e.,
protein with an amino acid pattern that matches the requirements for mice.
10.A.5.a.3. Maintenance
The few estimates of maintenance requirements for dietary protein in mice indicate that a 5%
protein diet, with good quality protein, is sufficient to sustain adult body weight (Tobin et al.,
2007). In fact, in adults, restriction of protein to 4% (casein), compared with 26%, typically
increased lifespan for multiple strains of mice (Leto et al., 1976; Goodrick, 1978; Stolzner,
1977). In rats, high protein diets are associated with kidney damage; in mice, however, a
comparable association of dietary protein and kidney damage has not been reported (Tobin et
al., 2007).
10.A.5.b. Fat and essential fatty acids

For growth and maintenance of most strains, diets of 46% fat weight/weight (w/w) are
generally appropriate (Knapka et al., 1977). For breeding, strain variation exists for the optimal
dietary fat content, which ranges from 412%. For example, BALB/c mice may perform better
with diets of 8% fat, compared to 4% or 12% (Knapka et al., 1977); however, diets with fat
content above 6% could promote obesity in other strains, which may reduce fertility. General
guidelines for dietary fat content do not exist specifically for poorly reproducing strains, and
optimal amounts should be determined by each researcher.
Both linoleic and "-linolenic acids are considered essential fatty acids. Linoleic acid is a
precursor to arachadonic acid and other omega-6 fatty acids, and arachadonic acid can substitute
in the absence of dietary linoleic acid. Although "-linolenic acid is necessary for the synthesis
of certain prostaglandins, the NRC has not yet determined a specific requirement for it.
Interestingly, animal fats are poor sources of the essential fatty acids. For example, about four
times more lard, compared to soya or corn oil, is needed to satisfy the requirement for linoleic
acid.
10.A.5.c. Carbohydrates and fiber

Complex carbohydrates provide the predominant energy source in natural diets. Crude fiber is
the indigestible material remaining after a defatted feed sample is successively boiled in mild
acid and then base, which digests proteins and starches and removes the amino acids and soluble
carbohydrates. Total carbohydrate value overestimates the amount of carbohydrate available for
metabolism because it includes insoluble (crude) fiber. Typically, the amount (in percent by
weight) of crude protein, crude fat, and crude fiber will be provided as the proximate analysis
with each bag of feed. The remaining weight is made up of carbohydrate, moisture, and ash.
10.A.5.d. Ash
Ash is the inorganic material that remains after burning a feed sample at a minimum of 525 C
for 1218 hours, depending on the temperature. Ash is composed of minerals; it is used in
proximate analysis as a rough measure of the amount of minerals in a feed sample. Natural
ingredient diets typically contain 48% ash.
10.A.5.e. Essential amino acids and vitamins

Amino acid requirements for maximal growth rates for mice are provided by the NRC (1995).
Although the optimal amount of total protein differs for reproduction, growth, and maintenance,
available information indicates that the relative amounts of each essential amino acid remain
about the same for all three physiological states (Tobin et al., 2007). Essential amino acids for
mice, as specified by the NRC (1995), are listed in Table 10.1,
Essential nutrients for mice.
Should you be concerned about
phytoestrogens in the diet?
The NRC (1995) also lists essential vitamins (Table 10.1) and
their estimated levels required for growth, which probably are
also suitable for reproduction. No estimates have been provided
for maintenance. Vitamins are added to natural ingredient diets at
levels usually well above minimal requirements to allow for
processing losses, possible inefficiencies in absorption, and
losses during storage. Because autoclaving diminishes certain
vitamins, diets specified as autoclavable are fortified for
autoclave-sensitive vitamins so that minimal requirements
typically are still met following autoclaving. However, because
autoclaves and autoclaving protocols vary from site to site, and
because the temperature and steam penetration will vary even
within a pallet of feed, actual amounts of vitamins in each batch of feed can vary considerably.
Diets manufactured specifically for autoclaving should never be fed to mice without autoclaving
due to the possibility of vitamin A or D toxicosis.
Today, with the increased use of soy products,

there is some question about the biological
effects of phytoestrogens in food. If this is a
concern for you, we recommend conducting a
bioassay to determine if the diet you are using
contains a level of estrogenic activity high
enough to interfere with your study. One of the
most sensitive measures of physiologically
relevant estrogen is uterine weight in
ovariectomized females (Gordon et al., 1986;
Mobbs et al., 1985).
Conditions of storage and method of feed preparation contribute to the loss of vitamin potency.
This loss differs considerably among various vitamins. Whereas loss of most vitamins over a 6month period ranges from 525% in pelleted food, loss of menadione can range from 5080%,
depending on the specific form of the vitamin; loss of vitamin D3 can range from 2065%
(Tobin et al., 2007). Storage losses depend on the moisture content of the feed, the
environmental temperature and humidity, and on the packaging (e.g., vacuum packing). (For
information on storage, see 10.A.4, On-site storage of feed.)
10.A.5.f. Minerals, including calcium and phosphorus

More than twenty minerals are considered essential (Table 10.1). They are categorized as
macroelements (elements at concentrations greater than 80mg/kg in the body) and trace
elements. Although minerals are derived from the various ingredients in the feed, a mineral
premix will often be added to provide appropriate levels and balance among the various
minerals. The level of each mineral in a feed sample is assayed from an ash sample using
specific spectroscopy techniques.
Although requirements in mice for most minerals have not been determined in detailed studies,
Reeves et al., (1993) report that the main standard purified diets, AIN-76A, AIN-93G (for
growth), and AIN-93M (for maintenance), have not been linked to mineral deficiencies.
A particular concern for rodent diets is the ratio of calcium to phosphorus. In rats, deposition of
calcium phosphate crystals in the kidney (nephrocalcinosis) is a relatively common condition
(e.g., Cockell et al., 2002) that is related to both levels of dietary calcium and the ratio of
calcium to phosphorus. A more generalized calcium mineralization, called dystrophic
calcinosis, has been reported for some mouse strains. This condition involves deposition of
calcium in soft tissues, particularly the heart and kidney, in susceptible strains (Van den Brock
et al., 1997). Yuen and Draper (1983) reported that when B6D2F1 mice were fed a purified diet
containing 0.6% calcium (normal) and 1.2% phosphorus (an amount present in some diets),
kidney calcium levels were more than double the level in mice fed the 0.6% calcium with 0.3%
phosphorus. The relationship of dystrophic calcinosis to nephrocalcinosis is unknown. Tobin et
al. (2007) recommend that, for natural ingredient diets, where a considerable proportion of
phosphorus is bound in an unavailable form (phytates), calcium and phosphorus weight ratios of
at least 1 (molar ratios of 0.77) are acceptable, although a weight ratio of 1.2 may be safer.
(Total amounts of each mineral should be less than 1%; NRC requirements, even for breeding,
are only 0.5% for calcium and 0.4% for phosphorus.) For purified diets, where the phosphorus
is more available, Reeves et al. (1993b) recommend a weight ratio of 1.7.
More than 40 minerals have been suggested to have some essential role in the health of the
mouse. Besides the 13 minerals and trace elements that have been identified as essential in
studies of mice or rats (Table 10.1), and that are typically added to commercial rodent diets in a
mineral premix, numerous elements have been ascribed some essential function, but are
required in such low amounts that the requirement is thought to be met by the concentrations
found in the ingredients of natural-ingredient diets or in drinking water. In contrast, in purified
diets, some of these elements may be missing (Reeves et al., 1993a). For example, long-term
survival (beyond two years) of rats fed the purified diet AIN-93M (maintenance) was lower than
on a natural-ingredient diet (Duffy et al., 2002), and the benefit of diet restriction was
diminished for rats on AIN-93M.
10.A.6. Quality control

Typically, near infrared spectroscopy is used for proximate analysis to rapidly determine
concentrations of protein, fat, fiber, and ash in feed. Chemical analysis is used for determination
of caloric content and concentrations of essential nutrients.
Reputable manufacturers provide batch analysis certificates when they ship feed. These
certificates provide information on proximate analysis, analysis of selected nutrients, and of
selected contaminants. It is good practice, however, to use the services of an independent
laboratory to confirm nutrient concentrations in your feed at least annually. This gives you
precise values for food under storage conditions at your facility. This is especially important if
you autoclave your food.
10.A.7. What we do at The Jackson Laboratory

At The Jackson Laboratory, we use several standard diets. For most production colonies, we use
a closed formula, custom diet based upon the NIH-31, 4% fat (w/w) or 6% fat (w/w) diet
(LabDiet 5LG6/5K52, 4%; 5K52/5K67, 6%). In certain breeding colonies, we use a
comparable formulation that is a minimum of 10% fat (LabDiet 5K20). All of our mouse food
is decontaminated before use. For most mice, we sterilize mouse food by autoclaving. For
specialized needs in some colonies, we use pasteurized or irradiated food. The diets for our
production mice are available on the strain datasheets (www.jax.org/jaxmice/query), under the
Health & husbandry tab. For additional information, telephone us at 1-800-422-6423 (North
America) or 1-207-288-5845 (International) or email us at [email protected].
We check autoclaved feed for hardness and clumping, which are common consequences of the
autoclaving process. To ensure that the autoclaved pellets are not too hard for the mice, we
regularly conduct hardness tests on our autoclaved feed. We follow strict SOPs and reject
pellets that exceed our hardness limit. To break up any clumping, animal care technicians break
up large chunks while the feed is in the bag, and break up smaller clumps as required when
feeding the mice.
To precisely determine the nutrient levels in the diet and evaluate the performance of our
autoclaves, we use an independent testing laboratory to analyze feed twice yearly. Normally we
test protein, fat, fiber, ash, calcium, and phosphorus levels in January and July; we test vitamin
A, vitamin B, and lysine in April and October. We follow strict SOPs for food collection and
analysis.
We never store food for longer than six months after the mill date.
10.B. Treating water

10.B.1. Guidelines for safe water
Water for mice must be treated to minimize microbiological contamination. To date, although
no organization has published specific guidelines for safe water, several water treatment
methodsincluding autoclaving, acidification, hyperchlorination, reverse osmosis, and
ultraviolet light exposureare in common use. Both the NRC (1995, 1996) and AALAS (2006)
provide details.
There is no standard for the type of water to provide mice: tap, bottled, or distilled. Tap water
has widespread variations, such as in mineral content, general hardness, or presence of flouride,
but the generally accepted convention is that if water is good enough for the community, it is
good enough for the mice. Please note, however, that this axiom does not recognize the potential
for the influence of water variation on research results. And, because there is no concerted effort
to standardize water composition, the best general strategy for a researcher is to use a consistent
source of water and consistent treatment method.
It also is important to ensure that your water delivery system is clean. If you have an automatic
watering system, this means following appropriate maintenance per the manufacturers
recommendations. If you use water bottles, they should be sanitizedor even sterilized
between uses.
10.B.2. What we do at The Jackson Laboratory

At The Jackson Laboratory, to suppress the growth of bacteria and mold in the water we use in
all mouse colonies, we treat water with hydrochloric acid (HCl) to a pH of 2.83.1. In our trials,
this pH level suppressed growth of Pseudomonas aeruginosa for more than five weeks. To
replace any vitamin K that is destroyed by autoclaving the mouse food, we also add menadione
sodium bisulfate (MSB) to the water at a rate that results in an average concentration of 0.40
mcg MSB/ml of water. Water bottles are filled, capped, and wrapped in plastic in a central
facility and shipped to individual mouse rooms.
10.C. References
American Association for Laboratory Animal Science (AALAS). 2006. Laboratory Mouse
Handbook. (Gografe SI, ed.) Memphis, Tennessee.
Baldelli B. 1967. Gamma radiation for sterilizing the carcasses of foot-and-mouth disease virus
infected animals, Microbiological problems in food preservation by irradiation. International
Atomic Energy Agency, Vienna. pp. 7785.
Cockell KA, LAbbe MR, Belonje B. 2002. The concentrations and ratio of dietary calcium and
phosphorus influence development of nephrocalcinosis in female rats. J Nutr. 132:252256.
Duffy PH, Lewis SM, Mayhugh MA, McCracken A, Thorn BT, Reeves PG, Blakely SA,
Casciano DA, Feuers RJ. 2002. Effect of the AIN-93M purified diet and dietary restriction on
survival in Sprague-Dawley rats: implications for chronic studies. J Nutr. 132:101107.
Eggum BO. 1979. Effect of irradiation on protein and amino acids in laboratory rodent diet,
Decontamination of animal feeds by irradiation. International Atomic Energy Agency, Vienna.
pp. 5567.
Ford DJ. 1979. Observations on the influence of irradiation on fat and vitamin A in dry
laboratory cat diets, Decontamination of animal feeds by irradiation. International Atomic
Energy Agency, Vienna. pp. 7781.
Goodrick CL. 1978. Body weight increment and length of life: the effect of genetic constitution
and dietary protein. J Gerontol. 33:184190.
Gordon MN, Osterburg HH, May PC, Finch CE. 1986. Effective oral administration of 17 betaestradiol to female C57BL/6J mice through the drinking water. Biol Reprod. 35:10881095.
Guo JY, Li X, Browning JD Jr, Rottinghaus GE, Lubahn DB, Constantinou A, Bennink M,
MacDonald RS. 2004. Dietary soy isoflavones and estrone protect ovariectomized ERalphaKO
and wild-type mice from carcinogen-induced colon cancer. J Nutr. 134:179182.
Isler D, Brubacher D. 1999. Effect of sterilization on vitamin retention in laboratory animal
feed, Proceeding of the International XII ICLAS and VII FELASA Joint Meeting. Tur-Mari JA,
Orellana-Muriena JA (eds). London, Laboratory Animals Ltd. pp. 242248.
Knapka JJ. 1997. Natural-ingredient diets: managing the variation in dietary nutrient
concentrations. Lab Anim. 26:4042.
Knapka JJ, Smith KP, Judge FJ. 1977. Effect of crude fat and crude protein on reproduction and
weaning growth in four strains of inbred mice. J Nutr. 107:6771.
Leto S, Kokkonen GC, Barrows CH Jr. 1976. Dietary protein, life-span, and biochemical
variables in female mice. J Gerontol. 31:144148.
Mobbs CV, Cheyney D, Sinha YN, Finch CE. 1985. Age correlated and ovary dependent
changes in relationships between plasma estradiol and luteinizing hormone, prolactin and
growth hormone in female C57BL/6J mice. Endocrinology. 116:813820.
National Research Council. 1995. Nutrient Requirements of Laboratory Animals, Fourth
Revised Edition. National Academy Press, Washington, DC.
National Research Council. 1996. Guide for the Care and Use of Laboratory Animals.
Grossblatt N (ed). National Academy Press. Washington, DC.
Reeves PG, Nielsen FH, Fahey GC Jr. 1993a. AIN-93 purified diets for laboratory rodents: final
report of the American Institute of Nutrition ad hoc writing committee on the reformulation of
the AIN-76A rodent diet. J Nutr. 123:19391951.
Reeves PG, Rossow KL, Lindlauf J. 1993b. Development and testing of the AIN-93 purified
diets for rodents: results on growth, kidney calcification and bone mineralization in rats and
mice. J Nutr. 123:19231931.
Stoltzner G. 1977. Effects of life-long dietary protein restriction on mortality, growth, organ
weights, blood counts, liver aldolase and kidney catalase in Balb/C mice. Growth. 41:337348.
Tobin G, Stevens KA, Russell RJ. 2007. Nutrition, in The Mouse in Biomedical Research,
2nd Edition, Vol. III, Normative Biology, Husbandry, and Models. Fox JG et al. (eds). American
College of Laboratory Animal Medicine Series; Academic Press, Elsevier, Burlington, MA. pp.
321383.
Van den Broek FA, Beems RB, van Tintelen G, Lemmens AG, Fielmich-Bouwman AX,
Beynen AC. 1997. Co-variance of chemically and histologically analyzed severity of dystrophic
cardiac calcification in mice. Lab. Anim. 31:7480.
World Health Organization (WHO). 1999. High-dose irradiation: wholesomeness of food
irradiated with doses above 10kGy. World Health Organisation, Geneva.
Yuen DE, Draper HH. 1983. Long-term effects of excess protein and phosphorus on bone
homeostasis in adult mice. J Nutr. 113:13741380.
229
Chapter 11: Recordkeeping and Identification of

Mice
Joanne M. Currer, Dorcas Corrow
Accurate recordkeeping is critical to a colony manager. In a production colony, accurate records
allow you to trackand maximizeproduction of your colony and monitor the health and
genetic integrity of your mice. In a research colony, accurate recordkeeping is a mandatory
requirement to avoid the corruption of data.
The objective of this chapter is to provide some guidelines for recordkeeping activities
necessary in both production and research colonies. Well also explain some of the
recordkeeping strategies we use at The Jackson Laboratory.
11.A. Identifying individual mice ....................................................................................230
11.A.1. Identification methods ...............................................................................230
11.A.2. What we do at The Jackson Laboratory ...................................................231
11.B. Keeping day-to-day records ...................................................................................232
11.B.1. Recommendations and strategies ..............................................................232
11.B.2. What we do at The Jackson Laboratory ...................................................233
11.C. Choosing colony management software................................................................234
11.C.1. Advantages of a colony management system ..........................................234
11.C.2. Considerations when choosing a colony management system ...............234
11.C.3. The Jackson Laboratorys Colony Management System (JAX-CMS)
for research mouse colonies ......................................................................235
11.D. References ...............................................................................................................235
11.A. Identifying individual mice

11.A.1. Identification methods
The five most common ways of identifying individual mice are ear punch, ear tag, tattoo, toe
clip, and microchip. Table 11.1 summarizes the advantages and disadvantages of each method.
Further details, including references, are provided at www.jax.org/jaxmice/faq/idsystem.
Table 11.1. Advantages and disadvantages of common mouse identification methods.
Identification
method
Advantages
Disadvantages
Ear punch
When done by experienced technician,

procedure is quick and accurate.
Cannot be administered until mouse

is 3 weeks old.
Works best when numbers are
limited from 199.
May be altered or lost through
fighting or grooming.
Mistakes are difficult, perhaps
impossible, to reconcile.
Immobilizing mice while retaining
access to ear pinnae requires
extensive practice. For less
experienced technicians, it may be
necessary to anesthetize the mouse to
accommodate more legible punching.
Ear tag

procedure is quick.
Provides a wide range of ID numbers.
More expensive than ear punching.

Ear tag is often lost over time
through grooming or fighting.
Ear often becomes inflamed.
Tattoo
On all but heavily pigmented tails, tattoo

remains visible throughout the mouses
entire life.
Can be used on infant mice (tail or toe
pad); it is not disabling (as is toe
clipping).
When used on infant mice, tattoos

fade as animal grows.
Requires special equipment.
Toe clipping
Unambiguous method for identifying

pups after 4 days of age.
procedure is quick and accurate.
Not recommended for weanlings or

older mice.
Anesthesia is recommended if pup is
older than 7 days.
Permanently affects ability to grip;
may affect grooming.
Microchip
(subcutaneous
transponder)
Provides unambiguous, non-invasive

identification.
Lasts throughout the life of the mouse.
Combined with computerized recording,
mouse numbers can be transferred
directly to a computer, eliminating
transcription errors.
Chips can be recycled.
Mice must be 45 weeks of age

before being chipped.
Chips are more expensive than other
methods.
Implantation requires anesthesia.
Chapter 11: Recordkeeping and Identification of Mice 231

We use multiple methods of mouse identification at The Jackson Laboratory. If we need to
identify specific mice in our production colonies, we use ear punches (Figure 11.1). In our
research colonies, we may use ear punches or ear tags. For some studies, such as aging studies,
when it is essential that identifiers are readable for more than one year, we use microchips.
11.A.2.a. Our ear punch codes

Figure 11.1 illustrates the ear punch codes we use at The Jackson Laboratory. These codes
allow us to distinguish 99 mice. When we need to unambiguously identify 15 or fewer mice, we
sometimes use a subset of the codesthe punches for 01, 03, 10, and 30, which are on the
rostral and caudal edges of the ear pinnae and are very easy to distinguish from each other.
Using this method, codes would represent just the following numbers: 1, 3, 4, 10, 11, 13, 14, 30,
31, 33, 34, 40, 41, 43, 44. (Note: Sometimes, customers may receive JAX Mice that have ear
clips. While not an official ID system, the clips provide a way to identify mice within a cage
for genotyping purposes.)
Figure 11.1. Dorsal view of ear punch coding used at The Jackson Laboratory.
Adapted from Dickey (1975).
11.A.2.b. Our pedigree numbering system for JAX Mice

At The Jackson Laboratory, our pedigree system for inbred strains was designed to track
individual animals and their ancestral relationships in our production colonies. This system
allows our colony managers to unambiguously identify and remove any mice that could
compromise the genetic integrity of the inbred line. Each breeding unit (a sisterbrother mated
pair) within a foundation stock (FS) is given a unique pedigree number that is entered into the
pedigree register.
When we transfer mice from an FS to a pedigreed expansion stock (PES) to begin colony
expansion, we trace the full sibling breeding units by expanding the parental FS pedigree
number to track the generations removed from the FS pair as well as the specific litter from that
mating. Figure 11.2 illustrates our pedigreed numbering system and provides several examples
of pedigree numbers for specific PES mice of our C57BL/6J (000664) strain. (For a description
of our production colony structure and its advantages, see 8.B.1, Our mouse colony structure:
how it helps us maintain genetic quality control.)
Figure 11.2. Pedigree numbering system used for inbred mice at The Jackson Laboratory
We also have standard operating procedures (SOPs) that address issues related to lengthy
pedigree numbers and numbering systems for non-standard pedigrees. If you have any questions
about pedigrees of any JAX Mice, please call Customer Service at 1-800-422-6423 (North
America) or 1-207-288-5845 (International), or email us at [email protected].
11.B. Keeping day-to-day records

Keeping accurate records for an entire colony of mice is a challenge. For some mice, the most
relevant data represent their ancestry and birthdates; for other mice, relevant data must cover the
animals entire life, including dates and effects of treatments and date of death. Data also must
be stored securely. Over the years at The Jackson Laboratory, we have developed some
recordkeeping strategies and techniques that work for our production colonies as well as our
research colonies.
11.B.1. Recommendations and strategies

The birth record for a mouse pup should include a unique ID number that is linked to the unique
ID numbers of its parents. Other information generally includes strain or genotype, generation,
and dates of birth and weaning. Breeding records also might include pedigree number (if
applicable); dates of mating setup, observation of vaginal plugs (if applicable), dates of
parturition; quantities and sexes of pups born and weaned; date retired from breeding; other
observations. In a research facility, daily recordkeeping can also include treatments, dates of
treatments, date of death, and reason for death.
Technicians without access to a data entry program must handwrite information on cage cards,
and perhaps in pedigree books. Cage cards of multiple colors can help distinguish groups of
mice. To avoid problems with illegible handwriting, we recommend the use of either sharpened
pencils with lead of a medium hardness (greater than 2.5 HB) or permanent marking pens with
fine points. Softer lead may smear, standard ink may bleed, and markers with broad or flattened
tips may create unclear text or numbers.
We recommend taking the time to set up SOPs or shortcut codes or both for certain studies.
As examples, in a study that relies on necropsies, both the person who necropsies the mice and
the pathologist who reads the reports must know exactly what distinguishes a lump from a
light pink mass from a tumor.
Store cage cards and other paper-based data in a safe place. Label storage boxes or file drawers
clearly, including strain and date. Remember that, if and when you need records (for example, if
you suspect genetic contamination), you probably will not have the luxury of time to search
through thousands of records to find the ones you need. Back up computer data regularly. If
necessary, store backup files in a separate building.

11.B.2.a. Production and repository colonies
In our production and repository colonies we have recently implemented a state-of-the-art
computer system that integrates our colony management, ordering, and invoicing systems.
Because we know exactly how many of each strain of JAX Mice are available at any given
time, when our customer service representatives get an inquiry or an order, they can rapidly
provide current, accurate information. Once an order is placed, shipping documents and
invoices are automatically created, speeding delivery and simplifying billing.
The data analysis features of our system enable our colony managers to easily review breeding
records and to manage anticipated requirements for mice so they can set up breeding
accordingly. This integrated system will help us achieve our goals of providing the best
customer service possible and of managing our colonies so that we have JAX Mice available
when researchers need them.
11.B.2.b. Research colonies

In our research colonies, it is the responsibility of investigators to maintain and organize their
own data. Some investigators keep handwritten records. Some use combinations of handwritten
records and Microsoft AccessTM or Microsoft Excel. Others use computer systems such as
The Jackson Laboratorys Colony Management System (JAX-CMS), a multi-user relational
database management system for managing animal colonies in a research environment (see
11.C.3). Any records on a computer connected to our network can be backed up automatically
on a daily basis.
11.C. Choosing colony management software

11.C.1. Advantages of a colony management system
Colony management software provides several advantages:
Accurate, complete records. A well-designed data entry form can screen data input and help
prevent missing data or erroneous data entry. A hand-held data entry device makes data entry
convenient.
Laser-printed cage card data. Printed cage cards can present complete informationincluding
full strain namesin identical formats and also prevent legibility problems related to faint or
illegible handwriting or smeared ink. Laser printing is permanent and will not bleed when
wet.
Flexible data analysis. Computerized data can be filtered and sorted to facilitate reporting and
analyses.
Thorough, efficient recovery from breeding errors and genetic contamination. Should
breeding errors occur, the pedigree can be tracked via the computer rather than by gathering
and sorting cage cards.
11.C.2. Considerations when choosing a colony management

system
When selecting a software package, considerations include the following:
Ease of data entry. Are input forms designed so they are logical for technicians to use? Will
you have enough terminals or data entry devices so that no one has to wait to enter data?
Types of tasks. Does the system accommodate any tasks you need to track? Is the system
flexible enough to accommodate any new activities you might want to track in the future?
Flexibility of reporting. Do the standard reporting and printing templates meet most of your
needs? Does the system allow you to design your own reports?
Compatibility with other software. Is the file structure compatible with, or can the files be
exported into, a software package you routinely use? This is especially critical if you like the
data analysis and reporting flexibility of packages such as Microsoft AccessTM or Microsoft
Excel and want to continue to use them with data captured by the new software.
Compatibility with Microsoft Excel is also important if people in your organization use
multiple types of statistical software.
This flexibility is especially relevant for future use of the data: Should the colony
management system become obsolete and unsupported, if you cannot use the data in another
system, they will be unusable unless you manually re-enter them or develop a way to convert
them.
Robustness. Is the system designed to accommodate the amount of data traffic you can expect
on a routine basis? Will it allow for expansion?
Barcode scanning. Can the system scan barcodes? This is an important feature if you use
microchips for mouse identification.
Product support. Is documentation technically correct and usable by your staff? Are quick
reference cards available? Is online help available? Is technical support available?
11.C.3. The Jackson Laboratorys Colony Management System

(JAX-CMS) for research mouse colonies
The Jackson Laboratorys Colony Management System (JAX-CMS) was written by researchers
at The Jackson Laboratory in response to demand within The Jackson Laboratory for a system
that would execute the core functionality of colony management from an intuitive, easy-to-use
interface. Since its initial release in 1998, it has been widely used within The Jackson
Laboratory and by a number of outside institutions.
JAX-CMS currently runs as a Microsoft
AccessTM application. It can be executed
remotely from UNIX or Macintosh
environments using technologies such as a
Citrix server. Features include the following:
Tracking of animal status, pedigree, mating
and litter records.
Logging of genotype.
Management of animal pens.
Printed cage cards.
Tracking of experimental data.
Advanced database queries.
Report generation.
Bulk data entry.
JAX-CMS is free!
JAX-CMS, tutorials and support are available
free to the public at
http://colonymanagement.jax.org. End user
support is provided through our moderated
listserv discussion group, which you can join
after you download the software.
11.D. References
Dickey MM. 1975. Keeping Records, in Biology of the Laboratory Mouse. Green EL (ed).
Dover Publications, NY.
237
Chapter 12: Introduction of New Mice into a

Colony
Joanne M. Currer, Dorcas Corrow, Kevin Flurkey
The challenges of introducing new mice into a colony include preventing the introduction of
pathogens, managing the potential for genetic contamination, and acclimating the mice to their
new environment so that the physiological effects of any shipping stress have lapsed before they
are used for research.
The objective of this chapter is to provide guidelines for meeting these challenges. Well also
provide specific steps to take when you introduce JAX Mice into your facility. And well
highlight what we do at The Jackson Laboratory.
12.A. Precautions when introducing live mice..................................................................238
12.A.1. Protecting against pathogens .......................................................................238
12.A.2. Protecting against genetic contamination ...................................................238
12.A.3. Identifying and recovering a loss of phenotypic expression.....................238
12.B. Handling newly arrived mice ...................................................................................238
12.B.1. Recognizing and managing the physiological effects of stress
related to transportation ...............................................................................238
12.B.2. Special handling for newly arrived, wild-derived inbred mice.................239
12.B.3. What to do if you have an automatic watering system and your
newly arrived JAX Mice wont use it.......................................................240
12.C. What we do at The Jackson Laboratory ..................................................................240
Acknowledgments: We would like to thank Peggy Danneman for her valuable input to this
chapter.
12.A. Precautions when introducing live mice

12.A.1. Protecting against pathogens
Each mouse you introduce into a colony has the potential to carry infectious agents from its
previous colony. Once a new infectious agent becomes established in a colony, it is very
difficult and expensive to eradicate. And as infestations from new mice accumulate, a poorly
protected colony can become a menagerie of pathogens.
Even the shipping container can introduce
pathogens
Keep in mind that the outside of the shipping
container may have been exposed to a variety of
infectious agents. Before you unpack the mice, we
recommend disinfecting the outside of the
shipping container by wiping it thoroughly with a
solution of a disinfectant such as 70% ethanol.
When introducing mice into conventional colonies, if mice are

purchased from reputable suppliers or are transported from
another mouse room on site with higher pathogen protection
standards, precautions for pathogen protection are generally not
taken. For colonies in which pathogen protection is a concern,
however, quarantine of new mice is a necessity.
Quarantine procedures involve separation of new mice until you

are satisfied that their health status is equal to or higher than
that of other animals in the colony. Technicians must take special care to keep the mice separate
and to disinfect the caging system and changing areas to prevent the spread of any pathogen that
might be present. Another precaution is for technicians to handle quarantined mice only after all
other mice are cared for. (For details on pathogen protection, please see Chapter 7, Animal
HealthPreventing, Identifying, and Eradicating Microbial Contamination.)
12.A.2. Protecting against genetic contamination

When you introduce mice that are a new genotype, you must take precautions to ensure that
existing stock does not become genetically contaminated. If you cannot house the new mice in a
separate room, try to house them next to mice that have a different coat color. Keep diligent
records. If a mouse escapes, find it immediately. Do not run the risk that it might breed. Details
on preventing genetic contamination are provided in Chapter 8, Genetic Quality Control
Preventing Genetic Contamination and Minimizing Effects of Genetic Drift.
12.A.3. Identifying and recovering a loss of phenotypic expression

Because expression of a phenotype can depend on internal or external environments, when a
strain is introduced into a new colony, conditions may be sufficiently different to alter
phenotypic expression. For example, in most mouse models of inflammatory bowel disease
(IBD), a complex enteric flora is required to produce gut pathology in young adults. In colonies
where not all the required enteric flora are present, the phenotype is not expressed until middle
age.
It also is not unusual for a phenotype to be lost when a mouse strain is rederived. For example,
when the NONcNZO10/LtJ (004456) strain, a polygenic model for male type 2 diabetes, was rederived into a production barrier colony at The Jackson Laboratory, diabetes was attenuated. A
higher fat diet was required to reconstitute the phenotype. Although a genetic basis for any
phenotypic loss must be considered, altering the environment may restore the phenotype.
12.B. Handling newly arrived mice

12.B.1. Recognizing and managing the physiological effects of
stress related to transportation
When new mice arrive at your facility, they are not ready for research. Since they were packed
for shipment, they have been under extreme stress and their physical condition is not normal.
Elevated stress-related hormones have promoted catabolic states and inhibited anabolic states
that will have physiological effects for at least a week after arrival. Eating behavior,
aggressiveness, and numerous other biological systems related to stress response can be
affected. This response is so universal that any research results obtained from mice within 72
hours of receipt must be considered unreliable.
Chapter 12: Introduction of New Mice into a Colony 239
Keep in mind that even moving your mice from one mouse room to another within your facility
is stressful to them. Although the actual trip might be short, their new location might have
different odors, light levels, sounds, air circulation, temperatureseven new technicians. This
combined stress will affect some biological variables within minutes, especially those that are
influenced by epinephrine. The stress might not affect other
variables for 24 hours.
We recommend taking the following precautions when you
receive new mice:
Disinfect the shipping container and remove the mice as soon
as possible. Provide fresh water and food. Even though the
mice have been transported with a moisture source, they might
be hungry or relatively dehydrated.
Monitor the mice to ensure that they are drinking and eating.
If they are not drinking water using the water delivery system
in your facility, provide an alternate supply of water until they
are familiar with your system. If they are not eating, provide
an alternate food source or place some food on the cage floor.
How can you tell when mice are no longer

stressed and are ready for research?
One way to monitor effects of stress on specific
strains following shipping (or in specific
environments) is to monitor body weight. Body
weight recovery will stabilize when the mice have
adjusted to new conditions. If possible, compare
weight data on newly arrived mice against normal
mice of the same age, sex, and strain in your own
colony. Because an adult mouse at a stable weight
consumes, and burns, about 10% of its body
weight each day, body weight will rapidly reach a
new steady-state level in response to a change in
environment or nutrition. Typically one week is
sufficient time for adjustment.
So, just how long will it take for the physiology of your mice to
normalize in their new environment so they are ready for research? If the mice were moved to a
new facility in a vehicle such as an airplane, truck, or van, wait for a week before conducting
research. If the mice were moved from room to room within a facility, wait three days.
12.B.2. Special handling for newly arrived, wild-derived inbred mice

Wild-derived inbred mice present challenges additional to those of standard inbred mice. For
example, in contrast to most inbred mice, which run from light, wild-derived mice may run
toward light, presumably associating it with an escape route. And, they are generally
hyperactive and exceptionally quick to bolt. Following are several hints for unpacking a
shipment of wild-derived mice:
Provide an environment that will keep escapees contained. Place the entire shipping container
in a closed, hooded changing station or at the bottom of a deep container such as a sterilized
garbage can.
Before opening the shipping container, have a new cage ready.
If you have the space to maneuver, place an extra cage lid over the opening of the shipping
container. As you open the container, slide the lid into place over the opening and move it
around as needed to create smaller openings from which to remove the mice. (This strategy
also allows you to see the mice and perhaps anticipate escape moves.)
Because some wild-derived inbred mice tend to burrow in bedding, always check the bedding
thoroughly for any hidden mice. If the container has a shipping label, verify the quantity of
mice in the container with the quantity noted on the label.
After you have transferred your new wild-derived mice into their new cages and you are certain
that they are eating and drinking, try to disturb them as little as possible. For more information
on housing and caring for wild-derived mice on a routine basis, please refer to 9.C.3, Caring
for wild-derived inbred mice.
12.B.3. What to do if you have an automatic watering system and

your newly arrived JAX Mice wont use it
Mice at The Jackson Laboratory drink from water bottles with sipper holes in the bottles or
caps. Sometimes, upon arrival at an institution that uses an automatic watering system, JAX
Mice will notor do not know how touse it. This problem is more likely with very young or
recently weaned mice (i.e., shipped within 24 hours of weaning) and appears to be strain
dependent. (For example, anecdotal evidence suggests that some NZB/BlNJ [000684] mice
have difficulty adapting to a new water source.)
If your facility is equipped with an automatic watering system, we recommend that you make
sure your newly unpacked JAX Mice are drinking water from it. If you notice any symptoms
that might indicate a problemweight loss, lack of appetite or dehydration, for examplehere
are a few steps you might take:
Tap the water valve in the mouse cage until a small bead of water forms on the surface. Most
mice will find this water and recognize it as their new water source.
Place a water bottle on the cage or set a small container of water or semi-moist food or gel
pack on the floor of the cage. After a few days, remove the alternate water source and try the
automatic system again.
It is important to note that, if mice are not drinking adequate water, they are experiencing stress.
Before you use mice for research, be sure they have been drinking water normally for at least 48
hours.
12.C. What we do at The Jackson Laboratory

When we move mice from our production facilities to our research facilities at The Jackson
Laboratory, mice spend less than one hour in a shipping container. We follow strict entry
procedures through materials locks at the receiving mouse room. We also allow the mice to
acclimate to their new environment before using them for research.
When we move mice among our research colonies, we never introduce them into a room that
has a health status higher than that of the room in which they originated. We wrap the cages in
the materials lock of the room they are leaving and unwrap them in the materials lock of the
room they are entering. We do not conduct research on the mice until we know they are
acclimated to their new environment.
When we receive mice from outside The Jackson Laboratory or transfer mice from one of our
own researchers to our production facility, the mice are quarantined and rederived. These mice
are bred in a separate dirty facility and their offspring are introduced into the clean area of
our campus, following testing for excluded microorganisms. For information about our
importation program, please see Chapter 7, Animal HealthPreventing, Identifying, and
Eradicating Microbial Contamination.
241
Chapter 13: Breeding Strategies and Techniques

Joanne M. Currer, Dorcas Corrow, Marge Strobel, Kevin Flurkey
The obvious goal of a breeding colony is to provide healthy, genetically well-defined mice that
are suitable for use in research. Colony managers have an additional challenge: to do this in the
most efficient, cost-effective way possible.
The objective of this chapter is to provide guidelines for maximizing the breeding of your mice.
We include biological breeding data, factors that can affect breeding, and several techniques
that assist with breeding. At the end of the chapter, youll find a table to help you troubleshoot
breeding problems you might encounter.
It is worth noting that, although the logic of breeding strategies is quite straightforward, the
behavior of mice often is not. Even littermates might behave differently under very similar
circumstances. Thus, wise colony managers and animal caretakers customize strategies and
techniques that work best for their mice in their environment.
Note: This chapter covers general breeding strategies and techniques. For information about
breeding schemes for developing and maintaining specific categories of mice, see
Chapter 3, Categories of Laboratory Mice: Definitions, Uses, Nomenclature.
13.A. Factors that affect the breeding of laboratory mice ................................................242
13.A.1. Biological breeding data..............................................................................242
13.A.2. Environmental factors that can affect breeding performance ...................243
13.A.3. Strategies for setting up and monitoring breeding to optimize
colony production ........................................................................................244
13.A.4. General guidelines for successful breeding................................................244
13.B. Breeding schemes .....................................................................................................246
13.C. Sizing a breeding colony for a research program ...................................................246
13.D. Strategies for maintaining a line or strain without expansion ................................247
13.E. Using reproductive techniques .................................................................................247
13.E.1. Standard reproductive techniques ...............................................................247
13.E.1.a. Determining pregnancy: vaginal plugs and palpation ..............247
13.E.1.b. Timing pregnancies using the Lee-Boot and
Whitten Effects............................................................................248
13.E.1.c. Fostering a litter ..........................................................................249
13.E.2. Assisted reproductive techniques (ARTs) ..................................................250
13.F. Maintaining the genetic integrity of your colonies .................................................250
13.F.1. Preventing genetic contamination and minimizing genetic drift ..............250
13.F.2. Confirming phenotypes and genotypes ......................................................250
13.G. Troubleshooting breeding problems ........................................................................252
13.H. Resources...................................................................................................................253
13.I. References .................................................................................................................253
Acknowledgments: We would like to thank James Yeadon for his valuable input to this chapter.
13.A. Factors that affect the breeding of laboratory mice

Breeding performance of laboratory mice depends on both biological and environmental factors.
Some factors apply to all strains; others are strain dependent. Some factors relate specifically to
your own situation and requirements.
13.A.1. Biological breeding data

Table 13.1 provides a summary of general reproductive characteristics for mice. For many of our
most popular strains of JAX Mice, we provide more detailed information in Chapter 4,
Characteristics of Popular Strains of JAX Mice, Including Reproductive Performance. Also
see the JAX Mice strain database (www.jax.org/jaxmice/query) and the Mouse Phenome
Database (MPD; www.jax.org/phenome).
Table 13.1. Reproductive characteristics for most inbred strains of laboratory mice.
Characteristic
Normal value
Sexual maturity
48 weeks of age
Males usually reach sexual maturity by 6 weeks, females by 46

weeks.
Comments
Estrous cycle
4-day or 5-day cycle.
The normal cycle can be interrupted by mating, pheromones, vibration,

noise, and other environmental stresses.
Post-partum estrus
6- to 8-hour period
This is the estrous period females enter within a few hours after giving
birth. If a male is in the cage, mating and pregnancy are likely.
Ovulation rate
412 ova per estrus
Strain dependent.
Litter size
212+ pups (average 6

8 pups)
Strain dependent. Pattern is for litter size to increase, reach a peak at

about 34 months of age, then start decreasing.
Fertility rate
50100%
With some strains, all pairs of mice are fertile; with others, as few as
50% are.
Gestation length
1821 days
Gestation length is typically 1819 days for most strains; may be

longer if litters are smaller (4 or fewer pups) or mothers are older.
Time between litters
2250 days
Typically the shortest time between litters occurs between 34 months

of age (between the first and second litter), then progressively
increases.
Generation time
About 10 weeks
Strain dependent. Conception-to-conception time is determined as

follows: 3 weeks gestation, 34 weeks suckling, 13 additional weeks
until sexual maturity. But, generation time for the first litter is often
longer.
Weaning age
2128 days
In husbandry context, the age at which pups are removed from their
mother, not when they start eating solid food. Varies among strains;
depends on weanling size and maturity. Most strains are weaned at 21
days, some at 28 days. Do not remove pups from mother before 17
days unless they are transferred to a foster mother.
Total litters
28
Total litter number varies by strain. A total of 4+ litters is typical, but

some strains produce as few as 1 or 2 litters.
Reproductive lifespan
(female)
Terminates at 612
months of age
Strain dependent. For inbred strains, fecundity usually begins to

decrease with the 3rd litter. By 68 months, some females become
infertile, and litter size for most females of most strains has diminished
to the point that it is more economical to set up a new breeding pair.
Reproductive lifespan
(male)
Terminates at 12-14
months of age
Strain dependent. Fertility in some strains decreases starting at 10

months.
Delayed implantation
n/a
Implantation normally occurs during the fifth day after conception.

However, if a female is nursing, implantation may be delayed for more
than a week, during which time embryonic development is held in
suspension.
Seasonal breeding
fluctuations
n/a
Some strains are susceptible to changes in breeding behavior based on

season.
Chapter 13: Breeding Strategies and Techniques 243
13.A.2. Environmental factors that can affect breeding performance

Whether you are maintaining a large production colony or simply breeding several pair of mice
for a small experiment, one of the most important things you can do to foster successful
breeding is to provide your mice with a quiet, comfortable, stable environment, free from noise
and vibration, with a consistent light cycle. You cannot overestimate the adverse affect that
environmental stress can have on breeding. Table 13.2 provides information that can help you
alleviate stress and improve the breeding performance of your laboratory mice.
Table 13.2. Environmental factors that can affect breeding.
Factors
Action to promote successful breeding
Comments
Location of
cages
Avoid locating cages near a heavily trafficked or noisy

area, such as near a door or sink or a loudspeaker used
for paging.
Place cage racks several inches from the wall to prevent
building vibrations from transferring to the cages.
Changes in levels of noise and vibration can

decrease breeding performance and may induce
mothers to resorb litters, cannibalize their pups,
or stop breeding.
Construction-related noise and vibrations may
be especially problematic.
Lighting
Maintain a single, consistent, lighting cycle. The most

common cycles are 14:10 (on:off) and 12:12.
For wild-derived mice, use less intense lighting.
Disruption of the light cycle may have an

adverse effect on breeding.
Barometric
pressure
Maintain a stable barometric pressure.
Falling barometric pressure can cause some

strains to become hyperactive, which reduces
breeding performance.
Temperature
and humidity
Keep the temperature at 1626 C (6479 F)

Keep the humidity at 4060%.
Thermoneutral temperature for mice is around

2728 C (8082 F). In contrast, for humans, it is
about 2223 C (7274 F).
Air quality
and odors
Keep the room air fresh, free from strong odors.

Establish a no perfume policy for caretakers,
technicians, or anyone who works with the mice.
Use clean forceps or clean (or new) gloves for each
cage.
Mice are extremely sensitive to strong or

noxious odors, but they like their own scent to
be strong in their environment.
Noxious fumes may reduce breeding
performance.
Handling
Work gently, slowly, and quietly when handling

breeding mice.
Try to regularly assign caretakers to the same cages so
that the mice receive consistent care with familiar
handling and odors.
Avoid changing cages more often than once a week; if
females are ready to give birth, skip cage changing until
pups are 2 days old or you can see milk spots.
Minimize handling and checking on the mice, especially
if mice are pregnant or giving birth, or have new litters.
Unless absolutely necessary, do not handle pups until
they are 3 days old.
Laboratory mice respond best to calm,

consistent handling.
Often, mice do not like new technicians.
Wild-derived mice are especially sensitive to
handling stress.
Bedding and
nesting
material
Provide nesting materials in the cage, especially if

bedding (such as pellets from corn cob) does not lend
itself to nesting.
The addition of material such as Kimwipes or

Nestlets can promote nesting.
Nesting behavior is strain dependent.
Diet
Provide food with a dietary fat content of 411% fat

w/w.
If mice have bad teeth, broken teeth (e.g., from gnawing
or malocclusion), no teeth, or other phenotypes that
affect their ability to eat normal mouse food, provide an
alternate food supply, perhaps either ground or
dampened food.
If mice cannot reach the normal water or food supply,
provide access to both on the cage floor.
The optimal percentage of fat in the diet, with

respect to fecundity, is strain dependent.
Optimal fat content ranges from 412% w/w; a
commercially available breeder diet with 9% fat
w/w works well for most strains of mice.
13.A.3. Strategies for setting up and monitoring breeding to

optimize colony production
Some breeding strategies involve timing and setup issues: when to set up mating, when to
swap breeders, when to replace breeders, how to improve breeding behavior. Table 13.3
provides guidelines for some of these issues.
Table 13.3. Strategies for maximizing productivity of a breeding colony.
Factors
Action to promote successful breeding
Comments
When to set up
breeding
Mate mice when they are 68 weeks old.
Note that it is not unusual for the first

litter to be smaller than the second or
third, which are typically the largest.
When to foster
pups
Foster pups
- if the mother does not nest the pups right away but
leaves them scattered around the cage , or
- if milk spots do not appear in the pups by the time they
are 24-hours old.
If you need offspring from a female who

is a poor mother, plan ahead to have foster
mothers ready when she gives birth.
Housing 2 females together will often
allow them to work together and
successfully raise 2 litters.
When to replace
breeding pairs
for optimal
performance
Replace breeding pairs as their reproductive performance

declines (typically 68 months of age; see Table 13.1.)
For a large colony, maintain a stable supply of breeding
pairs at various ages by replacing a specific percentage
on a weekly or monthly basis.
A colony of mixed-age breeders produces

a more consistent quantity of pups than
does a colony with mice of the same age.
When to replace
individual
female breeders
Replace female breeders when they

- produce no litter within 60 days of pairing (unless this
delay is normal for the strain),
- produce no litter within 60 days of their last litter, or
- produce litters but wean no pups for 23 litters.
When to replace
individual male
breeders
Replace male breeders

- when they reach 1 year of age, or
- if they are infertile with a young, fertile female.
When to cull a
litter
Reduce the number of pups in a litter if the mother is

having problems feeding the pups.
Some mothers may be unable to provide

milk for more than a few pups.
For segregating strains, remove unwanted
pups as soon as they can be phenotyped or
genotyped.
How to improve
breeding
behavior
With young females, use experienced males.

Isolate males for 2 weeks before pairing.
Rotate males within a strain among cages.
Males mature later than females; therefore

age at first litter for same-aged breeding
pairs is often determined by the male.
13.A.4. General guidelines for successful breeding

1. Breed healthy animals.
Specific acute illnesses that affect breeding include parvovirus (losses at 710 days) and
MHV (losses at weaning).
Chronic infectious illnesses that affect breeding include Pneumocystis (pneumonia) for
immunodeficient mice and Helicobacter spp. (if associated with colitis).
Infestation by ectoparasites, such as mites, can impair breeding.
Obese males often lose interest in breeding, and obese females are less likely to get pregnant.
If you must breed animals that are unhealthy, consider assisted reproductive techniques, pup
fostering, or rederivation.
2. Know your animals.

Make allowances for strains with characteristics that require special housing or care. For
example, some males, such as those of the SJL/J (000686) strain, attack their mates and
offspring. With very aggressive males, you may need to remove the male as soon as you
observe a vaginal plug (13.E.1.a). Also, do not place a new male in a cage with a female and
her litter; he may kill the pups. (This instinct is suppressed if the male is present when the
female gives birth.)
In cases where a constitutive disease such as type 1 diabetes will seriously impact breeding, it
may be possible to use a disease prevention strategy to keep the breeders disease free through
the reproductive period. For example, with NOD/LtJ (001976) breeders, the injection of a
single dose of complete Freunds adjuvant (CFA) at five weeks of delays the onset of
diabetes.
Be aware that interaction of a mutation with the genetic background may affect breeding
performance. If you transfer a mutation to a new background by backcrossing, maintain
earlier backcross generations until you are certain that the new background does not affect
any phenotypes of interest, especially those related to reproductive performance and survival.
3. Keep meticulous and accurate breeding records; review them

regularly.
Analyze breeding performance on a regular basis, especially the time between litters, litter
size, born:wean ratio. Adopt a detective-like demeanor and cultivate habits such as the
following:
Monitor genotype ratios for breeder units so you know what to expect.
Investigate deviations in breeding performance and phenotype immediately.
Consider strain characteristics when analyzing productivity. For example, females of some
strains routinely lose their first litters. Others, such as some 129 substrains, are poor
mothers.
Compare the breeding performance of the strain in your colony with data provided by your
supplier. If breeding data are not available for mutant strains, use data for the inbred strain
background. But recognize that all mouse colonies, even within a facility, are different and
that strains that breed well in one colony may not do as well in another. Thus, standard
values should not be considered absolute performance standards. Rather, they should be used
as guidelines to indicate the breeding potential of the strain and to help identify breeding
problems.
4. Choose a female:male breeding ratio based on your need for pedigree

vs. productivity
Choices of female:male ratios include
pair mating,
trio mating (two females and one male that remain in the cage together), and
harem mating (generally two females, with a male that might be rotated to other cages).
Most strains produce more progeny per cage with trio mating because inbred mice can tolerate
the relatively high density and all adult cage mates generally help care for the pups. Thus, for
strains that have small litters or are poor parents, harem mating may be a viable strategy. Keep
in mind, however, that if you use trio or harem mating and want to maintain a pedigree lineage,
you must house females separately when they become pregnant.
Another issue is whether to leave the male in the cage with a pregnant female or females or to
remove him from the cage. Removing the male can lengthen the time interval between litters in
two ways: First, if he is not in the cage during post partum estrus, which occurs shortly after a
female gives birth, a mating opportunity is lost. Second, once he is removed, we recommend
delaying his return until all pups have been weaned and removed. Otherwise, he may kill the
pups, even if they are his. In contrast, if the male remains in the cage, he can impregnate the
female as soon she gives birth or at the first estrus after her pups are weaned. Furthermore, the
males instinct to kill pups is suppressed if he is present during the pregnancy.
13.B. Breeding schemes

Choice of breeding scheme depends on the strain you are breeding. In this handbook, we discuss
breeding and maintenance schemes for specific categories of mice in Chapter 3, Categories of
Laboratory Mice: Definitions, Uses, Nomenclature.
13.C. Sizing a breeding colony for a research program

The exact quantity of mice for a study is determined by the experimental design, the variance of
the phenotype, and the desired statistical power. (For an illustration of using power analysis to
calculate quantities of mice required for an experiment, see Appendix L, Simplifying Power
Analysis to Determine Sample Size.) Especially in cases where specific genotypes are
required, it may be surprising to learn how many mice must be produced to get the required
quantity. For example, assume that on a weekly basis you need 20 males that express a
recessive, infertile phenotype. Only 1/4 of the mice you produce will express the recessive
phenotype (with heterozygous-by-heterozygous mating), and only 1/2 of those will be male.
Thus, to get 20 males with the recessive phenotype, you will need to produce 160 mice per
week.
Once you know the quantity of mice you need to produce and the production schedule, the next
decision is whether to breed the mice or purchase them on a regular basis from a supplier. If you
choose to breed the mice, you must determine the quantity of breeders to purchase. This
decision is based on values for strain productivityaverage pups per litter, wean:born ratio,
average number of litters per breeding female, and rotation period of the females. For many
strains of the most popular JAX Mice, this information is provided in 4.B, Reproductive
performance, and in the JAX Mice strain database (www.jax.org/jaxmice/query). Additional
information on some strains of JAX Mice, as well as inbred strains from other suppliers, is also
provided in the Mouse Phenome Database (MPD; www.jax.org/phenome). It is important to
keep in mind that these breeding data represent guidelines for a strain, and are not a guarantee of
a given productivity. In fact, a more relevant source for this information would be the
experience you or a colleague at your institution has had for your strain of interest or a similar
strain.
You also must decide whether to breed your own replacement breeders or purchase them from
your supplier. Consider that purchasing replacements from your original supplier can help
minimize genetic drift in your colony. If you do choose to breed your own replacements, set up
a schedule as stringent as the one for producing the experimental mice so that they will be
available when you need them.
A few words about inbreeding a line of heterogeneous mice: Typically, a line will become less
fertile within about three generations and may eventually become infertile. Make plans to
refresh your breeding stock or set up extra lines at the beginning of your program.
13.D. Strategies for maintaining a line or strain without

expansion
Often, researchers may wish to maintain a newly-generated strain without expanding it. A
common reason to do this is to retain valuable mice while awaiting program funding. One
challenge is to maintain the strain as efficiently as possible while protecting against its loss.
Another challenge is to minimize the development of a substrain background. Following are
several strategies to consider:
Maintain a minimum of two generations of mice, with each generation consisting of two or
three sisterbrother breeding pairs (total of four to six pairs). Do not eliminate any older
generation until a younger generation is proven fertile. Unless you have a concern about
breeding performance, such as with inbreeding depression, set up each new generation from
only one breeding pair of the parental generation.
Closely monitor breeding performance. As performance declines with age, promptly set up
the next generation of breeders.
Try to keep the age range of your breeding pairs between two and eight months of age.
Breeding pairs older than eight months may become infertile and suddenly stop breeding,
without exhibiting a progressive decline in litter size.
When maintaining a mutation on a standard inbred background, consider backcrossing the
strain every 10 generations to prevent substrain divergence.
Consider cryopreservation of the strain, so that the unique genetic characteristic (for example,
mutation, congenic region, new strain) can be recovered in the event of breeding failure or a
catastrophe such as fire or flood.
13.E. Using reproductive techniques

For the purposes of this handbook, we have divided reproductive techniques into two groups:
Standard reproductive techniques that require no special equipment and that are
straightforward to learn.
Assisted reproductive techniques (ARTs) that require special equipment and very specific
training.
13.E.1. Standard reproductive techniques

Standard reproductive techniques are used to determine and time pregnancies and to foster pups.
These techniques may seem simple and old fashioned, but when used with artful skill by
experienced technicians, they are some of the most valuable colony management tools available.
13.E.1.a. Determining pregnancy: vaginal plugs and palpation

Although there is no accurate early pregnancy test for mice, there is an easy and accurate way to
tell if breeding has occurred recently: the presence of a copulatory (or vaginal) plug in the
females vagina. The copulatory plug is a waxy, solid mass of cream-colored, coagulated
ejaculate that is produced by the males seminal vesicle and coagulating gland. (One of the
plugs purposes is to prevent other males from mating with the female.)
Generally, vaginal plugs remain intact for 1012 hours post mating. Because mating usually
occurs over a period of 1560 minutes about 46 hours into the dark cycle, the best time to look
for vaginal plugs is as early into the light cycle as possible, before they dissolve or become
dislodged. The nature and depth of the vaginal plug can be a strain and age characteristic: it is
superficially evident in some strains or in young females, but deep in the vagina in other strains
and in older females. If the plug is not visible when looking at the vaginal opening, technicians
can use a blunt, flat, autoclaved toothpick or blunt disinfected metal probe or forceps to open the
vagina slightly and expose the plug.
Although a vaginal plug does not confirm conception, it does prove that mating has occurred.
Even mating with a vasectomized maleone of the steps in creating pseudopregnant females
produces a vaginal plug. The likelihood of pregnancy ranges from about 30100%, but it is
stress and strain dependent (see sidebar). We confirm pregnancy with palpation after the 10th
day of the pregnancy. (The day the vaginal plug is found is
day zero.)
The likelihood of pregnancy following mating is
strain dependent. For most strains, the rate of
pregnancy among estrus-suppressed (group-housed)
females that were induced to ovulate by housing with
a male is highest for females with vaginal plugs found
the third day after being set up with a male. C3H/HeJ
(000659) and BALB/cJ (000651) strains are examples
(table below). C57BL/6J (000664) females are an
exception: 39% of females with vaginal plugs on the
rd
3 day were pregnant; 69% of females with plugs on
th
the 4 day were pregnant.
Day
plug is
found
Rate of pregnancy for these strains

C3H/HeJ
(000659)
BALB/cJ
(000651)
rd
100%
44%
th
62%
31%
3
5
Source: Frequently asked questions (husbandry) at

www.jax.org/jaxmice/faq.
We do ship female mice in which we have observed a

vaginal plug, but we guarantee pregnancy only after we have
confirmed with palpation. We prefer to ship pregnant
females between the 11th and 15th day of pregnancy, because
they seem to withstand the rigors of shipping better at this
stage of gestation. Up to day 11, hormonal maintenance of
pregnancy is mediated through the hypothalamus and
pituitary; during this period, a given stress is more likely to
cause complete termination of the pregnancy (through fetal
resorption) than after day 11, when the corpora lutea
maintain the endocrine support of pregnancy independently
of the hypothalamus and pituitary. For information on
purchasing plugged or pregnant JAX Mice, contact
Customer Service at 1-800-422-6423 (North America) or 1207-288-5845 (International).
13.E.1.b. Timing pregnancies using the LeeBoot and Whitten Effects
The Lee-Boot Effect (Van Der Lee and Boot, 1955) describes the phenomenon of estrus
suppression in a group of densely-housed female mice that is removed from male mouse urine
for 28 days. The Whitten Effect (Whitten, 1956) describes the process of a female in anestrus
being induced into estrus by exposure to male mouse urine.
You can take advantage of both of these effects to time and coordinate pregnancies:
1. To suppress estrus, house at least five females as densely as possible for 28 days. Keep all
male mice at least four feet away in all directions, including front and back.
Note: To adhere to your ACUC guidelines for housing density, you may need to use large
cages such as weaning cages.
2. To induce the females to resume their estrous cycles simultaneously, expose them to male
mouse urine by placing dirty bedding in the cage for at least three days. On the third day, set
up your breeding. Typically females will go into estrus and breed on the third night.
Note: Only the first estrus will be synchronized.
3. Starting on day 4, check for vaginal plugs.
13.E.1.c. Fostering a litter

Litter fostering is used when mothers are unavailable or unable to care for their pups. Two
common fostering situations are following hysterectomy derivation and when a genetic defect
prevents the mother from lactating. In research colonies, foster mothers typically come from the
among the breeders. For hysterectomy derivation, foster mothers are specifically prepared in
SPF colonies.
The fostering procedure is relatively straightforward: Replace some or all pups from a foster
mothers natural litter with pups from the litter you are trying to save.
13.E.1.c.1. Considerations
When fostering a litter, the younger the pups are, the better.
Choose a foster mother that has successfully weaned a litter in the past and that currently has
a healthy, well-fed litter of her own that is as close in age as possible to the age of the foster
pups.
For identification purposes, choose a foster mother whose natural offspring are a different
color than the foster pups. This is an obvious precaution when mixing natural and foster pups.
But even when replacing the entire litter, there is always a chance that a natural pup can be
buried under the cage bedding and not removed with its littermates.
Generally, try to limit the size of the foster litter to six pups or fewer. Of course, this number
is strain dependent and should be based on experience. But the foster litterall foster pups or
the combination of foster pups and natural offspringshould contain no more pups than the
natural litter. (Changing the litter size can affect the foster mothers milk supply.) If
necessary, split the litter between two foster mothers.
13.E.1.c.2. How to foster a litter of pups

1. Transfer the foster mother to a holding pen. If you are mixing natural offspring with the foster
pups, leave the appropriate number of the mothers pups in the pen; remove the others.
2. Place the foster pups into the foster mothers home pen and cover them with nest bedding so
they acquire the scents of the foster mother and her natural pups. (One strategy is to rub some
feces from the foster mother on the fosterlings.)
Note: If any of the pups are cool to the touch, warm them with a heat lamp or heat pad.
3. Place the foster mother back in her home pen with the foster pups as soon as possible. The
mother will be stressed when she is separated from her litter, so do your best to minimize the
separation time.
4. Leave the foster mother and foster litter alone for about 30 minutes. Then, carefully check to
be sure the mother has accepted themwhether the pups are in the nest or have been kicked
out. If the foster pups are between about 6 and 36 hours old, check for milk spots.
5. For the next several days, check on the foster litter periodically to be sure that the foster
mother is feeding and caring for the foster pups, but try to disturb them minimally.
If, at any time, you notice that the foster mother is rejecting the foster pups, try spreading the
scent of the nest or any natural pups on the foster pups. Or, try fostering to another mother.
13.E.2. Assisted reproductive techniques (ARTs)

Assisted reproductive techniques (ARTs) represent technical procedures that require special
equipment and sometimes, dedicated facilities. Technicians must be trained in specific
techniques. ARTs provide ways to expand a colony, rederive a strain, and maintain or rescue a
strain that cannot or will not breed reliably. ARTs also are used to remove mice from the shelf
without losing the strain.
Table 13.4 provides an overview of several ARTs, their application, and considerations. Note
that ARTS are often used in combination. For additional information about ARTs and related
training, see 14.G. Resources.
13.F. Maintaining the genetic integrity of your colonies

13.F.1. Preventing genetic contamination and minimizing genetic
drift
If you breed laboratory mice, it is imperative that you follow breeding and colony management
practices that prevent genetic contamination and minimize the effects of genetic drift. Prevent
genetic contamination by following stringent breeding and recordkeeping protocols. Minimize
genetic drift by replenishing your breeding stocks on a regular basis with mice of the same
strain from your original supplier. For details, see Chapter 8, Genetic Quality Control
Preventing Genetic Contamination and Minimizing Effects of Genetic Drift.
13.F.2. Confirming phenotypes and genotypes

Sometimes, phenotypes can be lost through
breeding. This can occur as a result of a
breeding error, but it also is a predictable
outcome when you breed certain types of mice.
For example, when you breed transgenic mice,
transgenes may be unstable in early
generations.
If the phenotype of interest is physically
observable, or if the phenotype is linked to an
observable marker (such as a specific coat
color), it is easy to determine its presence or
absence. However, often phenotypes of interest
are not physically observable or do not appear
when an animal is young. In these cases,
genotyping with a biological assay may be
necessary to ensure that the mutant allele is
present in the mouse.
If you need to genotype your JAX Mice or

have questions about genotyping
The Jackson Laboratory website provides several
ways to access information related to the
genotyping of JAX Mice:
Display the datasheet for a strain of JAX Mice

and link to genotyping protocols:
Browse a list of protocols (also search by gene,
stock number or primer):
www.jax.org/jaxmice/pubcgi/protocols/protocols.sh
Link to supplemental genotyping protocol
information (e.g., genomic DNA extraction
methods):
www.jax.org/imr/supp_proto
For further assistance, email us at
[email protected] or call Tech Support at 1-800422-6423 (North America) or 1-207-288-5845
(International).
Information about genotyping methods is

provided in 2.E, Genotyping: what it is and how it is used.
Table 13.4. Assisted reproduction techniques (ARTs): definitions, applications, considerations.

Technique and definition
When to use
Considerations
Hysterectomy derivation:
Pups are taken via caesarean
section from the birth mother and
fostered with a clean foster
mother.
Importation of a new mouse strain

into facility with higher level of
pathogen protection.
Rederivation (due to health status or
strain restoration).
Females are sacrificed; males are not.

If done because of pathogen contamination,
pups must be monitored for pathogens.
Good strategy if rederivation is necessary,
IVF is not proven for the strain, or few mice
are available.
Ovarian transplantation:
Fresh or thawed ovary (or 1/2 or
1/4 of ovary) is surgically
implanted in the ovarian bursa of
4- to 5-week-old female of
histocompatible strain.
When females cannot successfully

support fetuses, give birth, or care
for pups.
Example: Homozygous B6C3Fe
a/a-Csf1op/J (000231) females fail to
lactate, and homozygotes of both
genders are extremely fragile. We
transplant ovaries from a
homozygous (op/op) female into a
recipient female of a
histocompatible strain.
When yield is not important as long
as you get something.
Because you only need part of an ovary, one

female can provide tissue for up to 8
recipients.
Allow 12 weeks of healing before breeding.
First litter might be delayed.
If the recipients ovaries were not completely
removed, she may bear some of her own pups.
Therefore, a recipient of a different coat color
enables identification of any offspring from
her residual ovaries.
In vitro fertilization (IVF):

Eggs are collected from
superovulated females, fertilized
in vitro with fresh or thawed
sperm.
When females are of questionable

health status.
When you need embryos for
cryopreservation.
When you have only 1 male and
multiple females.
Can accommodate ratio of many females to 1

male.
Embryo transfer:
Embryoscreated via IVF,
thawed, or removed from
fertilized females of unacceptable
health status and flushedare
implanted into pseudopregnant
females of high SPF health status.
Rederivation.
Strain rescue.
Rapid expansion of colony.
Up to 15 embryos can be implanted per

female.
If transplanting fewer than 4 embryos, add
carrier embryos during transfer.
Consider using recipients that are readily
available, stay trim, have large infundibulum,
have a coat color that minimizes confusion
with natural pups, and have good mother
phenotype.
Intracytoplasmic sperm injection

(ICSI):
Insertion of frozen or thawed
sperm head into egg cytoplasm in
vitro.
IVF with dead or thawed

cryopreserved sperm.
Sperm do not need to be live.

Sperm can be collected from dead male if
sperm is collected and cryopreserved as soon
as possible.
Embryo flushing (following in

vivo fertilization):
Superovulated females are mated;
oviducts are collected and
flushed.
When cryopreserving embryos.

When IVF technology is
unavailable.
Superovulation:
Females are induced into
ovulating a greater number of
eggs than normal via injection
with gonadotrophins.
Often used in combination with in

vitro fertilization or in vivo
fertilization and embryo flushing.
To create embryos for
cryopreservation.
Superovulated females at 2135 days of age,

weighing 1214 g, produce the greatest
number of fertilized eggs.
Response to gonadotrophin injection is strain
dependent; preliminary dose injections may be
necessary.
Pseudopregnancy:
Females are induced into the
neuroendocrine status of the first
half of pregnancy by mating with
a vasectomized male.
As first step to prepare recipient for

embryo transfer.
Mating is confirmed with a vaginal plug.
13.G. Troubleshooting breeding problems

Table 13.5 will help you identify and resolve common breeding problems. For breeding
information specific to popular strains of JAX Mice, see Chapter 4, Characteristics of Popular
Strains of JAX Mice, Including Reproductive Performance. Within the strain information in
that chapter, technician notes often provide anecdotal breeding observations and hints from
our animal care technicians. Also see the Mouse Phenome Database (MPD;
www.jax.org/phenome). For breeding information on each strain of JAX Mice, refer to
individual strain datasheets, available at www.jax.org/jaxmice/query.
Table 13.5. Breeding problems and possible resolutions.
Problem
Mice are not breeding.

Females are not getting pregnant.
Possible resolution
A:
B:
C:
D:
E:
F:
G:
H:
I:
J:
Make sure you have male and female breeders.

Add nesting material specifically designed for that purpose.
Try a different diet, for example, one with more or less fat.
Minimize stressincluding human contact with the mice and
activity and noise in the room. Construction-related vibrations,
even outside the building, can disrupt breeding. If possible,
move mice to a quieter area.
Try a 14:10 light cycle.
Make sure mice are healthy and able to breed (for example,
not too obese or too old). Try healthier, younger animals.
If you never see vaginal plugs, try a new male.
Determine whether the problem is the male or female: pair a
proven breeder female with the male and a proven breeder
male with the female.
Surgically evaluate the reproductive tract. If the female
appears normal, try low dose gonadotrophins, ovarian
transplant, IVF; if the male appears normal, try IVF.
Research the strain reproductive characteristics. For a
transgenic, check the effect of the transgene on breeding. For a
strain carrying a mutation, check the effect of the mutation.
Adjust the breeding strategy accordingly.
Mice get pregnant but you never

see pups (females are resorbing
fetuses).
D (above): The most common cause of fetal resorption is stress.
Individual breeders are not

producing an expected number of
pups.
B, C, D, E, F, H, J (above)
Females give birth, but dont raise

their pups.
Pups disappear or do not survive.
D, J (above)
K: If you introduced a male to a cage with pups, he may have
killed them. Wait to add a male until all pups have been
weaned and removed.
Colony productivity has dropped.
L: Check for environmental factors that might have changed.

Consider room conditions (temperature, vibrations, building
construction, odors, etc.), caretaker, and diet. If more than one
cage, area, or strain is affected, expand the search. If possible,
restore environment to previous conditions.
13.H. Resources
In addition to the chapter references, following are some resources that provide information
about breeding and ARTS:
Web-based resources
The Jackson Laboratory website: www.jax.org
Access to details on ARTs techniques and cryopreservation; information about workshops on
shipping and reconstituting frozen mouse embryos, cryopreservation of mouse germoplasm,
surgical techniques for the laboratory mouse; individual strain data sheets.
Technical support and literature webpage: www.jax.org/jaxmice/support
Links to online literature and requests for literature, including resource manuals, newsletters,
and JAX Notes; online requests for technical support.
Mouse Genome Informatics (MGI) listserve webpage:
www.informatics.jax.org/mgihome/lists/lists.shtml
Subscription form to join our MGI email list service.
Print-based resources
Appendix J, Cryopreservation, in this handbook.
Silver LM. 1995. Mouse Genetics, Concepts and Applications. Oxford University Press.
(Also available online at www.informatics.jax.org/silver.)
Staff of The Jackson Laboratory. 1968. Biology of the Laboratory Mouse, Second Edition.
Dover Publications, Inc., NY.
13.I. References
Van Der Lee S, Boot LM. 1955. Spontaneous pseudopregnancy in mice. Acta Physiol
Pharmacol Neerl. 4:442444.
Whitten WK. 1956. Modification of the oestrous cycle of the mouse by external stimuli
associated with the male. J. Endrocrinol. 13:399404.
255
Chapter 14: Emergency Planning

Joanne M. Currer, Dorcas Corrow
Colony managers often think of emergencies in terms of major disasters such as fires, floods
and earthquakes. But chemical spills and short power outages can result in an emergency event,
too, as can suspicious letters or packages. Today, many colony managers also recognize the
need to plan for the possibility of a pandemic and the resulting loss of employees.
All emergency planning is based on risk assessment: How much loss are you willing to accept?
How much are you willing to spend to prevent a loss that may never happen? Or to recover from
one that did?
The objective of this chapter is to provide some basic information about emergency planning as
well as an overview of what we do at The Jackson Laboratory. The focus of this chapter is on
the effects of an emergency on an animal facility, not an entire organization.
14.A. Developing your plan................................................................................................256
14.A.1. Minimizing the initial effect of an emergency .........................................256
14.A.2. Keeping your animals safe ........................................................................256
14.A.3. Minimizing the loss of data .......................................................................257
14.A.4. Returning to normal operations.................................................................257
14.A.5. Managing a loss of employees ..................................................................257
14.B. What we do at The Jackson Laboratory ..................................................................258
14.C. References .................................................................................................................258
Acknowledgments: We would like to thank John Fitzpatrick and Janice Von Brook for their
valuable assistance with this chapter.
14.A. Developing your plan

Emergency plans have five major objectives: to minimize the initial effect of an emergency, to
keep animals safe, to minimize loss of data, to return to normal operations as quickly as
possible, and to manage a loss of employees.
14.A.1. Minimizing the initial effect of an emergency

To minimize the initial effect of an emergency, you must determine the scope of the event and
initiate first response steps as quickly as possible. An emergency plan should include ways to
quickly assess the emergency, procedures for immediate containment of the emergency, and if
necessary, evacuation of people and animals from your facility. Considerations include, but are
not limited to, a published list of responsible parties and responsibilities, a warning system (e.g.,
fire alarms), evacuation drills, a trained security force, trained floor monitors, and prearrangements with local authorities.
Procedures for keeping people safe should be
appropriate for your institution and must be
your highest priority. Perhaps youll need
trained medical personnel on site. Besides basic
medical supplies, you might need protective
equipment for first responders.
What about insurance?

Consider the real value of lost research animals,
research data, and equipment when arranging
for insurance coverage. Consult with experts to
determine whether options such as business
interruption or extra expense coverage or both
make sense for your organization. Appropriate
coverage can provide critical assistance to a
recovery effort. And the process of an insurance
audit might expose risky behavior that can be
corrected.
Minimizing the effect of an emergency also

includes planning to avoid it. For example, in
an area susceptible to flooding, a wise strategy
would be to house animals above ground. A
wiser strategy might be to house them above possible water levels during a flood. As always,
the cost to avoid a disaster must be balanced against the cost of the lost assets.
14.A.2. Keeping your animals safe

To keep your animals safe throughout an emergency, it is important to provide them fresh air,
water and food in a suitable environment. You must be concerned about microbial
contamination of any animals you move. Only your institution can determine the costbenefit
ratio of saving vs. destroying animals that may have been contaminated by any microbial agent.
It is always wise to have a backup plan for
recovering from a loss of animals. Strategies
include maintaining animals at another location
(while avoiding the inadvertent development of
a substrain) and cryopreserving embryos,
ovaries or sperm off site.
How The Jackson Laboratory can help with

your animal backup plan.
The Jackson Laboratory offers several JAX

Services related to cryopreservation and
recovery of mouse strains. To learn about how
these programs can help you plan for and
recover from emergencies, visit our disaster
planning webpage at
www.jax.org/jaxservices/disasterplanning.
Keep in mind that once a pathogen barrier in a

facility is broken, you must wait to reopen the
facility until its condition is restored to an
acceptable health standard. Thus, you might need to house animals in a temporary facility for a
period much longer than the initial emergency.
Chapter 14: Emergency Planning 257
14.A.3. Minimizing the loss of data

For any computer data, strategies include regular backups of institutional and research data to a
server off site or over the Internet. You may need to set up special backup procedures for laptop
computers, which may not be connected to
your network on a regular basis.
Copy and store any critical paper-based data at
a remote location or in containers or file
cabinets resistant to fire or water or both.
14.A.4. Returning to normal

operations
Plans for redeploying mouse rooms should be
no less stringent than those for biosecurity
breaks. (For details, see Chapter 7, Animal
HealthPreventing, Identifying, and
Eradicating Microbial Contamination.) Of
course, following an emergency, recovery
might be on a much larger scale.
Specific issues related to pandemics

Pandemics present 2 specific challenges: First,
pandemics affect the work force, not the animals.
Therefore, you will have just as many animals to
care for, but not as many personnel with which to
do so. Second, pandemics can be of a lengthy
duration. They are expected to occur in waves,
which decline in severity as the disease runs its
course.
Considerations include the following:
Transportation in and out of an affected
geographical area could be suspended during a
pandemic. The implication is that enough food
and water (for mice and employees), fuel for
emergency generators, etc. must be planned for
and in place before the pandemic strikes.
If the emergency involves loss of housing for

your employees, arrangements for temporary
housing can benefit both employees and your
institution.
Ways of doing business will be altered as social

distancing is practiced. Face-to-face contact will
be reduced in favor of telephone conversations,
email, and teleconferences. Having protocols in
place can prevent confusion, especially when
the pandemic first appears.
Having backup equipment at another site or

planning ahead for replacement of equipment
is also wise.
Staff preparedness involves planning and

prevention at home as well as at work, both to
protect against the disease and do whatever
possible to minimize its effects.
In times of crises, scientific institutions often

do whatever they can to help. Assistance can
include housing of animals and research space.
Arranging ahead for this type of help can
minimize confusion and uncertainty when you
are in the middle of an emergency.
Focusing on critical functions rather than

departments or titles can concentrate necessary
personnel and energy on tasks that must be
accomplished even under the most trying of
circumstances.
14.A.5. Managing a loss of employees

In the event of a pandemic or any event that results in loss of employees, you must cope with a
reduced work force. An obvious strategy to plan for this issue is cross-training of employees.
But remember that effective cross training involves more than just animal care. You also might
need to make arrangements for employee shortages in animal care support, including the wash
area, janitorial services, shipping, and another other critical areas of support.
14.B. What we do at The Jackson Laboratory

At The Jackson Laboratory, we have standard operating procedures (SOPs) to manage
emergencies at our facilities in Bar Harbor, Maine, and West Sacramento, California. We have
specific SOPs for such events as fire, flood, earthquakes, bomb threats, contaminated letters or
packages, chemical spills, and pandemics. Our security force and a designated group of
employees are fully trained on these procedures and are responsible for managing any necessary
implementation. We regularly remind employees to be watchful for any suspicious activities on
or around our facilities.
To ensure the welfare of our employees and
animals during a power outage, we have
emergency generators in our facilities in Maine
and California. And, we stock emergency
supplies of food and water for mice. All
supplies are substantial enough for a lengthy
situation.
We train our employees in good health
practices, including prevention of and response
to a pandemic. Managers and employees are
cross-trained in multiple areas of
responsibilitywith a focus on critical
functionsto ensure that animals will be well
tended even if we experience a reduction in
workforce.
Our cryopreservation facilities, which store
both our own and customers biological
material, are located in a secure area. We also
store duplicate cryopreserved biologicals offsite.
Our institutional computers are backed up
daily. We have redundant backups stored at
multiple sites. And, we have a disaster plan in
place to restore data as necessary.
14.C. References
We know a little about dealing with fires

The Jackson Laboratory has twice experienced
serious firesin 1947 and 1989.
October 17,1947, a fire that started in a bog about 6
miles from our facility spread throughout Mount
Desert Island, the 108-square-mile island on which
The Jackson Laboratory is located. By the time the
fire was declared out on November 14, (National
Park Service, 2008) more than 17,000 acres of
Mount Desert Island were destroyed, as was much
of The Jackson Laboratory and its stock of mice.
Fortunately, Dr. Little and the staff of The Jackson
Laboratory had shared their research mice freely,
and because the scientific community recognized
the value of The Jackson Laboratory and our mice,
they partnered with us to help restore our facilities
and our mouse stocks.
May 10, 1989, a 5-hour fire that started in a
construction area in a mouse room destroyed about
40% of our production facility and more than
400,000 mice. But many mice in affected buildings
were saved, and many more throughout the campus
were unaffected. We lost no strains of mice.
By May 23 we were shipping mice. We also assisted
researchers dependent on JAX Mice to maintain

the momentum of their research by helping them set
up their own mouse colonies. Within days of the fire
we were rebuilding our facilities, and by spring 1990,
we were operating at 80% of pre-fire capacity (The
Jackson Laboratory Staff, 1989). Reconstruction
employed a more modular building design, which
makes our facilities less susceptible to the spread of
fire or contamination.
National Park Service. 2008. Fire of 1947.

www.nps.gov/acad/historyculture/fireof1947.htm (retrieved 2/13/08).
The Jackson Laboratory Staff. 1989. The Jackson Laboratory Fire. JAX Notes #438.
http://jaxmice.jax.org/jaxnotes/archive/438a.html (retrieved 4/22/08).
259
Chapter 15: Human Health ConcernsMouse

Allergies, Bites, Zoonotic Disease
Peggy Danneman, Kathleen Pritchett-Corning, Joanne M. Currer, Kevin Flurkey
Although working with mice is a relatively low-risk pursuit, three areas of potential risk exist:
exposure to mouse allergens, injury from animal bites, and exposure to zoonotic disease.
Our objective for this chapter is to provide an overview of these issues and some strategies for
addressing them. We will also highlight what we do at The Jackson Laboratory and provide
resources where you can find further information.
15.A. Mouse allergens ......................................................................................................260
15.A.1. The most common offending allergen: Mus m1 ....................................260
15.A.2. Protection from laboratory animal allergies (LAAs) .............................260
15.B. Animal bites ............................................................................................................261
15.C. Zoonotic disease......................................................................................................261
15.D. What we do at The Jackson Laboratory ................................................................262
15.D.1. Allergies....................................................................................................262
15.D.2. Bites ..........................................................................................................262
15.D.3. Zoonotic disease...................................................................................262
15.E. Resources.................................................................................................................263
15.F. References ...............................................................................................................263
15.A. Mouse allergens

In the United States, among the population of people who work with mice, approximately 10%
routinely develop a laboratory animal allergy (LAA) to mice (JAX Notes, 1999). Although an
LAA can be a debilitating condition, sometimes resulting in severe physical reactions such as
anaphylactic shock, reactions usually are much less severemore commonly associated with
nasal symptoms (sneezing, discharge), respiratory symptoms (wheezing, shortness of breath),
cutaneous symptoms (rash, hives) or ocular symptoms (watering, redness). Workers with a
history of atopic disease are at higher risk of becoming sensitized to laboratory animals.
15.A.1. The most common offending allergen: Mus m1

The main murine protein that causes allergic reactions in humans is Mus m1 (mouse urinary
protein [MUP] in older literature), one of the many proteins in mouse urine. Mus m1 is a
lipocalin protein that serves as a pheromone carrier. It is produced in the liver, and although it is
excreted primarily in the urine, it also may be found in the hair follicles and dander of mice.
Males produce approximately four times as much Mus m1 as females.
15.A.2. Protection from laboratory animal allergies (LAAs)

An obvious solution to an LAA is to limit total exposure to the animals. But often, this option is,
at best, only partially workable. Following are several strategies for minimizing the effects of
allergic reaction to mouse antigens:
Caging and environment. The most effective caging system for minimizing LAA exposure is
ventilated caging operated under negative pressure (Reeb-Whitaker and Harrison, 1999).
Filter tops on non-ventilated cages will confine allergens, but their use must be balanced with
their potentially detrimental effect on the cage micro-environment. Innovative room
ventilation designs also can help improve the dilution and removal of airborne contaminants
in a mouseroom. Harrison (2001) discusses options.
Institution-wide husbandry practices. Specify workplace conduct rules and standard operating
procedures (SOPs), such as changing cages in ventilated hoods (Schweitzer et al., 2003) and
prohibiting dry sweeping in animal facilities (Reeb-Whitaker and Harrison, 1999).
Minimizing or, preferably, prohibiting animal traffic in personnel areas will help to protect
sensitive individuals from unnecessary exposure to animal allergens.
Personal protection. Consider LAAs when developing SOPs for entry to and exit from mouse
rooms. Any procedure that prevents transmission of pathogens from humans to mice, such as
those used in SPF colonies, also helps to limit exposure of humans to animal allergens.
Components of these SOPs include frequent hand washing and use of booties, gowns with
tight, rib-knit cuffs, gloves, and dust masks. Use of facility uniforms for animal caretakers
and other individuals who spend a considerable amount of time in animal rooms will not only
protect the individual worker but minimize the potential for carrying animal allergens to other
parts of the facility or outside the facility (e.g., home). Facility uniforms should be laundered
in the facility or by a professional laundry service.
For workers who have symptoms of LAA or a history of asthma and are concerned about
severe reactions to mouse allergens, personal protective equipment such as custom-fitted
respirators or powered air-purifying respirators (PAPRs) provide high-efficiency particulate
air (HEPA)-filtered air directly to the worker.
Most minor allergic symptoms can be treated with over-the-counter medications such as
antihistamines or topical creams. More serious symptoms, especially respiratory ailments,
should be treated by a physician.
Chapter 15: Human Health ConcernsMouse Allergies, Bites, Zoonotic Disease 261
15.B. Animal bites

If irritated or handled incorrectly, laboratory mice may bite. Although the use of gloves helps
prevent injury to the skin, sometimes teeth do break through the gloves and the skin, creating
small puncture wounds. Animal bites are always of concern, but laboratory mouse bites are of
less concern than bites from most other animals. Nonetheless, even SPF mice, which are free of
organisms that tend to cause disease in mice, still carry common bacteria in their mouths that
can cause wound infections. Thus, any bite should be cleaned thoroughly with soap and water.
(Note: Although people may associate the risk of tetanus with animal bites, the tetanus agent
Clostridium tetani is not commonly found in laboratory mice. Nonetheless, vaccination against
tetanus is commonly recommended when a human is bitten by any animal.)
Perhaps the greatest concern with bites from laboratory mice is allergic reaction. In particular,
workers with a minor allergy to mice may have an exaggerated allergic reaction to a mouse bite
if it breaks the skin. If swelling appears around the bite area, an occupational health care worker
should be contacted to evaluate the need for treating and monitoring the wound. Anaphylaxis, a
serious medical condition, can occur in highly sensitized individuals and requires immediate
medical attention.
If the bite is from a wild-caught mouse, or a mouse exposed to wild-caught mice, there is
greater concern (see 15.C, Zoonotic disease). A report should be made through appropriate
institutional channels. Information about the health status of the mouse, if known, should be
reported to an occupational health care worker for further evaluation.
15.C. Zoonotic disease

Most modern mouse colonies are kept in facilities designed to exclude wild mice and are
regularly tested for various pathogenic organisms, including those transmissible to humans
(zoonotic). Reputable suppliers of laboratory mice are especially vigilant.
However, wild miceand even domestic laboratory micedo have a potential for infection
with and transmission of zoonotic diseases. Especially if investigators are using wild-caught
mice in the laboratory, screening of representative animals for zoonotic organisms is highly
recommended. If long-term use of wild-derived animals is anticipated, rederivation should be
considered.
Zoonotic agents that are most likely to be carried by laboratory mice include lymphocytic
choriomeningitis virus (LCMV), Salmonella spp., and Streptobacillus moniliformis (rat bite
fever). In addition, wild mice may also carry other zoonotic organisms, including Hantaan virus,
Seoul virus, Sin Nombre virus, Leptospira spp., or Rodentolepsis (formerly Hymenolepsis)
nana.
Any animal infected with a zoonotic organism should be euthanized or housed in a containment
facility, because many zoonotic bacteria, viruses, and fungi can persist in an animal even after
treatment, resulting in a continued threat to the colony and the potential for further human
infection.
The potential for mouse-derived biological products (e.g., serum or cell lines) to carry
pathogenic organisms should be kept in mind. To protect both mouse and human health, such
products should be screened for pathogenic and zoonotic organisms prior to use in the
laboratory.
15.D. What we do at The Jackson Laboratory

15.D.1. Allergies
At The Jackson Laboratory, we include information about mouse allergies in our orientation for
all new employees. We provide additional information to any employee who works with mice.
We have a formal procedure for reporting possible allergic reactions, and, if warranted, we can
screen for allergic reactions in our on-site health office. We recommend treatment based on
severity of reaction.
We take animal allergies seriously at The
Jackson Laboratory
Researchers at The Jackson Laboratory have
been studying mouse allergies since 1980the
biological perspective as well as the effects on
our employees and institutional strategies for
lessening those effects. Several published
studies are referenced throughout this chapter.
Our strict SOPs for mouse room setup and husbandry, which
were originally designed to protect mice against pathogens, also
help control allergens. We monitor mouse rooms and public areas
to determine levels of airborne mouse allergens, and we take
corrective action when necessary. We also provide personal
protective equipment for any employee who requires it.
Our experience is that a majority of LAAs are relatively mild.

Most affected employees manage their allergy by adhering to our
SOPs for entry to and exit from mouse rooms, which include use
of gloves and gowns in all mouse rooms at The Jackson
Laboratory. We also have a formal respiratory protection
program, which is required for all personnel who work in animal
areas and have a history of animal allergies or asthma. This program is voluntary for employees
interested in preventive protection. (It is worth noting that employees rarely need such extreme
protection.) If allergies cannot be managed using respirators or PAPRs, an employee will be
transferred to another position that involves less or no exposure to mice.
Currently, we are partnering with Johns Hopkins

University to study occupational mouse allergies
and asthma. We also conduct annual medical
surveillance for our employees who are at risk.
15.D.2. Bites
At The Jackson Laboratory, to minimize injury from animal bites, we train technicians in safe
animal handling practices. We require the use of protective gloves when handling mice. Any
bite wounds are reported to our Health Office and treated and monitored accordingly.
15.D.3. Zoonotic disease

In our mouse colonies, we regularly screen for zoonotic pathogens. Although it has been
decades since we last found any of these organisms in any of our established coloniesthe only
zoonotic agent ever found in any of our established colonies was Salmonella, which was
eradicated in the 1960sour emergency response policy dictates euthanasia of any infected
mice along with complete depopulation of any remaining mice in the room.
Mice imported from other institutions are rederived, primarily to eliminate the potential of
introducing unwanted mouse pathogens into our colonies. Prior to rederivation, all newly
imported mice are housed in a strict quarantine facility and handled with great care based on
their potential to harbor zoonotic organisms. Similarly, we screen all biological products of
rodent origin for organisms, including zoonotic organisms, that might threaten mouse or human
health. (For information about our screening and importation procedures, see Chapter 7,
Animal HealthPreventing, Identifying, and Eradicating Microbial Contamination.)
Chapter 15: Human Health ConcernsMouse Allergies, Bites, Zoonotic Disease 263
15.E. Resources
Selected Publications:
Bush RK, Stave GM. 2003. Laboratory animal allergy: an update. ILAR J. 44:2851.
Curtin-Brosnan JM, Eggleston PA, Paigen BJ, ONeil EA, Hagberg KA, Matsui EC. 2007.
Respiratory protection and incident skin test sensitivity among laboratory mouse workers. J
Allergy Clin Immunol. 119(Supplement 1):S65.
Division of Occupational Health and Safety. 2003. The National Institutes of Health Laboratory
Animal Allergy Prevention Program (LAAPP). Web access:
http://dohs.ors.od.nih.gov/publications.htm
Institute for Laboratory Animal Research. 2001. ILAR Journal. Entire Volume 42, Issue 1.
Matsui EC, Diette GB, Krop EJM, Aalberse RC, Smith AL, Eggleston PA. 2006. Mouse
allergen-specific immunoglobulin G4 and risk of mouse skin test sensitivity. Clin Exp Allergy.
36:10971103.
Newcomer CE and Fox JG. 2007. Zoonoses and Other Human Health Hazards, in The Mouse
in Biomedical Research. Vol. II Diseases, 2nd Edition. Academic Press, New York, pp. 719746.
Reeb-Whitaker CK, Harrison DJ, Jones RB, Kacergis JB, Myers DD, Paigen B. 1999. Control
strategies for aeroallergens in an animal facility. J Allergy Immunol. 103:139146.
Web resources:
Centers for Disease Control and Prevention: www.cdc.gov
National Institute for Occupational Safety and Health (NIOSH):
NIOSH Safety and Health TopicAsthma and Allergies: www.cdc.gov/niosh/topics/asthma
Preventing asthma in animal handlers: www.cdc.gov/niosh/animalrt.html
15.F. References
Harrison DJ. 2001. Controlling exposure to laboratory animal allergens. ILAR J. 42:1736.
JAX NOTES. 1999. Frequently asked questions about JAX Mice. JAX NOTES. 479:68.
Reeb-Whitaker CK, Harrison DJ. 1999. Practical management strategies for laboratory animal
allergy. Lab Animal. 28:2530.
Schweitzer IB, Smith E, Harrison DJ, Myers DD, Eggleston PA, Stockwell JD, Paigen B, Smith
AL. 2003. Reducing exposure to laboratory animal allergens. Comp Med. 53:437492.
265
Chapter 16: Vivarium Staff Development and

Contribution
Joanne M. Currer, Kevin Flurkey
Researchers may know the genetics of mice down to the nucleotide, but often, technicians are
more familiar with normal strain-specific characteristics and behaviors. In some ways, they
know the mice best. Day after day, conscientious technicians keep animal colonies running
smoothly, by caring for the animals, defending the pathogen barrier, and helping assure the
genetic integrity and health of the animals. Should a problem arise, a well-trained, experienced
technician will discover it at an early stage andwith the appropriate authoritytake timely
action that can minimize damage.
The reputation of a staff that unfailingly maintains high quality mice can also directly affect an
organizations finances. In a production environment, an exemplary reputation affects revenue
by warranting the confidence of customers. In a research environment, an exemplary reputation
affects grant funding by inspiring the confidence of peer reviewers. Thus, a well-trained,
involved animal care staff is a valuable resource for an entire organizationnot just for colony
managers.
The objective of this chapter is to highlight some issues related to training, communicating with,
and maximizing the involvement of your staff. We also provide details about our training
programs and several other strategies we use at The Jackson Laboratory.
16.A. Training and career development for vivarium personnel ...................................266
16.A.1. Considerations..........................................................................................266
16.A.2. What we do at The Jackson Laboratory .................................................266
16.B. Effective communications ......................................................................................269
16.B.1. Considerations..........................................................................................269
16.B.2. What we do at The Jackson Laboratory .................................................270
Acknowledgments: We would like to thank Marcia Picard and Dorcas Corrow for their
valuable input to this chapter.
16.A. Training and career development for vivarium

personnel
16.A.1. Considerations
16.A.1.a. Training
Simply put, if you are managing a production or research mouse colony, you need a well-trained
staff. Protecting your mice from pathogenic and genetic contamination is time-consuming,
meticulous work. If it is performed casually, your coloniesand research conducted at your
institutionwill suffer. One of the best ways to ensure that animal care is done well is to ensure
that technicians understand the importance of even mundane tasks that are designed to assure
health and genetic quality. Training, both on-the-job and classroom, is essential. It is important
to note that on-the-job training does not imply informality. Although the training environment
may be less formal than that of a classroom, objectives must be operationally defined, and
evaluation and demonstration of proficiency must be specific.
Also, it is important to provide ongoing training. As technology changes, your staff must be
well equipped to handle any advancements in husbandry and relevant research practices.
16.A.1.b. Career development

Some employees are eager to learn and advanceby increasing their skills, by learning more
about the science and technology behind the work they do, by improving animal welfare, and by
seeking new responsibilities. It is important to provide opportunities for these employees to
continue their growth and advance their careers. Other employees are very happy doing one job
well. Remember to recognize them for their consistent contribution.
And, remember the team that supports the technicians. Workers who wash, autoclave, and
deliver supplies also must adhere to exacting standards. Ensure that they get recognition and
advancement opportunities.

It is an understatement to say that we are proud of our animal care technicians at The Jackson
Laboratory, which, at the time this book was published, numbered at approximately 250. We
know that our global reputation as one of the most reliable sources of genetically defined
laboratory mice depends on the work our caretakers and technicians do day after day, year after
year. We employ men and women who understand the seriousness of their work. We provide
training and incentives to build their skill sets, and we recognize and reward hard work and
dedication.
16.A.2.a. Training specific to The Jackson Laboratory

Following is overview information related to the training we offer our animal technicians. Detail
is provided in Table 16.1.
16.A.2.a.1. New hire, on-the-job training

Phase I. Upon hiring, animal care trainees attend orientation and receive extensive on-the-job
training. Throughout this probationary period, employees receive ongoing coaching as well as
three formal evaluations, which require that they show understanding and proficiency of
standard operating procedures (SOPs) related to their job requirements.
Upon completion of Phase I training, supervisors meet with trainees, evaluate their
performance, skills, and preferences, and assign them to one of three areasProduction,
Research Animal Facilities (RAF), or RAF Repository (where we maintain our special mutant
strains).
Phase II. Phase II training involves on-the-job instruction and evaluation tailored to
Production, RAF, or RAF Repository.
Chapter 16: Vivarium Staff Development and Contribution 267
Phase III. Phase III training involves on-the-job instruction and evaluation tailored to the
highest level barrier areas in Production. These areas house Foundation Stocks, Pedigree
Expansion Stocks, and Pedigree colonies that distribute mice to other Production areas.
16.A.2.a.2. Required classroom training

We require that our technicians attend a formal course in addition to on-the-job training:
Laboratory Animal Sciences. The Laboratory Animal Sciences course supplements on-the-job
training. Technicians take this course after completion of primary training, generally six
eight months after they are hired. Much course material is drawn from the Assistant
Laboratory Animal Technician (ALAT) training material provided by The American
Association for Laboratory Animal Science (AALAS). Evaluation includes multiple quizzes
and final written and practical exams.
16.A.2.a.3. Elective classroom training

Elective classroom training includes the following, all of which adhere to Animal Care and Use
Committee (ACUC) and Association for Assessment and Accreditation of Laboratory Animal
Care International (AAALAC) guidelines:
Foundation of Basic Genetics
Beyond Basic Genetics
Biomethods
Surgery
A majority of our technicians attend both genetics courses, and approximately 75% of our
technicians have completed biomethods training successfully.
16.A.2.b. Other training

16.A.2.b.1. Technician training
Training curriculum and materials from AALAS are incorporated into our required Laboratory
Animal Sciences course. Employees also can use the AALAS materials as a self-study guide.
We offer the Assistant Laboratory Animal Technician (ALAT) exam on site. Once certified,
employees receive a monetary bonus. Although ALAT certification is not required for
promotion, typically about 75% of the animal care technicians at The Jackson Laboratory are
ALAT certified.
Higher levels of AALAS certification include the following, both of which offer a monetary
bonus: Additional training in animal husbandry and certification as a Laboratory Animal
Technician (LAT), and training in colony management and biotechnical skills (such as surgery)
and certification as Laboratory Animal Technologist (LATg). LATg certification is especially
important for jobs in our research and services groups. Although AALAS courses are self-study,
exams are held at The Jackson Laboratory.
16.A.2.b.2. Management training

We recognize the importance of an effective supervisory and management team. Many of our
supervisors and managers are trained and certified by the Institute for Laboratory Animal
Management (ILAM), an AALAS educational program targeted to managers in the laboratory
animal science industry. The 2-week course is taught 1 week per year over a 2-year period.
Topics include management concepts, enhanced communication, team building, and
networking.
On an ad hoc basis, The Jackson Laboratory provides off-site leadership training that comprises
team building and coaching for supervisors and mangers who qualify.
Table 16.1. Training opportunities available to animal care personnel at The Jackson Laboratory
Training/
Required/
Class
Elective
Length
Content
On-the-Job,
Phase I
Required
12 weeks
Overview of The Jackson

Laboratory, employee
policies, and benefits
Basic husbandry,
including animal handling
and cage changing
Breeding
On-the Job,
Phase II
Required
4 weeks
Based on requirements specific to Production, RAF, or

RAF Repository.
Follows Phase I
training.
On the Job,
Phase III
Elective
12 weeks
High level barrier area

Mutant stock colony
maintenance
Basic genotyping
Our pedigree numbering
system
Follows Phase II
training.
Laboratory
Animal
Science
Required
14 weeks,
1 afternoon
per week
Genetics
Chemical safety
Nomenclature
Recordkeeping
Diagnostics
Structure of organs,
tissues, and cells
Genetic quality control
Breeding
Mouse room environment
Animal health
Drug therapy
Research techniques
Biological and genetic
terms and concepts
Career development
Sometimes taken
concurrently with
on-the-job
training.
Foundation
of Basic
Genetics
Elective
15 weeks,
1 afternoon
per week
Cell cycle
Genes and chromosomes
Rules of heritability
Concepts of gene therapy

Mitochondrial genetics
Beyond
Basic
Genetics
Elective
15 weeks,
1 afternoon
per week
Mouse karyotype
Mitosis and meiosis
Oogenesis and
spermatogenesis
In vitro fertilization
Preimplantation
development
Relationship of mouse
genetics to human health
Biomethods
Elective
Multiple
afternoons;
length
depends on
topics and
student skill
levels
Required methods:
Animal handling and
restraint
Sexing newborn mice
Injections
Euthanasia
Tail tipping
Ear notching
Blood sampling
Optional methods:
Cardiac puncture
Other identification
methods (ear tagging,
microchip implantation,
toe clipping, tattoo)
Taught on an as
needed basis;
often customized
to a particular
group of students.
Surgery
Elective
Multiple
afternoons;
length
depends on
topics and
student skill
levels
More than 30 various

surgical techniques,
including
Catheterizations
Implantations
Denervations
Cannulations
Organectomies
Taught on an as
needed basis;
often customized
to a particular
group of students.
Recordkeeping
Materials handling
Pathogen monitoring
Deviant identification
Basic genotyping
Safety
Comments
Initiated upon
hire.
Chapter 16: Vivarium Staff Development and Contribution 269
16.A.2.c. Career advancement

Within our production and operations organization, we have multiple levels of trainee and
technician positions. We reward initiative and hard work and regularly promote from within.
Many former technicians have advanced to such positions as room supervisors, managers, and
senior managers. Former technicians who moved into our research facilities now hold such
positions as research assistants and technical support personnel.
Under our Shared Services program, vivarium technicians may
choose to work part time with researchers. For a set amount of
time per week, technicians perform research oriented tasks under
the supervision of a member of the scientific staff. This is a way
for vivarium technicians to broaden their knowledge base and
gain critical skills for career advancement. Our Shared Services
program has greatly facilitated introduction of animal care
technicians to full-time jobs in research.
16.B. Effective communications
Tuition reimbursement for post-secondary

education
At The Jackson Laboratory, we encourage all of
our employees to take an active role in their
education and career advancement. All technicians
are eligible to participate in our lab-wide tuition
reimbursement program, which applies to
successful completion (grade C or above) of
courses given by an accredited post-secondary
institution. We also offer short term, interest-free
loans through a local credit union for up front
payment of tuition.
16.B.1. Considerations
One way to ensure that a mouse colony runs smoothlyand that technicians know exactly what
is expected from themis to develop and document any procedures or protocols for tasks that
must be repeated in a consistent manner. This is especially critical when it comes to any
institutional policy or standard operating procedures (SOPs) directly related to colony
management (including animal care, protection from pathogens, safety, etc.). The more detailed
this documentation is, the more consistently the tasks will be performed. Goals are to make it
easy for technicians to learn and review procedures, and to remove subjectivity from
performance evaluation.
Of course, communication works best when it is 2-way. This includes regular meetings, and it
requires an environment where technicians are recognized as valuable team members.
Encourage comments and problem solving. Critically evaluate comments you receive.

At The Jackson Laboratory, we have detailed SOPs, formalized across the organization, for all
tasks our technicians must perform. These include procedures for cleaning and sanitation of the
facilities, animal care, and safety, as well as for compensation and benefits. These procedures
are available on our internal website; some are posted throughout our campus. Whenever an
animal care technician learns or undertakes a new responsibility, he or she must sign off on any
relevant SOPs.
In our production facility we hold bi-weekly room supervisor meetings to disseminate
information and discuss issues. We also hold quarterly open forums for our entire animal care
staff, where our management team discusses whats happening in other parts of The Jackson
Laboratory.
We encourage communications from our technicians, especially regarding changes to improve
efficiency or ease stress for the mice or themselves. An example: One of our technicians,
concerned about the unavoidable stress on mice when their cages are changed, redesigned a
mouse-holding forceps to provide maximum grasping power with minimum pinching.
Management listened and, in fact, The Jackson Laboratory pursued a patent for this design.
In our production facilities, we have a know your mice program that encourages technicians
to look for unique characteristics or behaviors of their mice. It is through this program that we
formally collect comments on physical appearance, behavior, and breeding that are the basis of
the technician notes that we include on strain datasheets for JAX Mice and in Chapter 4,
Characteristics of Popular Strains of JAX Mice, Including Reproductive Performance.
In our research colonies, we have a sick and injured animal program that provides a formal
way for technicians to make decisions about when to involve researchers and veterinarians in
the care of individual mice. Because the characteristics of a research animal may be normal for
that specific animal, it is important that the technicians use good judgment to ensure both the
welfare of the animal and the validity of the research. Details of this program are provided in the
sidebar in Section 7.B.3, Our monitoring procedures.
The Senior Management Team at The Jackson Laboratory has initiated a program of quarterly
forums, open to all employees. One goal of the open forums is to address any issue raised by
any employee. Comments and questions can be submitted through a variety of channels.
Additional goals of the program are to foster positive and constructive working relationships at
all levels, and to facilitate understanding of the roles of The Jackson Laboratory in the field of
biomedical research.
271
Chapter 17: Ordering JAX Mice and JAX Services

Contact Information for Customer Service and Technical
Support; Frequently Asked Questions
To place an order or for Customer Service:
To expedite the order process:
Telephone:
United States: 1-800-422-6423

International: 1-207-288-5845
Monday through Friday
8:00 AM to 6:00 PM Eastern Time
Fax:
1-207-288-6150
Email:
[email protected]
Please provide the following information

About your institution:
Complete billing and shipping addresses.
Names, telephone numbers, fax numbers,
and email addresses of buyer and primary
researcher.
Web form:
www.jax.org/jaxmice/orders
Mail:

Customer Service
610 Main Street
Bar Harbor, Maine
04609-1526 U.S.A.
About your order:

Purchase order number (and release
number, if applicable).
Order type: one-time shipment or
standing order.
Requested delivery date(s).
For Technical Support:

Telephone:
United States: 1-800-422-6423

International: 1-207-288-5845
Monday through Friday
8:00 AM to 6:00 PM Eastern Time
Web form:
www.jax.org/jaxmice/micetech
Email:
[email protected]
For JAX Services:

Telephone:
1-800-422-6423
1-207-288-6294
Website:
www.jax.org/jaxservices
Email:
[email protected]
About the mice:

Stock number and full strain name.
Genotype.
Quantity, age, and gender required.
If you are a new customer:

To establish an account to order JAX Mice
and JAX Services, please complete our
new account form, available on our website:
www.jax.org/jaxmice/orders/newcustomer
For general information about The Jackson

Laboratory:
Telephone:
1-207-288-6000
Web:
www.jax.org
Mail:

600 Main Street
Bar Harbor, Maine
04609-1526 U.S.A.
272 Section V: Ordering JAX Mice and JAX Services
If I am in Europe or Asia, how do I order JAX Mice?

Customers in Europe and Asia can purchase JAX Mice one of two ways:
Directly from Customer Service at The Jackson Laboratory.
From one of our authorized distributors or breeders in Europe or Asia. For an up-to-date list
and contact information, visit our website (www.jax.org/jaxmice/orders/international).
If you have any questions, please contact Customer Service. One of our international agents will
answer your questions and help you with your order.
Can I set up a delivery schedule for my order of JAX Mice?

We can schedule shipment of your JAX Mice per your requirements. Contact Customer
Service for assistance.
Are there ways to reduce the lead time for my order of JAX Mice?
To expedite delivery of an order, consider the following:
Partial shipments of smaller quantities of mice.
Increased range of acceptable ages.
Males and females vs. males or females only.
How are JAX Mice shipped?

We ship JAX Mice in protective polypropylene containers with air filters designed to provide
maximum air flow and pathogen protection. (Air filter specs: media, 100% #5 polypropylene;
basis weight, 2.25 ounces per square yard; nominal thickness [1 ply], 17 mils; air permeability,
125 cubic feet per minute per square foot.) We supply each container with bedding, a water
source, and the normal feed for the mice being shipped. Supplies are adequate to accommodate
mice for up to 10 days. We conduct the entire packing process in the facility in which the mice
were raised.
Generally, we ship JAX Mice to the United States and Canada via our dedicated ground
transportation network. All trucks are specially engineered with environmental control systems
that facilitate sanitation and air flow and ensure as safe and stress-free a ride as possible. Once
we put the JAX Mice on the truck at our facility, they remain on the truck in this tightly
controlled environment until they are delivered to your site.
Sometimes it is imperative that we ship JAX Mice via air. Because air travel requires loading
and unloading of the animals in a variety of environments, we only use carriers that have proven
to be reliable partners and who are sensitive to the needs of animal transport. If your order
requires air shipment, we will work with you to ensure safe, reliable shipment of your JAX
Mice.
We schedule all shipments to minimize the time the mice are in transit.
For questions about shipping, please contact Customer Service.
Chapter 17: Ordering JAX Mice and JAX ServicesContact Information; Frequently Asked Questions 273
Can I order pregnant JAX Mice?

We distribute pregnant mice of some popular strains of JAX Mice to most locations. We
guarantee pregnancy for mice shipped after the 10th day of pregnancy, following confirmation of
pregnancy using palpation. We prefer to ship mice between gestation days 11 and 15.
We also distribute female mice in which we have observed a vaginal plug, which indicates
mating, not pregnancy. Because of the uncertainty of whether these mice are pregnant, we do
not guarantee their pregnancy.
For more information, for a current list of strains for which we ship pregnant mice, or to
schedule a shipment of pregnant mice, please contact Customer Service.
What should I do when my JAX Mice arrive?

Before your shipment of JAX Mice arrives, we suggest alerting your receiving department that
you are expecting them. This notification can help avoid the problem of live animals sitting on a
receiving dock for an extended period of time.
When you receive your shipment of JAX Mice, we recommend that you do five things as soon
as possible.
On the shipping dock:
1. Before you accept delivery of the mice, carefully inspect the shipping container for any
visible damage. If you notice anything wrong,
a. Describe it on the delivery manifest before you sign and return it to the driver.
b. Immediately contact Customer Service at The Jackson Laboratory.
2. Check the shipping label to be sure that the JAX Mice listed are the strain, genotype and age
you ordered. If you have any questions or concerns, immediately contact Customer Service.
3. To ensure the health and welfare of your JAX Mice, place themin the sealed shipping
containerin a safe place until they are delivered to a mouse room. A well-ventilated area,
away from direct sunlight is best. Avoid temperatures below 8 C (46 F) or above 29 C
(84 F).
When you are ready to unpack the mice in a mouse room:
4. Before you unpack your JAX Mice, disinfect the outside of the shipping container by wiping
it thoroughly with a disinfectant such as 70% ethanol. Although the mice were packed under
extremely strict health regulations at The Jackson Laboratory, the outside of the shipping
container may have been exposed to microbes since it left our shipping dock (especially if the
mice were shipped via air). Taking the time to clean the container thoroughly before
unpacking the mice can help ensure that the health status of your JAX Miceand your
facilityremains high.
5. As soon as you open the container, check on the mice. They may need food or water.
Note: At The Jackson Laboratory, our mice drink water from bottles. If your facility uses an
automatic watering system, be aware that the mice may need help learning how to use it.
For strategies, refer to 12.B.3, What to do if you have an automatic watering system and
your newly arrived JAX Mice wont use it.
What if there is a problem with my JAX Mice when I receive them?

If you have any problem with your newly arrived JAX Mice, immediately contact Customer
Service. If the mice appear sick, you also may want to contact your staff veterinarian.
Note: Due to animal health issues, mice cannot be returned to The Jackson Laboratory. A
customer service representative will advise what you should do.
Why do the coat colors of F2 hybrid JAX Mice sometimes differ from
order to order?
At the time this handbook was printed, we offered two strains of F2 hybrid JAX mice
B6129PF2/J (100903) and B6129SF2/J (101045). These hybrids segregate on coat color, and we
generally group mice of the same color when we ship them. This means that if you reorder the
same F2 hybrid, you might get mice of a different color. Check the shipping label. If you
suspect a problem, contact Customer Service.
Should I genotype my JAX Mice when they arrive?

We guarantee the genotype of all JAX Mice that we distribute. It is always a good idea,
however, for you to confirm the genotype before undertaking studies.
When are newly arrived JAX Mice ready for research?

Due to the lingering effects of shipping stress on their physiology, mice will not be ready for
research for at least one week. During this time, however, mating pairs can be placed together.
For details on introducing JAX Mice into your colony and readying them for research, please
refer to 12.B, Handling newly arrived mice.
Should I try to duplicate the same diet used by The Jackson Laboratory
to maintain my JAX Mice?
The requirements for a specific diet depends on the individual strain or mutation. Sometimes it
is important to duplicate the diet we use at The Jackson Laboratory to assure expression of a
phenotype of interest. For example, we maintain the diabesity strain NONcNZO10/LtJ (004456)
on a 10% fat diet (LabDiet 5K20) to express the diabetes phenotype. For dietary requirements
for any strain of JAX Mice, please check the strain datasheet (www.jax.org/jaxmice/query).
Should I expect phenotypic differences from published descriptions of

JAX Mice that have been maintained in standard SPF vivaria if my
vivarium is at full barrier status?
Certain phenotypes require the exposure to microorganisms that may be considered
unacceptable in some vivaria. For example, the development of atherosclerotic plaques in mice
may be diminished in vivaria that are full barrier status. For additional discussion, refer to 7.A,
Developing an animal health plan, in chapter 7. For information about specific strains of
JAX Mice, refer to the strain datasheet (www.jax.org/jaxmice/query) or contact Tech Support.
Is there a difference between JAX Mice from Bar Harbor and

Sacramento?
We offer a selection of JAX Miceincluding inbred and genetically-engineered strains and
hybridsfrom Sacramento based on customer requirements. We adhere to the same exacting
standards for research, genetic and health monitoring, animal husbandry, and customer service
in California as we do in Maine.
Because our breeding colonies in Sacramento are refreshed monthly using foundation stocks
from Bar Harbor, JAX Mice from Sacramento and Bar Harbor are genetically identical.
Chapter 17: Ordering JAX Mice and JAX ServicesContact Information; Frequently Asked Questions 275
What does it mean to register interest in a new strain?

Each year, nearly 300 new mouse strains become available from The Jackson Laboratory. Some
of these mice are from our own investigators, but many are strains that are donated by
investigators from other institutions. The process of readying the strain for distribution includes
importation, rederivation, colony building, and quality testing, which can take from 612
months. During this period, researchers can register interest in the strain, which places them
on a waiting list for the mice.
Researchers receive confirmation of the registration and get advance notice (typically about
three weeks) of the pending availability of the strain. They then have the option to place an
order for the strain. (When the mice are available, these orders are filled on a first comefirst
served basis according to the date on which interest was registered.) Note that registering for a
strain in no way obligates a researcher to purchase a strain.
For information on a specific strain of JAX Mice for which we are registering interest, refer to
the strain datasheet at www.jax.org/jaxmice/query. For information on registering for a strain,
including a list of strains currently being readied for distribution, visit
www.jax.org/jaxmice/interestlist or contact Customer Service.
Do I have to pay licensing fees for JAX Mice?

At The Jackson Laboratory, one of our goals is to provide researchers with mouse models
unencumbered by license restriction. However, some of the mouse strains we distribute were
genetically engineered at other institutions and may require licensing for commercial use.
Generally, academic and non-profit organizations are exempt from license restrictions of these
types, but it is the responsibility of each institution to abide by all licensing and use
requirements that might apply.
For any strain of JAX Mice that requires a licensing agreement or that has use restrictions, we
include relevant information in the strain datasheet (www.jax.org/jaxmice/query). The note
Use Restrictions Apply will be displayed in the Availability area of the datasheet. For details
of the use restriction, select the Terms of Use tab.
If you have questions about license restrictions, please review the information about conditions
of use on our website at www.jax.org/jaxmice/cou. Or contact the Tech Transfer Office at
[email protected]. Please include the stock number with your inquiry.
For more information

To order technical literature, including a JAX Mice Catalog, visit
www.jax.org/jaxmice/support.
For frequently asked questions, visit www.jax.org/jaxmice/faq.
For any other assistance, please contact Customer Service.
277
Chapter 18: JAX Services

One of the missions of The Jackson Laboratory is to enable research throughout the world. A
significant way we do this is by providing JAX Services to the global research community.
JAX Services include a wide range of technologies. Each service was originally developed as a
way for our own researchers at The Jackson Laboratory to share resourcesequipment and
expertise. Today we offer many of these same benefits to
researchers throughout the world.
We generally group individual JAX Services into five basic

categories:
Breeding and colony management
Cryopreservation and recovery
Phenotyping and efficacy testing
Genetic analysis and research services
Study-ready induced models
JAX Services are designed to be flexible, either used individually
or bundled, and tailored to meet a wide variety of research needs
for both large and small organizations.
Where to get information about JAX

Services
Phone:
1-800-422 6423 (North America)
1-207-288-6294 (International)
8:00 a.m. to 6:00 p.m., EST (or EDT), Monday
through Friday
Email:
[email protected]
Online:
JAX Services catalog:

www.jax.org/jaxmice/literature
This chapter provides just a brief overview of JAX Services. For more detail, please visit our
JAX Services website (www.jax.org/jaxservices) or request a copy of our JAX Services
Catalog (www.jax.org/jaxmice/literature). To consult with us about how JAX Services can
augment your research program, please contact us at the telephone number or email address
shown above.
Breeding and colony management

Aging service
Breeding and housing mice until they reach an age when you require them.
Applicable strains: Your research mice or any strain of JAX Mice. Note that we also maintain
colonies of several strains of JAX Mice that we routinely have available at specific ages. For a
list of these strains, visit www.jax.org/jaxservices/aging.
Breeding services
Breeding and maintenance of your mice at our facility, per your specifications; shipment to you
per your schedule. This service also can be used to create F1 or F2 hybrids, to backcross
progeny, or to maintain special stocks carrying multiple gene mutations or transgenes.
Dedicated supply services
Shipment of a specific quantity of JAX Mice according to your schedule. Use when you need
one shipment of a large quantity of JAX Mice or a regular supply of JAX Mice.
Applicable strains: Any strain of JAX Mice, but generally used for strains that are in one of our
repositories, strains not bred in large quantities, or strains that are difficult to breed.
Rederivation services
Speed rederivation (via IVF) with sperm cryopreservation (for transgenic, knockout, and
single gene mutation mice)
Cryopreservation of sperm (at least 16 straws) from at least two males from your colony. On
your schedule, use of in vitro fertilization (IVF) to create live mice (10 minimum) that are
shipped back to you. The service is typically completed within 1012 weeks from the time we
receive your mice. Applicable to transgenic, knockout, and single gene mutation mice on the
most commonly used genetic inbred lines, including BALB/cByJ (001026), BALB/cJ (000651),
C3H/HeJ (000659), C57BL/6J (000664), DBA/1J (000670), DBA/2J (000671), FVB/NJ
(001800), NOD/ShiLtJ (001976), hybrid combinations of these background strains, B6;129
hybrids.
Standard rederivation (for inbred and homozygous mice)

Importation and rederivation of your micefour to five males and six to ten females from your
colony; shipment to you of all the specific pathogen free (SPF) mice (minimum of two pair
guaranteed) that we produce.
Applicable strains: Any strain, but the service is particularly appropriate for inbred and
homozygous mice.
Speed expansion service

Use of in vitro fertilization (fresh or frozen sperm) and implantation of embryos into host
females to provide accelerated expansion of a line of mice. Used for rapid expansion of a colony
(for example, a small number of unique mutant mice), especially when you need a quantity of
mice at the same age, if you have just a few viable males.
Strain rescue service

Importation of mice that have stopped breeding; use of assisted reproductive techniques to
rescue the strain.
Sponsored strain distribution

Rederivation and distribution of your research mice. For an overview, see Appendix K,
Donating or Submitting a Strain of Mice to The Jackson Laboratory. For full details, visit
www.jax.org/jaxservices/sponsoreddistribution.
Chapter 18: JAX Services 279
Cryopreservation and recovery

Following are summaries of our JAX Services related to cryopreservation. For general
descriptions of cryopreservation techniques, see Appendix J,
Cryopreservation.
Our cryopreservation team can come to you
Cryostorage and recovery services

Cryopreservation of your mouse strain and storage of the frozen
material in our secure facilities. Upon your request, either
shipment of frozen material or recovery of the frozen material and
shipment of liveborn mice.
IVF embryo cryopreservation service
We can deploy teams of reproductive specialists

to your facility to cryopreserve large numbers of
strains. This service is ideally suited for
institutions or investigators with large rederivation
projects or substantial backlogs of strains that
must be cryopreserved. Our teams can routinely
cryopreserve 120 strains or more on site in a
week.
Use of sperm from two male donors for in vitro fertilization of ova
from superovulated donor females; cryopreservation of embryos and rapid recovery upon
request.
Applicable strains: Your males and our females of these strains of JAX Mice: BALB/cByJ
(001026), C57BL/6J (000664), DBA/2J (000671), FVB/NJ (001800), NOD/ShiLtJ (001976).
Custom (homozygous embryo) cryopreservation service

Cryopreservation of inbred, mutant, and genetically modified lines of mice that cannot be
cryopreserved under the conditions of our standard cryopreservation services. Requires male
and female mice from your colony.
Sperm cryopreservation & recovery service

Cryopreservation of sperm from two male mice from your colony.
Upon your request, either shipment of frozen material or recovery
of the frozen material and shipment of liveborn mice.
Applicable strains: Any mouse strain.
Phenotyping and efficacy testing

In Vivo services
Sperm cryopreservation is now a viable

alternative at The Jackson Laboratory.
Historically, the use of sperm cryopreservation
was limited by poor recovery rates. Researchers
at The Jackson Laboratory are funded to study
ways to improve cryopreservation methods. In the
spring of 2006, we developed patent pending
techniques that greatly improve the recovery of
frozen sperm for strains for which recovery was
poor (Ostermeier et al. 2008). This advancement
enhances the application of sperm
cryopreservation as a colony management tool.
Implementation of treatment studies using mice housed and treated

at The Jackson Laboratory. Areas of research include obesity and
type 2 diabetes, type 1 diabetes, inflammation and autoimmunity, neurodegenerative and
neuromuscular disorders, and xenografts.
Applicable strains: Your mice or JAX Mice.
Compound evaluation services

Maintenance and treatment of your mice at our site. Optional services include evaluation of
blood, serum, plasma, urine, and feces; and, necropsies and collection of tissue for
histopathology, IHC, and gene expression.
Applicable strains: Any stock of mice or strain of JAX Mice.
Phenotyping services
Model characterization, drug target validation, and efficacy testing in mouse models of disease;
based on a broad selection of noninvasive physiological tests.
Genetic analysis & research services

Gene expression service
Nucleic acid preparation, chip/array hybridization, and detailed statistical analysis, using unique
statistical tools developed at The Jackson Laboratory.
Gene mapping service

Mapping of a spontaneous genetic mutation or non-targeted transgenic mutation using SNP
markers; based on tissue from a genetic cross between your mice and an appropriate strain of
JAX Mice.
Genome scanning service

Genotyping of your mice using single nucleotide polymorphism (SNP) markers; based on tissue
sent to us. This service is especially useful when creating speed congenics, confirming strain
identity, monitoring genetic purity.
Speed congenic development service

Creation of a congenic strain of mice using genotyping, reducing development time from 2.53
years to about 1.5 years.
QTL mapping service

Advanced identification of quantitative trait loci (QTLs) using selected markers from our
validated panel of more than 2,000 SNP markers. Includes genotyping of DNA samples from a
cross and the application of specialized statistical methods for QTL discovery.
Study-ready induced models

Aging service
Breeding and housing mice until they reach an age when they are useful as models of late onset
disease or normal aging.
Applicable strains: Your research mice or any strain of JAX Mice. Note that we also maintain
colonies of several strains of JAX Mice that we routinely have available at specific ages. For a
list of these strains, visit www.jax.org/jaxservices/aging.
Alopecia areata surgical model

Development of mice surgically induced to develop alopecia areata.
Applicable strains: Strains on the C3H/HeJ (000659) background.
Diet-induced obesity (DIO) service

Treatment of mice to produce diet-induced obesity. Options include our shipping pre-treated
mice to you or performing further procedures in our facilities.
Applicable strains: C57BL/6J (000664); other strains upon request.
STZ-induced diabetes service

Treatment of mice with a multiple, low dose, streptozotocin (STZ) protocol that induces
pancreatic islet damage and subsequent diabetes.
Applicable strains: A/J (000646), BALB/cJ (000651) and FVB/NJ (001800) males are resistant;
C57BL/6J (000664) males are moderately susceptible; males of strains CBA/J (000000) and
NOD/ShiLtJ (001976) are highly susceptible.
Chapter 18: JAX Services 281
VCD-induced model of menopause

Development of research models of perimenopause that can be used to study the interaction of
menopause with age-related, chronic, cumulative diseases such as heart disease, diabetes,
cancer, osteoporosis, and stroke.
Applicable strains: five genetic backgroundsB6.129S7-Ldlrtm1Her/J (002207), a strain with
normally high serum cholesterol levels and extremely high levels when fed an atherogenic diet;
B6.129P2-Apoetm1Unc/J (002052), another strain with high serum cholesterol levels; C3H/HeJ
(000659), an atherosclerosis-resistant strain; C57BL/6J (000664), an atherosclerosis-susceptible
strain; and NZBWF1/J (100008), a model of systemic lupus erythematosuswith an option to
adapt the model on other backgrounds.
Surgical and histological services

Histology service
Tissue collection, tissue fixation, embedding, sectioning, straining; shipment of blocks and/or
slides.
Applicable strains: Your mice or any strain of JAX Mice.
Surgical and tissue collection services

A wide variety of standard surgical procedures and bio-specimen, organ and tissue collection,
with the option of custom surgery.
Other research services

Mouse DNA Resource
Genomic DNA suitable for Southern blotting and amplification by PCR. Most DNA is extracted
from spleen or brain and spleen of pedigreed male mice. Some DNA, however, is extracted
from other tissues, and some is extracted from female mice. For details, call 1-207-288-6414,
fax 1-207-288-6074, or email [email protected].
Applicable strains: Most strains of JAX Mice. For a current list, visit www.jax.org/dnares.
References
Ostermeier GC, Wiles MV, Farley JS, Taft RA. 2008. Conserving, distributing and managing
genetically modified mouse lines by sperm cryopreservation. PLoS ONE. 3(7):e2792.
doi:10.1371/journal.pone.0002792.
283
Chapter 19: The Jackson LaboratoryWest

In 1999 The Jackson Laboratory opened a facility in West Sacramento, California. Our
objective was to provide a source for mice and related services in demand by academic, nonprofit, pharmaceutical and biotechnology researchers in California and western North America.
Since then, our staff and offerings have expanded as customer needs have warranted. We now
provide a number of JAX Mice and JAX Services from The Jackson LaboratoryWest.
Overview of The Jackson LaboratoryWest facilities

We view The Jackson LaboratoryWest as an extension of our Bar Harbor facilities. We
adhere to the same exacting standards for research, genetic and health monitoring, animal
husbandry, and customer service in California as we do in Maine.
Mouse rooms
Mouse rooms in Sacramento are maintained in a
manner consistent with rooms of our highest health
status in Bar Harbor.
Where to get more information

About The Jackson LaboratoryWest:
www.jax.org/jaxmice/jaxwest
Breeders are received monthly from Bar Harbor

foundation stocks. Genetic monitoring is conducted in
Bar Harbor.
Veterinary care and husbandry
About JAX Services:

Telephone:
1-800-422-6423 (North America)
Email:
[email protected]
Web:
The Comparative Pathology Laboratory at The
University of California at Davis provides health
monitoring and veterinary care for all mice in our
Sacramento facility. Standards are consistent with those for our Bar Harbor facility. For details
on husbandry at The Jackson LaboratoryWest, visit www.jax.org/jaxmice/jaxwest/husbandry.
Overview of JAX Mice and JAX Services available from The

Jackson LaboratoryWest
Strains of JAX Mice
We offer a selection of JAX Miceincluding inbred and genetically-engineered strains and

hybridsfrom Sacramento based on customer requirements. For a list of strains currently being
bred and shipped from The Jackson LaboratoryWest, visit
www.jax.org/jaxmice/jaxwest/strains.
JAX Services
Several of our JAX Services are available at The Jackson LaboratoryWest. Our ongoing
goal is to provide the exact, customized services that best meet the needs of the research
programs of our customers on the West Coast. One of our most popular offerings is JAX In
Vivo Services, which includes compound evaluation services and phenotyping services. Areas
of research include obesity and type 2 diabetes, type 1 diabetes, inflammation and
autoimmunity, neurodegenerative and neuromuscular disorders, and xenografts. We also offer
breeding services based in high health status barrier rooms or flexible film isolators.
For details on these and other JAX Services, please contact us as indicated above.
285
Appendix A: Strain Nomenclature Quick Reference

This appendix includes three tables related to nomenclature:
Table A.1. Mouse strain nomenclature quick reference: examples, definitions, and comments.
Table A.2. Abbreviations of inbred mouse strain and substrain names used in hybrid names.
Table A.3. Nomenclature symbols and abbreviations used within strain names.
For more information about mouse nomenclature, including full guidelines set by the
International Committee on Standardized Genetic Nomenclature for Mice, visit the Mouse
Nomenclature Home page at www.informatics.jax.org/mgihome/nomen.
Table A.1. Mouse strain nomenclature quick reference: examples, definitions, and comments.
Name
Category and definition
Convention, comments, explanations
129
C57BL
C3H
DBA
Inbred strain: developed by

intercross sibling mating (one
lineage) for at least 20 consecutive
generations.
Uppercase alphabetic and alphanumeric

characters, starting with an alphabetic
character.
Exception: Names assigned before adoption of
current nomenclature rules may start with
number or include lowercase alphabetic
characters.
C57BL/6J
DBA/1LacJ
CBA/CaGnLeJ
Inbred substrain: branch of an

inbred strain separated by 20 or
more generations.
Inbred strain name, forward slash (/), ILAR

code(s)*.
CAST/EiJ
MOLD/RkJ
Wild-derived inbred strain:

developed by importation of wild
mice followed by intercross sibling
mating for at least 20 generations.
Wild strain name, forward slash (/), ILAR

code(s)*.
B6D2F1/J
F1 hybrid: first outcrossed

generation of 2 inbred strains.
Abbreviation of strain of mother, abbreviation

of strain of father, F1, forward slash (/),
ILAR code(s)*.
Note: Female strain abbreviation is always
given first.
(See Table A.2 for strain abbreviations.)
B6129SF2/J
F2 hybrid: first intercrossed

generation of F1 hybrid siblings.
Name of F1 parental hybrid, F2, forward

slash (/), ILAR code(s)*.
C57BL/6J-Aw-J/J
Inbred strain carrying a mutation.

Note: For details about the mutation,
check with the supplier. For JAX
Mice, refer to the strain datasheet, at
www.jax.org/jaxmice/query.
Background strain name, hyphen (-), gene

symbol/allele (italicized), forward slash (/),
ILAR code(s)*.
Note: Nomenclature does not reflect whether
the strain is heterozygous (segregating inbred
strain) or homozygous for the allele.
B6129PF1/J-Aw-J/A w
F1 hybrid carrying a mutation.
Same as in previous row, with name of F1

hybrid as background strain.
C57BL/6-Prf1tm1Sdz/J
Inbred strain carrying a targeted

mutation.
Background strain name; hyphen (-); gene

symbol/allele (italicized), targeted mutation
number (tm#) and allele identifier (italicized
superscript); forward slash (/); ILAR codes*.
C3H/HeJ-Mgrn1md/J
*For Institute for Laboratory Animal Research (ILAR) codes, visit http://dels.nas.edu/ilar_n/ilarhome/search_lc.php.
286 Appendixes
Table A.1. Mouse strain nomenclature quick reference: examples, definitions, and comments. (continued)
Name
B6;129S4-Nos1tm1Plh/J
Targeted mutation on a stock derived

from 129S4 ES cells and C57BL/6J
mice.
Same as in previous row, except

abbreviations of the parental genotypes are
separated by a semi-colon (;). If this stock is
being backcrossed, this nomenclature
indicates less than 5 backcross generations.
C57BL/6-Tg(CAG-EGFP)131Osb/
LeySopJ
Transgenic strain: includes genetic

material from a different strain or
species.
Recipient strain, -Tg, insert designation

(in parentheses), line number and originator,
forward slash (/), ILAR code(s)*.
STOCK-Tg(B19-RNAi:Il3)241Ckn/J
Transgenic strain on a mixed

background.
Same as in previous row, with STOCK

designation to represent a mixed
background of 3 or more founder strains,
founders of unknown genetic background,
or outbred founders.
B6.129P1-Lama2dy/J
Congenic or incipient congenic strain:

in which a genetic locus is transferred,
via outcrossing, from a donor to a
recipient, followed by backcrossing for
at least 5 generations. An incipient
congenic has been backcrossed for 59
generations; a full congenic requires 10
backcross generations.
Note: For details about the number of
backcross generations for a particular
strain, check with the supplier. For
JAX Mice, refer to the strain datasheet
at www.jax.org/jaxmice/query.
Abbreviation of recipient strain, period (.),

abbreviation of donor strain, hyphen (-),
genetic locus and allele of interest (in
italics), forward slash (/), ILAR code(s)*.
B6.Cg-Ay/J
Congenic strain, with locus of interest

from a mixed donor stock.
Same as in previous row, with Cg

replacing name of donor strain to indicate
mixed donor stock.
Congenic strain, with multiple loci from

different sources.
Same as in previous row, with multiple loci

of interest.
BXD1/TyJ
BXD2/TyJ
BXD5/TyJ
Recombinant inbred (RI) strain:

generated by outcrossing 2 inbred
strains (to create F1s), intercrossing of
F1s (to create F2s), inbreeding single
lineages of siblings into multiple inbred
strains.
Abbreviation of strain of mother, X,

abbreviation of strain of father, numeral
indicating line number within the panel,
NONcNZO5/LtJ
NONcNZO10/LtJ
Recombinant congenic (RC) strain:

generated by outcrossing 2 inbred
strains (to create F1s), backcrossing of
F1s to one of the parental strains
(recipient strain) for 1 or 2 generations
(N2, N3), inbreeding single lineages of
N3 siblings for 14 generations (F1F14)
into multiple inbred strains.
Uppercase abbreviation of female founder,

c, uppercase abbreviation of male
founder, line number in the panel, forward
slash (/), ILAR code(s)*.
Appendix A: Nomenclature Quick Reference 287
Table A.1. Mouse strain nomenclature quick reference: examples, definitions, and comments. (continued)
Name

A/J
C57BL/6J-Chr 1 /NaJ
Chromosome substitution strain (CSS;

sometimes called a consomic strain):
generated by outcrossing 2 inbred strains (to
create F1s), backcrossing of F1s with markerassisted selection for 9 generations (N1N9),
inbreeding single lineages of N9 siblings until
all markers for the target chromosome are
donor-type.
Full recipient strain name, hyphen (-),

chromosome number, donor strain
(superscripted), forward slash (/), ILAR
code(s)*.
Conplastic strain: type of congenic in which

the mitochondrial genome of one strain is
transferred to another strain.
Note: When a conplastic strain is part of a
CSS (consomic) panel, it is also considered a
CSS strain.
Full name of recipient strain, -mt, full name

of mitochondrial donor strain (superscripted),
Chromosomal aberration strain: includes

rearrangements of the normal chromosomal
structure.
Full background strain name, hyphen (-),

abbreviation of aberration, affected
chromosome(s) (in parentheses), series number
of the aberration, ILAR code(s)* of discoverer
or developer, forward slash (/), ILAR code(s)*.
Note: For translation of commonly used
aberration abbreviations, see Table A.3 in this
appendix. For translation of all abbreviations,
visit www.informatics.jax.org/
mgihome/nomen/anomalies.shtml.
Tac:ICR
Outbred stock: a genetically undefined

population.
ILAR code* for the institution holding the

stock, colon (:), the common strain root.
Table A.2. Abbreviations of inbred mouse strain and substrain names used in hybrid names.
129P
129P substrains
129X1
129X1/SvJ (000691)
CBy
BALB/cByJ (001026)
129P1
129P1/ReJ (001137)
A strains
D1
DBA/1 strains
129P2
129P2/OlaHsd
AHe
A/HeJ (000645)
D2
DBA/2 strains
129P3
129P3/J (000690)
AK
AKR strains
HR
HRS/J (000673)
129S
129S substrains
C57BL
C57L/J (000668)
129S1/Sv-Oca2+Tyr+KitlSl-J/J
B6
C57BL/6 strains
NZB
NZB strains
(000090)
B6Ei
C57BL/6JEi (000924)
NZW
NZW strains
129S1
129S1/SvImJ (002448)
B10
C57BL/10 strains
R3
RIIIS/J (000683)
129S2
129S2/SvPas
BR
C57BR/cdJ (000667)
129S4
129S4/SvJae
BALB/c strains
SJ or
J
SJL/J (000686)
129S5
129S5/SvEvBrd
C3
C3H strains
SM
SM/J (000687)
129S6
129S6/SvEvTac
C3Fe
C3HeB/FeJ (000658)
SW
SWR strains
129S7
C3Sn
C3H/HeSnJ (000661)
NZW strains
Numbers in parentheses are JAX

Mice stock numbers.
129S8
CB
CBA strains
(002027)
CBACa
CBA/CaGnLeJ (001143)
288 Appendixes
Symbol or
abbreviation
Use, definition
STOCK
Indicates a mixed background of 3 or more founder strains, founders of

unknown genetic background, or outbred founders. (Usage is unique to The
Jackson Laboratory.)
Separates strain name from information such as genetic data, ILAR code(s)* for
originator of the strain and institution that maintains the strain.
F#
Filial generations (sisterbrother matings)

Example: F120. The inbred strain has been sibling mated for 120 generations.
When followed by a question mark (F?), the number of filial generations is
unknown. ? is most often used when mice are imported into a repository and
inbreeding history is unknown or unsubstantiated.
Example: F?+19. Unknown number of filial generations, followed by sibling
mating for 19 generations.
N#
Backcross generations.
Example: N6. The stock has been backcrossed to the same recipient strain for 6
generations.
NE#
N equivalents. Used when creating a congenic with complex mating systems, to

indicate equivalence to normal backcrossed generations.
Example: NE10. The mating system has produced a level of homozygosity
equivalent to 10 backcross generations.
N#F#
Number of backcross generations (N) and number of filial generations (F).

Example: N8F20. The strain was backcrossed for 8 generations, and then
intercrossed by sibling mating for twenty generations.
For cryopreserved strains, the generation when the material was frozen.
Example: F26p27. The strain was cryopreserved after 26 filial generations;
since recovery, the strain has been mated for 27 additional filial
generations.
G#
Generations that cannot be defined using F or N notation. For example,

with advanced intercrossed lines, typically the first 2 generations are produced
by sibling matings to produce an F2 population; the next generation, produced
by a non-sibling intercross, is designated as the G3 generation. Subsequent
generations of non-sibling intercrosses are designated as G4, etc.
. (period)
In congenic strain names, designates at least 5 generations of backcrossing.

Note:
Congenic nomenclature is assigned after backcross generation 5
(N5). Congenics from N5 to N9 are called incipient congenics. A full
congenic requires a minimum of 10 backcross generations.
; (semi-colon)
In mixed stocks, separates names of recipient and donor strains or, for nondonor/recipient situations, separates strain names of female and male founders.
Indicates less than 5 filial generations or unknown number of filial generations.
: (colon)
In names of outbred stocks, separates the ILAR code* for the name of the
institution holding the stock from the name of the common strain root.
In names of advanced intercross lines, separates the ILAR code* of the
developer of the line from abbreviations of the strains of the founders and
generations of breeding.
In recombinant congenic strains, separates abbreviations of parental strain

names.
Appendix A: Nomenclature Quick Reference 289
(continued)
Symbol or
abbreviation
Use, definition
Cg
In names of congenic strains, indicates that a single locus from an undefined

(mixed) donor has been transferred or that multiple loci from different sources
have been transferred.
Chr
In names of chromosome substitution (consomic) strains, precedes the

chromosome number and the name of the donating strain.
mt
In conplastic strain names, precedes the strain name of the mitochondrial donor.
Tg
Indicates a transgenic strain; precedes the insert designation (in parentheses).
tm
Indicates a targeted mutation.
In recombinant inbred (RI) strain names, separates abbreviations of parental

strain names.
In
Is
Rb
T
Ts
Y
In chromosomal aberration strains, abbreviations for the aberrations.

In: inversion
T: translocation
Is: insertion
Ts: trisomy
Rb: Robertsonian
Y: Chr Y abnormality
(For additional abbreviations and information, visit
www.jax.org/jaxmice/type/chromosomal_abberati.)
291
Appendix B: 129 StrainsNomenclature and

Related ES Cell Lines
This appendix provides information about the 129 strain family: nomenclature and the
embryonic cell lines.
129 strain nomenclature

Extensive outcrossing, residual heterozygosity, and documented contamination in 129
substrains resulted in a complex history and confusing genetic relationships (Simpson et al.,
1997; Threadgill et al., 1997). Because of the extensive use of 129 substrains in targeted
mutagenesis, it became important to establish a consistent nomenclature. In 1999, Festing et al.
introduced new nomenclature for the 129 strains, which was approved by The International
Committee on Standardized Genetic Nomenclature. Tables B.1 and B.2 provide information
about the new nomenclature. For full nomenclature details, visit
www.informatics.jax.org/mgihome/nomen/strain_129.shtml.
Table B.1. New parental categories for 129 strains.
This strain designation
represents strains derived from
the original parental strain
a congenic strain made by outcrossing to introduce the steel locus
a congenic strain that originally carried the teratoma mutation
X
a strain where genetic contamination is documented*
*The 129X lines from The Jackson Laboratory have been fully inbred since the contamination event that
occurred early in the history of the line.
292 Appendixes
Table B.2. Revised nomenclature for 129 substrains.

Revised nomenclature
Abbreviation
129P1-Lama2dy
Old nomenclature
Full designation
(JAX Mice stock number)
129P1/ReJ-Lama2dy/J
(000641)
129/ReJ-Lama2dy
129P1
129P1/ReJ
(001137)
129/ReJ
129P2
129P2/OlaHsd
129/OlaHsd
129P3
129P3/J
(000690)
129/J
129X1
129X1/SvJ
(000691)
129/SvJ
129S1/Sv-Oca2+ Tyr+ KitlSl-J/J

(000090)
129/SV-p+ Tyr+KitlSl-J/+
129S1/SvImJ
(002448)
129/SV-p+ Tyr+Kitl+/J
129S2
129S2/SvPas
129/SvPas
129S4
129S4/SvJae
129/SvJae
129S5
129S5/SvEvBrd
129/SvEvBrd
129S6
129S6/SvEvTac
129/SvEvTac
129S7
129/SvEvBrd-Hprtb-m2
129S8
(002027)
129/SvEv-Gpi1c Hprtb-m2@J
129T1
129T1/Sv-Oca2+ Tyrc-ch Dnd1Ter/J

(000091)
129/ Sv-p+ Tyr c-ch Ter/+@Na
129T2/SvEms
(002064)
129/SvEms-Ter+?
129S1
129T2
129T2/SvEmsJ
129/SvEms-Ter+?/J
(002065)
Table source: www.informatics.jax.org/mgihome/nomen/strain_129.shtml
Phenotype and genotype
White-bellied, pink-eyed chinchilla,

dystrophic:
Aw/Aw
Oca2p Tyrc-ch/Oca2p Tyrc-ch
Lama2dy/Lama2dy
White-bellied, pink-eyed chinchilla,
(non-dystrophic; unaffected):
Lama2dy/+ or +/+ or +/?
White-bellied, pink-eyed chinchilla
Aw/Aw
Oca2p Tyrc-ch/Oca2p Tyrc-ch
White-bellied, pink-eyed, light
chinchilla
Aw/Aw
Oca2p Tyrc-ch Oca2p Tyrc
Albino
Aw/Aw
Oca2p Tyrc /Oca2p Tyrc
White-bellied agouti
Aw/Aw
White-bellied, chinchilla
Aw/Aw
Tyrc-ch/Tyrc-ch
Appendix B: 129 strain nomenclature and related ES cell lines 293
ES cell lines and related 129 strains

To minimize background genetic variation when creating recombinant mice using embryonic
stem (ES) cells, it is important to match the ES cells and the specific 129 substrain used as a
recipient. Table B.3 lists the ES cell lines and their 129 strains.
Table B.3. ES cell lines and their 129 strains.
ES cell line
129 strains and (JAX Mice stock number)
Coat color
AB1 (+Hprt1-bm2)
129S7/SvEvBrd-Hprt1b-m2
AB2.1 (+Hprt1-bm2)
129S7/SvEvBrd-Hprt1b-m2
AK7
129S4/SvJaeSor
CJ7 (+ Kitl-SlJ )
129S1/Sv-Oca2+ Tyr+ KitlSl-J/J*

(000090)
CP1
129S6/SvEv
D3
129S2/SvPas
E14TG2a
129 P2/OlaHsd
Pink-eyed chinchilla
EK.CCE
129S6/SvEv
HM-1 (Hprt1b-m1)
129 P2/OlaHsd
J1
129S4/SvJae
mEMS32
129P3/JEms
PJ1-5
129X1/SvJ
(000691)
Light chinchilla or albino
R1 (+Kitl-SlJ)
129X1/SvJ x 129S1/Sv-Oca2+ Tyr+ KitlSl-J/J*

(000691 x 000090)
RW-4
129X1/SvJ
(000691)
Light chinchilla or albino
TC1
129S6/SvEvTac
129S1/Sv-Oca2+ Tyr+ KitlSl-J/J*
W9.5 (+Kitl-SlJ )
(000090)
*Origin of 129S1/SvImJ (002448). (Adapted from Simpson et al., 1997.)
References
Festing MFW, Simpson EM, Davisson MT, Mobraaten LE. 1999 (updated 2007). Revised
nomenclature for strain 129 mice. Mouse Genome Informatics, The Jackson Laboratory, Bar
Harbor ME. (www.informatics.jax.org/mgihome/nomen/strain_129.shtml)
16:1927.
Threadgill DW, Yee D, Matin A, Nadeau JH, Magnuson T. 1997. Genealogy of the 129 inbred
strains: 129/SvJ is a contaminated inbred strain. Mamm Genome. 8:390393.
295
Appendix C: Origins and Relationships among

Common Strains and Substrains of Laboratory Mice
The relationships of the major inbred strains of laboratory mice are shown in Figure C.1. The
derivations of many substrains of six of the major strains are shown in Figures C.2C.7. These figures
show the progress of inbreeding in years and estimates of the numbers of generations. For a
comprehensive geneology chart of inbred strains, visit www.informatics.jax.org/mgihome/genealogy.
Figure C.1. The origins and relationships of some of the inbred strains of mice.
(Staats, 1980)
296 Appendixes
Figure C.2. Substrains of the A strain.
(Bailey, 1978)
Appendix C: Origins and Relationships among Common Strains and Substrains 297
Figure C.3. Substrains of the BALB/c strain.
(Bailey, 1978)
298 Appendixes
Figure C.4. Substrains of the CBA strain.
(Bailey, 1978)
Figure C.5. Substrains of the C3H strain.
(Bailey, 1978)
300 Appendixes
Figure C.6. Substrains of the C57BL strain.
(Bailey, 1978)
*The KS substrain is primarily C57BL/6 with contaminations from DBA/2 and BTBR strains (Petkov et al.,
2004). The KS substrain was sent to The Jackson Laboratory to help restore the C57BL/6 stock following the
fire in 1947.
For a poster that illustrates the history and development of todays C57BL/6 substrains, visit
www.jax.org/jaxmice/jaxnotes/512/512s.html.
Figure C.7. Substrains of the DBA strain.
(Bailey, 1978)
302 Appendixes
References
Bailey DW. 1978. Sources of Subline Divergence and Their Relative Importance for Sublines
of Six Major Inbred Strains of Mice, in Origins of Inbred Mice. Morse HC III (ed). Academic
Johnson KA, Robinson P, et al. 2004. An Efficient SNP System for Mouse Genome Scanning
and Elucidating Strain Relationships. Genome Res. 14:18061811.
Staats J. 1980. The Origins and Relationships of Some of the Inbred Strains of Mice, in
Handbook on Genetically Standardized JAX Mice. Heiniger H-J, Dorey JL (eds). The Jackson
Laboratory, Bar Harbor, ME. pp. 23.
303
Appendix D: Commonly-Used Inbred Strains and

Substrains of JAX MiceGenes and Research
Applications
Carol Linder, Barbara Witham
Over 400 different inbred strains are currently used in biomedical research (Festing, 1998).
Table D.1 summarizes the most commonly used parental strains, JAX Mice substrains, mutant
alleles of interest, and provides a guide to their application. For more information about research
applications of JAX Mice strains (including references), see the Find JAX Mice website at
www.jax.org/jaxmice/findmice.
Table D.1. Genetic characteristics and research applications of commonly-used inbred strains available
from The Jackson Laboratory.
Parental
strain
129
Substrains, JAX Mice

(stock number)
129P1/ReJ
129P3/J
129P3/JEmsJ
129P4/RrRkJ
129S1/SvImJ
129T2/SvEmsJ
129X1/SvJ
(001137)
(000690)
(002357)
(001198)
(002448)
(002065)
(000691)
Genes of interest
Tyrc-ch or Tyrc (not

129S1/SvImJ)
Oca2p/Oca2p (not
129S1/SvImJ)
Aw/Aw
Cdh23ahl
Disc1del
Polid
A/J
A/HeJ
A/WySnJ
(000646)
(000645)
(000647)
Tyrc
Tyrp1b
a/a
Hc0
Cdh23ahl
Dysf prmd (A/J)
Research applications
Cancer (low background incidence of

testicular teratomas)
General purpose
Neurodevelopmental defects (callosal
agenesis, incomplete penetrance); neuronal
and cognition defects, Disc1del)
Polymerase iota deficient (Polid )
Sensorineural (early hearing loss, Cdh23ahl)
Targeted mutagenesis (ES cell lines)
Cancer (high susceptibility to carcinogeninduced lung adenomas; useful for carcinogen
testing; late onset mammary tumors)
Cardiovascular (relatively resistant to dietinduced atherosclerosis)
Developmental biology (low background
incidence of cleft palate; high susceptibility to
cortisone-induced cleft palate)
General purpose
Immunodeficiency (specific complement
deficiency, Hc0)
Immunology (hybridoma production)
Progressive muscular dystrophy (Dysf prmd)
Susceptibility to hepatomas induced by
infection with Helicobacter hepaticus
AKR
AKR/J
AKR/CumJ
(000648)
(002720)
Tyr
Hc0
Soat1ald
Thy1a
Cancer (high leukemia strain due to retroviral

integration)
Developmental biology (hematopoietic
defects)
Diabetes and obesity (susceptible to dietinduced obesity)
Endocrine deficiency (adrenal cortex defects,
hypothalamus/pituitary defects, Soat1ald)
Note: relatively short lifespan
304 Appendixes
from The Jackson Laboratory. (continued)
Parental
strain
BALB/c

(stock number)
BALB/cJ
BALB/cByJ
BALB/cGaJ
BALB/cGrRkJ
BALB/cWtEiJ
(000651)
(001026)
(001905)
(000921)
(001311)
Genes of interest
Tyrc
Tyrp1b
A/A
Mdmg1BALB/cBy
(BALB/cByJ)
Hld (BALB/cJ, BALB/cByJ)
Cdh23ahl (BALB/cByJ)
General purpose
Cancer research (late onset mammary gland
tumors)
Developmental biology research
(hermaphroditism: sex chromosome
chimerism [BALB/cWtEiJ])
Immunology research (production of
monoclonal antibodies and hybridomas)
Autoimmunity (experimental allergic
encephalomyelitis (EAE), [BALB/cByJ and
BALB/cWtEiJ])
Neurobiology (callosal agenesis, incomplete
penetrance; high anxiety [BALB/cJ];
hippocampal lamination defect, Hld)
CBA
CBA/CaH-T(14 ;15)6Ca/J
(000655)
CBA/CaHN-Btkxid/J
(001011)
CBA/CaJ
(000654)
CBA/J
(000656)
C3H
C3H/HeJ
C3H/HeJSxJ
C3H/HeOuJ
C3H/HeSnJ
C3HeB/FeJ
C3HfB/BiJ
(000659)
(001824)
(000635)
(000661)
(000658)
(001908)
Pde6brd1 (CBA/J)
A/A
Btkxid
(CBA/CaHN-Btkxid/J)
Pde6brd1
A/A
MMTVTlr4Lps-d (C3H/HeJ)
Cancer (mammary tumor development,

hepatomas, lymphomas)
Cardiovascular (relatively resistant to dietinduced atherosclerosis [CBA/J])
Diabetes and obesity [CBA/CaJ]
Immunology (human X-linked
immunodeficiency and B cell defects
[CBA/CaHN-Btkxid/J]; experimental
autoimmune thyroiditis [CBA/J])
General purpose
Metabolism (exocrine pancreatic enzyme
deficiency [CBA/J])
Research tools (T6 translocation is a marker
to distinguish host from donor cells
[CBA/CaH-T(14;15)6/CaJ])
Cancer (mammary tumor development
enhanced by presence of exogenous mouse
mammary tumor virus, MMTV. Note:
Either embryo transfer or neonatal fostering
eliminates MMTV; hepatomas)
Cardiovascular (susceptible to dystrophic
cardiac calcinosis)
Dermatology (surgical model for alopecia
areata alopecia [C3H/HeJ])
General purpose
Immunodeficiency and inflammation
(Tlr4 Lps-d [C3H/HeJ])
Sensorineural (retinal degeneration,
Pde6brd1)
Note: Because of an inversion involving 20%
of Chr 6 in C3H/HeJ and probably in
C3H/HeJSxJ, they are not useful for mapping
loci in this region on Chr 6 (Akeson et al.,
2006).
Appendix D: Commonly-Used Inbred Strains and Substrains of JAX Mice 305
Parental
strain
C57BL

(stock number)
C57BL/6J
C57BL/6ByJ
C57BL/6JEiJ
C57BL/10J
C57BL/10ScSnJ
C57BL/10SxJ
C57BL/10SnJ
C57BL/10WtRkJ
C57BL/10ScNJ
C57BLKS/J
(000664)
(001139)
(000924)
(000665)
(000476)
(001822)
(000666)
(001197)
(003752)
(000662)
Genes of interest
a/a
Tlr4Lps-d (C57BL/10ScNJ)
Cdh23ahl (C57BLKS/J and
C57BL/6J)
Gluchos1C57BL/6J(C57BL/6J)
NntC57BL/6J(C57BL/6J)
Background for histocompatibility congenics

(C57BL/10ScSnJ, C57BL/10SxJ,
C57BL/10SnJ, and C57BL/10WtRkJ)
Cardiovascular (susceptible to diet-induced
atherosclerosis; resistant to dystrophic cardiac
calcinosis [C57BL/6])
Developmental (eye defects, hematopoietic
defects, skeletal defects [C57BL/6J])
Diabetes and obesity (susceptible to dietinduced obesity, hyperglycemia,
hyperinsulemia, and insulin resistance,
multiple QTLs for glucose homeostasis,
Gluchos and Nnt [C57BL/6J])
General purpose
Immunology and inflammation (Tlr4 Lps-d
[C57BL/10ScNJ])
Neurobiology (preference for alcohol and
morphine [C57BL/6J])
Research tools (background for transgenes,
spontaneous, and targeted mutations
[C57BL/6])
Sensorineural (early hearing loss. Cdh23ahl)
DBA
DBA/1J
DBA/1LacJ
DBA/2J
DBA/2BiJ
DBA/2DeJ
DBA/2HaSmnJ
(000670)
(001140)
(000671)
(001907)
(000052)
(000973)
Cdh23ahl
Hc0 (DBA/2)
Gpnmb (DBA/2J)
a/a
Tyrp1b
Tyrp1isa (DBA/2J)
Myo5ad
Autoimmunity (collagen-induced arthritis [not

DBA/2])
Cardiovascular (low susceptibility to dietinduced atherosclerosis; susceptible to
dystrophic cardiac calcinosis [DBA/2])
DBA/2J often contrasted with C57BL/6J
because of many polymorphic differences
between the two strains
General purpose (DBA/1J, DBA/2J)
deficiency, Hc0)
Neurobiology (epilepsy, audiogenic seizures
[DBA/2J]; extreme intolerance to alcohol and
morphine [DBA/2J])
Sensorineural (early hearing loss, Cdh23ahl;
glaucoma, GpnmbR150X, Tyrp1isa)
FVB
FVB/NJ
(001800)
Hc0
Pde6brd1
Tyrc
Fv1b
General purpose
deficiency, Hc0)
Transgenic production (large male pronuclei,
good breeder)
Sensorineural (retinal degeneration, Pde6brd1)
306 Appendixes
Parental
strain
NOD

(stock number)
NOD/ShiLtJ
(001976)
Genes of interest
Hc0
Tyrc
Cdh23ahl
Autoimmunity (unique MHC haplotype [H2g7

= Kd, Aad, Abg7, Enull, Db])
Developmental (hematopoietic defects)
Immunodeficiency (defective APC
immunoregulatory functions; defects in the
regulation of the T lymphocyte repertoire;
defective NK cell function; defective cytokine
production from macrophages; specific
complement deficiency, Hc0)
Type 1 diabetes
Wound healing (delayed and impaired)
NZB
NZB/BlNJ
(000684)
Hc0
a/a
Autoimmunity
F1 hybrid (NZBWF1/J [100008]) between
NZB/BlNJ and NZW/LacJ is widely used as a
human systemic lupus erythematosus
deficiency, Hc0)
SJL
SJL/J
(000686)
Dysf im
Autoimmunity (experimental allergic

encephalomyelitis [EAE])
Cancer (reticulum cell sarcomas, Hodgkins
disease)
Muscular dystrophy, limb-girdle (type 2B)
Pde6brd1
Tyrc

SWR
SWR/J
(000689)
Hc0
Pde6brd1
Tyrc
Autoimmunity (EAE)
Cancer (high incidence of lung and mammary
gland tumors in aging mice)
General purpose
deficiency, Hc0)
Metabolic disease (nephrogenic diabetes
insipidus with increasing age)
(Modified from Linder, 2006.)
References
313.
Festing MFW. 1998. Inbred Strains of Mice.
www.informatics.jax.org/external/festing/mouse/STRAINS (August 2008)
Linder CC. 2006. Genetic variables that affect phenotype. ILAR Journal. 47:132140.
For a complete list of references and more details, see the individual JAX Mice datasheets,
accessible at www.jax.org/jaxmice/query.
307
Appendix E: Coat Color Alleles for Popular Strains

of JAX Mice
This appendix includes several tables for reference purposes:
Table E.1. Coat color genes and alleles: current and old symbols, current names.
Table E.2. Common coat color genes and alleles for laboratory micerelated biological
systems and relative dominance.
Table E.3. Coat color phenotypes and genotypes for common strains of JAX Mice.
For information about the genetics of mouse coat color, see 2.G, Coat color genetics. For
information about all the coat color genes and alleles, visit www.informatics.jax.org.
Table E.1. Coat color genes and alleles: current and old symbols, current names.
Current symbol
Gene:
Old symbol
Name
Unchanged
Nonagouti
Allele: a
Gene:
Unchanged
Nonagouti (black or brown)
A or +
Unchanged
Agouti (wild-type), black hair with a subapical yellow band
ae
Unchanged
Extreme nonagouti
at
Unchanged
Black and tan
Aw
Unchanged
Ay
Unchanged
Yellow
Tyrp1
Tyrosinase-related protein 1
Allele: Tyrp1 or Tyrp1+
B or +
Tyrp1B-lt
Light
Tyrp1b
Brown
Tyr
Tyrosinase
Allele: Tyr or Tyr+
C or +
Gene:
Pigmented (wild-type)
ch
Chinchilla (light grayish-brown)
Tyrc-e
Extreme dilution
Tyrc
Albino
Myo5a
Myosin Va
Tyrc-ch
Gene:
Black (wild-type)
Allele: Myo5a or Myo5a+
D or +
Non-dilute (wild-type)
Myo5ad
Dilute
Oca2
Oculocutaneous albinism II
Allele: Oca2+
Normal pigment (wild-type)
Oca2p
Pink-eyed dilution
Gene:
308 Appendixes
Table E.2. Common coat color genes and alleles for laboratory micerelated biological systems and
relative dominance.
Gene
Symbol,
name
a
nonagouti
Allele
Chr
Symbol
Tyr
tyrosinase
Myo5a
myosin Va
Oca2
oculocutaneous
albinism II
(old p, pink-eyed
dilution)
Ednrb
endothelin
receptor type B
Mc1r
melanocortin 1
receptor
Mlph
melanophilin
(old ln)
U
umbrous
Pleiotropic effects on
ae
at
Black and tan
Aw
Ay
Yellow
Tyrp1 or
Tyrp1+
Black (wild type)
Tyrp1B-lt
Light
Hearing/vestibular/ear
Tyrp1b
Brown
Vision/eye
Tyr or Tyr+
Pigmented (wild-type)
Tyrc-ch
Chinchilla
Tyrc-e
Extreme dilution
Tyrc
Albino
Myo5a or
Myo5a+
Non-dilute (wild-type)
Myo5ad
Dilute
Oca2 or
Oca2+
Wild-type
Oca2p
Pink-eyed dilution
Vision/eye
14
Ednrbs
Piebald
Growth/size
Mc1rE-tob
Tobacco darkening
Mlphln
Leaden
unk
n/a
Relative dominance
Ay > Aw > A > a

A > at (dorsal)
at >A (ventral)
Nonagouti (black or
brown)
Agouti (wild-type)
(black hair with a
subapical yellow band)
Extreme nonagouti
A or +
Tyrp1
tyrosinase-related
protein 1
Name
Growth/size, skeleton
Craniofacial, vision/eye,
growth/size,
hearing/vestibular/ear
Anemia,
endocrine/exocrine
Obesity, adipose, behavior,
growth/size, homeostasis,
liver/biliary,
digestive/alimentary,
renal/urinary
Neurological degeneration
lethality/prenatal-perinatal,
homeostasis, nervous
system
Blood clotting disorders;

vision/eye
Tyrp1+ > Tyrp1b

Tyrp1b / Tyrp1b adds
brown tones to other coat
colors
Tyr+>Tyrc, Tyrc-ch, Tyrc-e
Tyrc*/ Tyrc*
compound recessive
alleles epistatically mask
other coat color genes
and alleles, and make
eyes pink.
Myo5a+ > Myo5ad
Myo5ad /Myo5ad dilutes
effects of other coat
color genes
Oca2+ > Oca2p
Oca2p/Oca2p dilutes
effects of other coat
color genes, and makes
eyes pink.
Umbrous (darkens
agouti mice)
unk = unknown
Additive with wild-type

(U/U darkens more than
U/+)
Appendix E. Coat Color Alleles for Popular Strains of JAX Mice 309
Table E.3: Coat color phenotypes and genotypes for common strains of JAX Mice.
Allele at common coat color loci
Strain
Coat color phenotype
a
(Chr2)
Tyrp1
(Chr4)
Oca2
(Chr7)
Tyr
(Chr7)
Myo5a
(Chr9)
129P1/ReJ
(001137)
Pink-eyed, white-bellied
chinchilla
Aw
Oca2p
Tyrc-ch
129P3/J
Pink-eyed, white-bellied,
(000690) light chinchilla
Aw
Oca2p
Tyrc-ch/Tyrc
Aw
Oca2p
Tyrc/Tyrc
129S1/SvImJ (002448) White-bellied agouti
Aw
129T2/SvEms/J
(002065) chinchilla
Aw
Tyrc-ch
Aw
Oca2p
Tyrc-ch/Tyrc
Aw
Oca2p
Tyrc/Tyrc
Albino
129X1/SvJ
Pink-eyed, white-bellied,
(000691) light chinchilla
Albino
A/HeJ
(000645) Albino
Tyrp1b
Tyrc
A/J
(000646) Albino
Tyrp1b
Tyrc
A/WySnJ
(000647) Albino
Tyrp1b
Tyrc
AEJ/GnLe/J
(000199)
ae/ae
Aw-J/a e
Dark black
Other
coat
color loci
Tyrc
hid*
(000649) Black
B6.129P2-Apoetm1Unc/J Black
(002052)
B6D2F1/J
(100006) Black
Myo5ad/+
BALB/cByJ
(001026) Albino
Tyrp1b/+
Tyrp1b
Tyrc
CByJ.RBF-Rb(8.12)
Albino
5Bnr/J
(001802)
Tyrp1b
Tyrc
BALB/cJ
(000651) Albino
Tyrc
BDP/J
(000652) Pink-eyed fawn
Tyrp1b
Tyrp1b
Oca2p
Myo5ad
at
Tyrc
Aw
AKR/J
(000648) Albino
AU/SsJ
BTBR T+ tf/J
(002282)
BUB/BnJ
BXSB/MpJ
Black and tan
(000653) Albino
White-bellied agouti,
(000740)
affected
C3H/HeOuJ
(000635) Agouti
C3H/HeSnJ
(000661) Agouti
C3HeB/FeJ
(000658) Agouti
C57BL/6ByJ (001139) Black
C57BL/6J
(000664) Black
C57BL/10J
(000665) Black
C57BL/10SnJ (000666) Black
tf*
* hid (hair interior defect) and tf (tufted) affect hair morphology or distribution, but not hair color.
310 Appendixes
Table E.3: Coat color phenotypes and genotypes for common strains of JAX Mice. (continued)
Coat color
phenotype
Strain
Other
coat color
loci
a
(Chr2)
Tyrp1
(Chr4)
Oca2
(Chr7)
Tyr
(Chr7)
Myo5a
(Chr9)
C57BLKS/J
(000662) Black
C57BR/cdJ
(000667) Brown
Tyrp1b
C57L/J
(000668) Leaden (grey)
Tyrp1b
C58/J
(000669) Black
CAST/EiJ
(000928) Agouti
Agouti
(000655)
CBA/CaHN-Btkxid/J
Agouti
(001011)
CBA/CaJ
(000654) Agouti
CBA/J
(000656) Agouti
CE/J
(000657) Greyish white
Aw
Tyrc-e
CXB7/ByJ
(000357) Black
CZECHII/EiJ (001144) White-bellied agouti
Aw
DBA/1J
(000670) Dilute brown
Tyrp1b
Myo5ad
DBA/1LacJ
Tyrp1b
Myo5ad
DBA/2DeJ
Tyrp1b
Myo5ad
DBA/2J
Tyrp1b
Myo5ad
DW/J Mlphln Pou1f1dw/J Agouti leaden

(000643)
FVB/NJ
(001800) Albino
HRS/J
(000673)
Without hair
Albino, unaffected
Tyrp1b
Tyrp1b
Tyrc
Tyrc
Tyrp1b
I/LnJ
JF1/Ms
Pink-eyed dilute
(000674) brown, piebald
(spotted)
Black spotted white
(003720)
coat, black eyes
Tyrc
Hrhr/Hrhr*
Hrhr/+
Oca2p
Myo5ad
Ednrbs
Ednrbs
(002106) Albino
LG/J
(000675) Albino
Tyrc
Tyrc
LP/J
(000676)
Aw
LT/SvEiJ
(006252) Grey-brown
Tyrp1B-lt
MA/MyJ
(000677) Albino
Tyrc
MOLF/EiJ
(000550) White-bellied agouti
Aw
MRL/MpJ
(000486) Albino, unaffected
Tyrc
Aw
MSM/Ms
(003719) White-bellied agouti
Mlphln
Myo5ad
Myo5ad
KK/HlJ
White-bellied agouti,
piebald
Mlphln
hr
*Although Hr (hairless) does not affect coat color, it does affect appearance.
+
Ednrbs
Appendix E. Coat Color Alleles for Popular Strains of JAX Mice 311
Table E.3: Coat color phenotypes and genotypes for common strains of JAX Mice. (continued)
Coat color
phenotype
a
(Chr2)
Tyrp1
(Chr4)
Albino
NOD/ShiLtJ (001976) Albino
Other
coat
color loci
Tyr
(Chr7)
Myo5a
(Chr9)
Tyrc
Tyrc
NON/ShiLtJ (002423) Albino
Tyrc
NOR/LtJ
(002050) Albino
Tyrc
NZB/BlNJ
(000684) Black
NZW/LacJ
(001058) Albino
Tyrp1b
Oca2p
Tyrc
P/J
(000679) Pink-eyed fawn
Tyrp1b
Oca2p
Myo5ad
PERA/EiJ
(000930) Agouti
PL/J
(000680) Albino
Tyrc
PWK/PhJ
(003715) Agouti
RBF/DnJ
(000726) Albino
Tyrc
RF/J
(000682) Albino
Tyrc
RHJ/Le
(000266) Albino
Tyrp1b
Tyrc
Without hair
Tyrp1b
Tyrc
Hrrh-J/
Hrrh-J
Albino, unaffected
Tyrp1b
Tyrc
Hrrh-J/+
Strain
NOD.CB17Prkdcscid/J
Oca2
(Chr7)
(001303)
RHJ/LeJ
(001591)
RIIIS/J
(000683) Albino
Tyrc
SEA/GnJ
(000644) Light brown agouti
Tyrp1b
Myo5ad
SEC/1GnLeJ (000270) Pink-eyed chinchilla
Tyrp1b
Tyrc-ch
SJL/J
(000686) Albino
Oca2p
Tyrc
SM/J
(000687)
Aw/a
a/a
Aw
Tyrc
Black
SPRET/EiJ (001146) White-bellied agouti

ST/bJ
(000688) Albino
Tyrp1b
SWR/J
(000689) Albino
Tyrc
WSB/EiJ
Agouti with head

(001145) blaze, variable belly
spotting, grayish coat
Mc1rE-tob
Although Hrrh-J (rhino) does not affect coat color, it does affect appearance.
Although the color pattern often appears to be white-bellied agouti, and is designated as such in some earlier publications, the
non-agouti gene has the A allele. The combination of frequent belly spotting and a coat dilution can give the illusion of a
white-bellied agouti phenotype.
313
Appendix F: Histocompatibility Haplotypes and Loci

This appendix includes several tables related to histocompatibility haplotypes and loci:
Table F.1:
H2 haplotypes for standard strains: allelic designations
Table F.2:
H2 haplotypes for specific categories of mice:

F.2.i. inbred strains
F.2.iv. recombinant congenic strains
F.2.ii. F1 hybrids
F.2.v. chromosome substitution (CS or consomic) strains
F.2.iii. recombinant inbred strains
F.2.vi. conplastic strains
Table F.3:
H2 haplotypes for H2-congenic strains: allelic designations
Table F.4:
Minor histocompatibility loci for inbred and congenic strains
Table F.1. H2 haplotypes for standard strains: allelic designations

Allelic designations for the H2 complex*
Haplo-
Class 1a
Class II
Class III
Class 1a
Class 1b
type
A!
A"
E!
E"
C4b
Qa-2
bc
T18
Qa-1
k2
g7
g7
g7
gx
g7
g7
dx
nb1
nb1
nb1
q2
s2
z
u
u
u
u
u
z
z
z
b
^ null
# unknown
*A! may be designated Ab; A" may be designated Aa; E ! may be designated Eb. E" may be designated Ea.
The former designation for C4b was S.
The E! chain is produced, but is not expressed on the cell surface because there is no E" chain to pair
with.
The Db-linked Lb allele is a functionally null variant.
314 Appendixes
Table F.2.i. H2 haplotypes for

inbred strains.
Strain
129P1/ReJ
129P3/J
Stock Haplonumber type
001137
000690
b
bc*
C57BL/10ScSnJ
000476
C57BL/10SnJ
C57BL/10SxJ
000666
001822
b
b
C57BL/10WtRkJ
001197
C57BLKS/J
000662
000667
k2
129P3/JEmsJ
002357
C57BR/cdJ
129P4/RrRkJ
129S1/SvImJ
001198
002448
b
b
C57L/J
C58/J
000668
000669
bc
k2
129T2/SvEms
129T2/SvEmsJ
002064
002065
b
b
CBA/CaGnLeJ
001143
000655
129X1/SvJ
000691
bc**
CBA/CaHT(14;15)6Ca/J
A/HeJ
A/J
000645
000646
a
a
CBA/CaHN
Btkxid/J
001011
A/WySnJ
000647
AKR/CumJ
AKR/J
002720
000648
k
k
CBA/CaJ
CBA/J
000654
000656
k
k
CE/J
000657
ALR/LtJ
ALS/LtJ
003070
003072
gx
nb1
DA/HuSnJ
000660
qp
DBA/1J
000670
AU/SsJ
000649
DBA/1LacJ
001140
B6 x IDH2/EiJ
BALB/cBy
002543
000650
b
d
DBA/2BiJ
DBA/2DeJ
001907
000052
d
d
BALB/cByJ
001026
DBA/2HaSmnJ
000973
BALB/cGaJ
001905
DBA/2J
000671
BALB/cGrRkJ
000921
DBA/8BiDsmJ
002860
BALB/cHeA
001255
BALB/cJ
BALB/cWtEiJ
000651
001311
d
d
BDP/J
000652
BPH/2J
003005
BPL/1J
003006
BPN/3J
BRVR/WrDvJ
003004
001891
d
k
BTBR T tf/J
002282
BUB/BnJ
C3H/HeJ
000653
000659
q2
k
C3H/HeJBirLtJ
C3H/HeJSxJ
005972
001824
k
k
C3H/HeOuJ
000635
C3H/HeSn
C3H/HeSnJ
000474
000661
k
k
C3HeB/FeJ
000658
C3HfB/BiJ
C57BL/6By
001908
000663
k
b
C57BL/6ByJ
001139
C57BL/6J
C57BL/6JEiJ
000664
000924
b
b
C57BL/10J
C57BL/10ScNJ
000665
003752
b
b
DDY/EFrkJ
002814
DDY/JclSidSeyFrk 002243
q
unk
s
DW/J Mlphln
Pou1f1dw/J
000643
EL/EFrkJ
002813
unk
EL/SuzSeyFrkJ
FL/1ReJ
001956
000023
b
k
FL/4ReJ
FVB/NJ
000025
001800
k
q
FVB/NMob
001491
HRS/J
HTG/GoSfSnJ
000673
000556
k
g
I/LnJ
000674
IDH2/Ei
000633
KK/HlJ
002106
LDH2/EiJ
001266
LG/J
LLC.A/CkcJ
000675
001200
d
unk
LP/J
000676
bc*
LT/SvEi
003588
MA/MyJ
MEV-W/TyJ
MRL/MpJ
MY/HuLeJ
000677
001856
000486
000265
k
unk
k
k
NH/KiPtJ
NOD/ShiLt
NOD/ShiLtJ
NON/ShiLtJ
NOR/LtJ
NU/J
NZB/BlNJ
NZL/LtJ
NZM391/J
NZM2410/J
NZO/HlLtJ
NZW/LacJ
NZW/Osu
P/J
PL/J
PN/nBSwUmabJ
PRO/1AReJ
PRO/ReJ
RBF/DnJ
RF/J
RHJ/LeJ
RIII/DmMobJ
RIIIS/J
SB/LeJ
SEA/GnJ
SENCARA/PtJ
SENCARB/PtJ
SENCARC/PtJ
003091
001289
001976
002423
002050
002019
000684
005067
003108
002676
002105
001058
003560
000679
000680
005052
000173
000059
000726
000682
001591
001088
000683
000269
000644
002746
002747
002748
k
g7
g7
nb1
g7
q
d2*
z
z
z
z
z
z
p
u
q
b
b
unk
k
d
r
r
b
d
q
q
q
SI/Col Tyrp1b
001045
d
Dnahc11iv/J
SJL/Bm
001902
s
SJL/J
000686
s2
SM/J
000687
v
SOD1/EiJ
001224
k
ST/bJ
000688
k
SWR/Bm
001900
q
SWR/J
000689 q2
WLC/MorJ
002600
unk
YBR/EiJ
000933
d
* (Fischer Lindahl K, 1997)
** (Kumanovics et al., 2002)
The Jackson Laboratory carries
this strain only as a background
genotype for a mutation or for
creation of an F1 hybrid.
(Fischer Lindahl K, 1997; Shen
FW, 1982)
(Shen FW, 1982)
Appendix F: Histocompatibility Haplotypes and Loci 315
Table F.2.ii. H2 haplotypes for

F1 hybrids.
AKXD11/TyJ
001003
AXB13/PgnJ
001826
AKXD13/TyJ
000765
AKXD14/TyJ
000779
AXB13a/PgnJ
AXB15/PgnJ
001684
001685
b
a
AKXD15/TyJ
000954
AXB19/PgnJ
001687
AKXD16/TyJ
000958
AXB19a/PgnJ
AXB19b/PgnJ
001686
001688
b
b
AXB23/PgnJ
AXB24/PgnJ
001690
001691
b
a
Strain
B6129PF1/J
100492
b/bc
B6129PF1/J
-Aw-J/Aw
100409
b/bc
AKXD18/TyJ
001093
B6129PF2/J
100903
b/bc
AKXD20/TyJ
001001
B6129SF1/J
101043
AKXD21/TyJ
001062
B6129SF2/J
101045
BRX58N1/TyJ
000753
000947
unk
AKXD22/TyJ
B6AF1/J
100002
b/a
BRX58N7/TyJ
000752
unk
AKXD23/TyJ
000780
BRX58N8/TyJ
000698
B6C3F1/J
100010
b/k
unk
AKXD24/TyJ
000969
000756
001022
b/k
BRX58N9/TyJ
B6C3FeF1/J a/a
unk
AKXD25/TyJ
000949
BRX58N11/TyJ
000750
B6CBACaF1/J
-Aw-J/A
unk
001201
b/k
AKXD27/TyJ
000764
BRX58N13/TyJ
000749
unk
001692
B6CBAF1/J
100011
b/k
BXA1/PgnJ
BXA2/PgnJ
001693
B6D2F1/J
100006
b/d
BXA4/PgnJ
001694
B6EiC3SnF1/J
001875
b/k
BXA7/PgnJ
001696
B6EiD2F1/J
003550
b/d
B6SJLF1/J
100012
b/s
BXA8/PgnJ
BXA11/PgnJ
001697
001699
a
b
C3D2F1/J
100004
k/d
AKXD28/TyJ
000957
AKXL5/Ty
000048
AKXL6/TyJ
000087
AKXL6A/TyJ
000757
unk
AKXL7/Ty
000324
AKXL8/Ty
000101
BXA12/PgnJ
001700
AKXL9/Ty
000325
BXA13/PgnJ
001701
C3FeB6F1/J
100016
k/b
C3FeB6F1/J
A/Aw-J
AKXL12/Ty
000326
001702
k/b
BXA14/PgnJ
001203
AKXL13/TyJ
000089
CAF1/J
100003
d/a
AKXL16A/TyJ
000404
unk
BXA16/PgnJ
BXA17/PgnJ
001703
001704
b
a
CB6F1/J
100007
d/b
AKXL17/TyJ
000088
BXA24/PgnJ
001710
CByB6F1/J
100009
d/b
AKXL17A/TyJ
000748
CByD2F1/J
100015
AKXL19/Ty
000086
BXA25/PgnJ
BXA26/PgnJ
001711
001999
a
a
CSJLF1/J
100019
d/s
AKXL21/TyJ
000782
BXD1/TyJ
000036
NZBWF1/J
100008
d/z
AKXL24/TyJ
000046
BXD2/TyJ
BXD5/TyJ
000075
000037
b
d
PLSJLF1/J
100299
u/s
AKXL29/TyJ
000042
AKXL37/TyJ
000044
BXD6/TyJ
BXD8/TyJ
000007
000084
d
b
AKXL38/TyJ
000328
BXD9/TyJ
000105
AKXL38A/TyJ
000747
unk
AKXL39/TyJ
003699
unk
BXD11/TyJ
BXD12/TyJ
000012
000045
d
d
AKXL43/TyJ
003700
unk
BXD13/TyJ
000040
BXD14/TyJ
BXD15/TyJ
000329
000095
b
b
BXD16/TyJ
BXD18/TyJ
000013
000015
d
d
Table F.2.iii. H2 haplotypes

for recombinant inbred
strains.
Strain
58NXL8/TyJ
000564
unk
129XAE/SvJ
001258
unk
129XAM/SvJ
001263
unk
AKXD1/TyJ
001005
AKXD2/TyJ
000776
AKXD3/TyJ
000959
AKXD6/TyJ
000777
AKXD7/Ty
001016
AKXD9/TyJ
000763
AKXD10/TyJ
001017
AKXL46/TyJ
003701
unk
AXB1/PgnJ
001673
AXB2/PgnJ
001674
AXB4/PgnJ
001676
AXB5/PgnJ
001677
AXB6/PgnJ
001678
AXB8/PgnJ
001679
AXB10/PgnJ
001681
AXB11/Pgn
AXB12/PgnJ
001682
001683
a
a
316 Appendixes
Table F.2.iii. H2 haplotypes

for recombinant inbred
strains. (continued)
Strain
CX8G/EiJ
001566
unk
NXSMU/EiJ
001663
CX8I1/EiJ
001570
unk
NXSMW/EiJ
001665
001666
d
v
CX8I2/EiJ
001571
unk
NXSMX/EiJ
CX8M/EiJ
001550
unk
NXSMZ/EiJ
001667
SWXJ2/BmJ
001072
SWXJ3/BmJ
001073
SWXJ4/BmJ
001074
SWXJ5/BmJ
001075
SWXJ6/BmJ
001076
q
s
SWXJ7/BmJ
001077
SWXJ8/BmJ
001078
SWXJ9/BmJ
001079
SWXJ10/BmJ
001080
SWXJ11/BmJ
001081
SWXJ12/BmJ
001082
s
s
q
BXD19/TyJ
000010
CX8N/EiJ
001532
unk
BXD20/TyJ
000330
CXB1/ByJ
000351
v
s
BXD21/TyJ
000077
CXB2/ByJ
000352
BXD22/TyJ
000043
CXB3/ByJ
000353
BXD23/TyJ
000098
CXB4/ByJ
000354
BXD24a/TyJ
005243
CXB5/ByJ
000355
BXD24b/TyJ
000031
CXB6/ByJ
000356
BXD25/Ty
000081
CXB7/ByJ
000357
BXD25/TyJRwwJ 006255
CXB8/HiAJ
001629
BXD27/TyJ
000041
CXB9/HiAJ
001630 Kb, Dd
BXD28/TyJ
000047
CXB10/HiAJ
001631
BXD29/TyJ
000029
SWXJ13/BmJ
001083
CXB11/HiAJ
001632
BXD30/Ty
000073
SWXJ14/BmJ
001084
CXB12/HiAJ
001633
SWXL4/TyJ
000074
BXD31/TyJ
000083
CXB13/HiAJ
001634
SWXL12/TyJ
000332
BXD32/TyJ
000078
CXJ1/SlkJ
001577
SWXL15/TyJ
000334
BXD33/TyJ
003222
CXJ3/SlkJ
001578
SWXL16/TyJ
000335
b
unk
q
b
BXD34/TyJ
003223
CXJ4/SlkJ
001579
SWXL17/TyJ
000336
BXD36/TyJ
003225
CXJ6/SlkJ
001580
BXD38/TyJ
003227
CXJ8/SlkJ
001581
BXD39/TyJ
003228
CXJ9/SlkJ
001582
BXD40/TyJ
003229
CXJ15/SlkJ
001583
BXD42/TyJ
003230
LXB3/TyJ
000754
BXH2/Ty1BedJ
002632
unk
LXPL/2TyJ
000303
unk
LXPL6/TyJ
000307
unk
LTXBJ/NaJ
002109
unk
LTXBO/SvJ
000402
NX129-1TyJ
BXH2/TyJ
000034
BXH4/TyJ
000011
BXH6/TyJ
000038
BXH7/TyJ
000014
BXH8/TyJ
000076
BXH9/TyJ
000008
BXH10/TyJ
000032
BXH11/TyJ
000039
BXH12/Ty
000080
BXH14/TyJ
000009
BXH19/TyJ
000033
BXH20/KccJ
003784
BXH22/KccJ
003786
BXJ2/TyJ
000096
unk
BXSB/MpJ
000740
CX8B/EiJ
001568
unk
CX8D/EiJ
001569
unk
q
s
q
q
Table F.2.iv. H2 haplotypes

for recombinant congenic
strains.
Strain
B6cC3-1/KccJ
003787
CBcNO6/LtJ
CBcNO7A/LtJ
002349
003052
k
k
CBcNO7B/LtJ
CBcNO7C/LtJ
003053
unk
003054
001193
unk
CBcNO7D/LtJ
003055
NX129-10/TyJ
000948
unk
NOcCB1/LtJ
002348
g7
NX129-18/TyJ
001539
unk
NONcNZO1/Lt
003668
nb1
NXSMC/EiJ
001651
NONcNZO3/Lt
003670
003671
nb1
NXSMD/EiJ
001652
NONcNZO4/Lt
NXSME/EiJ
001653
NONcNZO5/LtJ
004455
NONcNZO6/Lt
003673
nb1
NONcNZO8/Lt
003675
NONcNZO10/LtJ
004456
nb1
NXSMF/EiJ
001654
NXSMI/EiJ
001655
NXSML/EiJ
001656
NXSMN/EiJ
001657
NXSMP/EiJ
001659
NXSMQ/EiJ
001660
NXSMT1/EiJ
001661
NXSMT2/EiJ
001662
v
d
Table F.2.v. H2 haplotypes for chromosome

substitution (CS or consomic) strains.
C57BL/6J-Chr 11A/J/NaJ
004389
004390
Stock
number
Haplotype
004391
129S1/SvImJ-Chr Y C57BL/6J/NaJ
005548
004392
A/J-Chr Y C57BL/6J/NaJ
005546
004393
001452
004394
004395
004396
004397
004398
Strain
BALB/cByJ-Chr
YC57BL/6By/J
C3.SW/Lt-Chr Y C3HeB/FeChp/J
C3.SW/Lt-Chr Y SW/J
C57BL/6J-Chr 1PWD/Ph/ForeJ
002110
002111
005259
005995
005518
C57BL/6J-Chr YA/J/NaJ
004399
006226
C57BL/6J-Chr 2C3H/HeJ/J
006357
005260
C57BL/6J-Chr 11C3H/HeJ/J
006358
005261
C57BL/6J-Chr Y129S1/SvImJ/NaJ
005547
005996
005262
C57BL/6J-Chr 11.1PWD/Ph/ForeJ
005997
005998
006372
005263
005519
005264
Table F.2.vi. H2 haplotypes for conplastic strains

Strain
Stock
number
Haplotype
C57BL/6J-mtA/J/NaJ
005545
005761
NOD/Lt-mtALR/Lt/MxLt
005332
g7
005265
005266
005267
unk
005268
005269
C57BL/6J-Chr X.1PWD/Ph/ForeJ
005762
C57BL/6J-Chr X.3PWD/Ph/ForeJ
006227
C57BL/6J-Chr Y PWD/Ph/ForeJ
005270
004379
004380
004381
004382
004383
004384
004385
004386
004387
004388
318 Appendixes
Table F.3. H2 haplotypes for H2-congenic strains: allelic designations.

Haplotype
Strain
Stock Class
number Ia
K
A!

Class
Class II
III
Class Ia
Class Ib
A"
E! E"
C4b
D
L
Qa-2 T18 Qa-1
B10.A-H2a H2-T18a/SgSnJ
000469
ar1
B10.LG-H2ar1/J
001894
ar1
C3.LG-H2ar1/CkcCyJ
000440
as1
B10.S-H2as1(8R)/J
001760
k/s
AK.B6-H2b/J
002090
BKS.B6-H2b/J
001041
BRVR.B10-H2b/J
001892
C.B10-H2b/LilMcdJ
001952
D1.LP-H2b H2-T18b?/SnJ
000435
NOD.B10Sn-H2b/J
002591
bc
A.BY-H2bc H2-T18f/SnJ
000140
bc
C3.SW-H2b/SnJ
000438
bm1
B6.C-H2bm1/By
000368 bm1
bm1
B6.C-H2bm1/ByJ
001060 bm1
bm2
B6.C-H2bm2/ByJ
000364 bm2
bm3
C57BL/6J-H2bm3/EgJ
001156 bm3
bm4
B6.C-H2bm4/ByJ
000369 bm4
bm5
C57BL/6Kh-H2bm5/KhEgJ
001157 bm5
bm7
B6.C-H2bm7/KhEgJ
001158 bm7
bm10 B6.C-H2bm10/KhEgJ
001160 bm10
bm11 B6.C-H2bm11/KhEgJ
001161 bm11
bm12 B6(C)-H2-Ab1bm12/KhEgJ
001162
bm12
bm14 B6By(CBy)-H2-D1bm14/(HZW42)ByJ
000145
bm14
bm23 B10.D2-H2bm23/EgJ
001163 bm23
bp5
B10.F-H2bp5/(14R)J
001823
bq1
B10.MBR-H2bq1/SxEgJ
001154
B6.C-H2d/bByJ
000359
B6.C-H2d Mdmg1BALB/cBy/aByJ
000360
B10.D2-H2d/n2SnJ
000462
B10.D2-Hc0 H2d H2-T18c/o2SnJ
000460
B10.D2-Hc0 H2d H2-T18c/oSnJ
000461
B10.D2- Hc1 H2d H2-T18c/nSnJ
000463
BRVR.D2-H2d/J
001893
D1.C-H2d H2-T18c/SnJ
000437
dm1
B10.D2-H2dm1/EgJ
001164
dm1 dm1
Table F.3. H2 haplotypes for H2-congenic strains: allelic designations. (continued)

Haplotype
Strain
Stock Class
number Ia
K
A!

Class
Class II
Class Ia
Class Ib
III
A"
E! E"
C4b
D
L
Qa-2 T18 Qa-1
dm2
BALB/c-H2dm2/KhEgJ
001165
A.CA-H2f H2-T18a/SnJ
000472
B10.M-H2f/nMobJ
001068
B10.M-H2f H2-T18a?/SnJ
000459
fm2
B10.M-H2fm2/MobJ
000739
fm2
B10.HTG-H2g/2CyJ
001012
B10.HTG-H2g/3CyJ
000999
C3H.HTG-H2g H2-T18b?/SnJ
000443
g3
B10.D2-H2g3/(103R)EgJ
001151
g6
B6.C-H2g6/J
001429
g7
B6.NOD-(D17Mit21-D17Mit10)/LtJ
003300
g7
g7
g7
NON.NOD-H2g7/LtJ
001627
g7
g7
h2
B10.A-H2h2/(2R)SgSnJ
000468
h4
B10.A-H2h4/(4R)SgDvEgJ
001150
k/b
i3
B10.A-H2i3/(3R)SgDvEgJ
001149
b/k
i5
B10.A-H2i5 H2-T18a/(5R)SgSnJ
000467
b/k
i7
B10.D2-H2i7/(107R)EgJ
001153
ia
B10.D2-H2ia/(106R)EgJ
001152
B10.WB-H2j H2-T18b/SnJ
000445
C3.JK-H2j H2-T18b/SnJ
000441
B6.AK-H2k/FlaEgJ
001148
B6.AK-H2k/J
001895
C.C3-H2k/LilMcdJ
001951
k2
B10.BR-H2k H2-T18a/SgSnJ
000465
kp1
B10.P-H2kp1/(10R)SgJ
001825
AK.M-H2m H2-T18a/nSnJ
000470
B10.AKM-H2m H2-T18a/SnJ
000466
nb1
NOD.NON-H2nb1/LtJ
001626
nb1
nb1
o2
C3H-H2o2 C4b/SfSnJ
000473
C3.NB-H2p H2-T18c?/SnJ
000439
pa
B10.Y-H2pa H2-T18c/SnJ
000444
pb1
B10.F-H2pb1/(13R)J
001818
B10.D1-H2q/SgJ
002024
NOD.SW-H2q/J
002032
qp1
B10.DA-H2qp1 H2-T18b/(80NS)/SnJ
000464
320 Appendixes
Table F.3. H2 haplotypes for H2-congenic strains: allelic designations. (continued)

Haplotype
Strain
Stock Class
number Ia
K
A!

Class
Class II
Class Ia
Class Ib
III
A"
E! E"
C4b
D
L
Qa-2 T18 Qa-1
qp1
D1.DA-H2qp1/SnJ
000436
B10.RIII-H2r/(71NS)nMobJ
001069
B10.RIII-H2r H2-T18b/(71NS)SnJ
000457
LP-RIII-H2r H2-T18b/SnJ
000434
A.SW-H2s H2-T18b/SnJ
000471
B10.S-H2s/SgMcdJ
001953
sm1
B10.S-H2sm1/(12R)SgJ
001817
t1
A.TL-H2t1/SfDvEgMobJ
001067
t2
A-TH-H2t2/SfDvEgMobJ
001066
t4
B10.S-H2t4/(9R)/J
001650
s/k
B10.PL-H2u H2-T18a/(73NS)SnJ
000458
B10.SM H2v H2-T18b/(70NS)Sn-cw/J 000456
y1
B10.AQR-H2y1/KljMcdJ
001954
y2
B10.T-H2y2/(6R)SgDvEgJ
001155 q
q
q
q
^
q
d
d
a
a
^ null
# unknown
*A! may be designated Ab; A" may be designated Aa; E ! may be designated Eb. E" may be designated Ea. The former
designation for C4b was S.
The E! chain is produced, but is not expressed on the cell surface because there is no E" chain to pair with.
The Db-linked Lb allele is a functionally null variant.
Table F.4. Minor histocompatibility loci for inbred and congenic strains.
Locus
H1
Chr
Allele
H3
Strain
Stock
number
B10.D2-H1a/(58N)SnJ
000425
BDP/J
000652
C3H/HeSnJ
000661
CBA/CaJ
000654
CBA/J
000656
DBA/1J
000670
DBA/2J
000671
WC/ReJ-KitlSl/J
000693
129X1/SvJ
000691
A/WySnJ
000647
B6.C-Tyrc H1b Hbbd/ByJ

B10.129P-H1b Hbbd Tyrc Ea7a/(5M)oSnJ
B10.129P-H1b Tyrc Hbbd/(5M)nSnJ
B10.C-H1b Hbbd Tyrc/(41N)SnJ
BALB/cByJ
001026
C3.K-H1b/nSnJ
000413
C57BL/6ByJ
001139
C57BL/6J
000664
C57BL/10Sn/J
000666
C57BR/cdJ
000667
C57L/J
000668
Congenics
Donor strain
Backcrosses (N)
D2.WA/Sn
000383
BALB/cBy
15
000409
129P/Sn
11
000418
129P/Sn
11
000432
BALB/c
Non-inbred
11
C58/J
000669
P/J
000679
e
f
WB/ReJ KitW/J
CE/J
000692
000657
C57BL/6J
000664
C57BL/10J
000665
C57BLKS/J
000662
C57BR/cdJ
000667
C57L/J
000668
WB/ReJ KitW/J
000692
WC/ReJ-KitlSl/J
000693
129P3/J
000690
129X1/SvJ
000691
B10.LP-H3b/Sn
000421
LP/J
13
B10.LP-H3b H13b/(36NS)Sn
000422
LP/J
11
B10.UW-H3b we Pax1un at/SnJ
000419
UW/Le
CE/J
000657
000661
CeH/HeSnJ
C58/J
000669
322 Appendixes
Table F.4. Minor histocompatibility loci for inbred and congenic strains. (continued)
Locus
H3
Chr
Allele
Donor strain
Backcrosses (N)
DBA/2J
LP/J
000671
SWR/J
000689
B6.C-H3c/ByJ
001286
BALB/c
B10.C-H3c/SnJ
000429
BALB/c
11
B10.C-H3c H13? A/(28NX)SnJ
000433
BALB/c
BALB/cByJ
001026
B10.KR-H3d/SnJ
000424
KR/Di
11
B10.PA-Pldnpa H3e at/SnJ
000477
Wild-derived
34
129X1/SvJ
000691
BDP/J
000652
C57BL/6J
000664
C57BL/10SnJ
000666
C57BLKS/J
000662
C57BR/cdJ
000667
C57L/J
000668
C58/J
000669
DBA/1J
000670
DBA/2J
000671
A/HeJ
000645
A/WySnJ
000647
B6.C-H7b/By KitW-50J/J
000560
BALB/cBy(-H7b)
19
B10.C-H7b/(47N)SnJ
000430
BALB/c
BALB/cByJ
001026
C3H/HeSnJ
000661
DA/HuSnJ
000660
C57BL/6J
000664
C57BL/10SnJ
000666
C57BR/cdJ
000667
C57L/J
000668
C58/J
000669
129X1/SvJ
000691
B10.D2-H8b/(57N)SnJ
DBA/1J
000426
D2.WA/Sn
DBA/2J
000671
LP/J
000676
B6.C-H8c/(HW96)ByJ
000113
BALB/cByJ
001026
BALB/cBy
15
000676
(see H46H47)
9
H8
Congenics
000670
H7
Stock
number
DBA/1J
(continued)
H4*
Strain
14
14
000670
Locus
H9
Chr
unk
Allele
H11
H12
unk
unk
unk
Stock
number
A/HeJ
000645
A/WySnJ
000647
C3H/HeSnJ
C57BL/10SnJ
000661
000666
C57BR/cdJ
C57L/J
000667
000668
CE/J
000657
PL/J
000680
WB/ReJ Kitw/J
000692
B10.C-H9b/(45N)SnJ
000431
BALB/cByJ
CBA/CaJ
001026
000654
CBA/J
000656
DA/HuSn
LP/J
000660
000676
C57BL/10SnJ
000666
129P3/J
000690
B10.129P-H10b/(9M)SnJ
000132
C57BL/10/SnJ
000666
129P3/J
000690
B10.129P-H11b/(10M)SnJ
?
B10.D2-H11?/(55N)SnJ
A/WySnJ
000647
BDP/J
C3H/HeSnJ
000652
000661
C57BL/6J
000664
C57BL/10SnJ
C57BR/cdJ
000666
000667
C57L/J
000668
C58/J
CE/J
000669
000657
DBA/1J
DBA/2J
000670
000671
PL/J
000680
129X1/SvJ
000691
B10.129P-H12b/(6M)SnJ
000417
SWR/J
000689
H10
Strain
Congenics
Donor strain
Backcrosses (N)
BALB/c
129/J
000416
129/J
000428
D2.WA/Sn
129/J
10
7
324 Appendixes
Locus
Chr
Allele
H13
H16
H17
H18
12
Stock
number
Congenics
Donor strain
Backcrosses (N)
A/HeJ
000645
A/WySnJ
000647
AKR/J
000648
C57BL/6J
000664
C57BL/10SnJ
000666
C57BLKS/J
000662
C57BR/cdJ
000667
C57L/J
000668
CBA/CaJ
000654
CBA/J
000656
DA/HuSn
000660
RF/J
000682
SWR/J
000689
WC/ReJ-KitlSl/J
000693
129X1/SvJ
000691
B10.CE-H13b Aw/(30NX)SnJ
000427
CE/J
B10.LP-H13b Aw/Sn
000420
LP/J
11
B10.LP-H3b H13b/(36NS)Sn
000422
LP/J
C58/J
000669
CE/J
000657
DBA/1J
000670
DBA/2J
000671
LP/J
000676
C3H/HeSnJ
000661
SM/J
000687
B10.C-H3c H13? A/(28NX)SnJ
000433
probably KR/Di for H13
B10.KR-H13? A/SnJ
000423
KR/Di
11
C57BL/6ByJ
001139
B6.C-H15c/(HW13J)ByJ
BALB/cByJ
000382
BALB/cBy
11
C57BL/6ByJ
001139
B6.C-H16c/(HW13K)ByJ
BALB/cByJ
000381
BALB/cBy
11
C57BL/6ByJ
001139
B6.C-H17c/(HW14)ByJ
000130
BALB/cBy
17
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H18c/(HW17)ByJ
000380
BALB/cBy
12
BALB/cByJ
001026
H15
Strain
001026
001026
Locus
H19
H20
H21
H22
H23
H24
H25
H26
H27
H28
H29
H30
Chr
unk
unk
15
Allele
Strain
Stock
number
C57BL/6ByJ
001139
B6.C-H19hc/(HW20)ByJ
BALB/cByJ
000135
001026
C57BL/6ByJ
001139
B6.C-H20c/ByJ
000379
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H21c/ByJ
BALB/cByJ
000378
001026
C57BL/6ByJ
001139
B6.C-H22c Gpi1a/(HW38)ByJ
000377
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H23c/(HW53)ByJ
BALB/cByJ
000376
001026
C57BL/6ByJ
001139
B6.C-H24c Gpi1a/(HW54)ByJ
000123
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H25c/(HW65)ByJ
BALB/cByJ
000114
001026
C57BL/6ByJ
001139
B6.C-H26c/ByJ
000375
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H27c/ByJ
Congenics
Donor strain
Backcrosses (N)
BALB/cBy
11
BALB/cBy
17
BALB/cBy
17
BALB/cBy
12
BALB/cBy
15
BALB/cBy
16
BALB/cBy
15
BALB/cBy
18
BALB/cBy
15
BALB/cByJ
000374
001026
C57BL/6ByJ
001139
B6.C-H28c If1h/(HW110)dBy
000116
BALB/cBy
15
B6.C-H28c If1l/(HW81)aByJ
000146
BALB/cBy
16
B6.C-H28c If1l/(HW94)bByJ
000384
BALB/cBy
15
B6.C-H28c If1l/(HW97)cByJ
BALB/cByJ
000142
001026
BALB/cBy
15
C57BL/6ByJ
001139
B6.C-H29c/(HW88)ByJ
BALB/cBy
15
BALB/cByJ
000373
001026
C57BL/6ByJ
001139
B6.C-H30c/(HW105)ByJ
000138
BALB/cBy
14
BALB/cByJ
001026
326 Appendixes
Chr
Allele
H31
17
A/J
000646
C57BL/6J
000664
H32
17
A/J
000646
C57BL/6J
000664
C57BL/6ByJ
001139
B6.C-H34c/(HW22)ByJ
000136
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H35c/ByJ
000143
H34
H35
H36
H37
H38
H46
H47*
12
unk
19
Congenics
Donor strain
Backcrosses
(N)
BALB/cBy
16
BALB/cBy
16
BALB/cBy
15
BALB/cBy
14
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H36c/ByJ
000372
BALB/cByJ
001026
C57BL/6ByJ
001139
000371
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.C-H38c/By-KitW-56J/J
000495
B6.CH38c/(HW119)ByJ
22p
000370
BALB/cBy
18
BALB/cByJ
001026
AKR/J
000648
C3H/HeSnJ
C57BL/6J
000661
000664
C57BL/10J
000665
C57BL/10SnJ
C57BLKS/J
000666
000662
C57BR/cdJ
000667
C57L/J
C58/J
000668
000669
CBA/CaJ
CBA/J
000654
000656
SJL/J
000686
129P3/J
129X1/SvJ
000690
000691
B10.129P-H46b H47b/(21M)Sn
BDP/J
000414
000652
129P3/J
15
B6.C3Fe-H51 Hps1ep/ByJ
000050
C3HeB/FeJ
20
C3HeB/FeJ
000658
C57BL/6ByJ
001139
H51
Strain
Stock
number
Locus
Table F.4. Minor histocompatibility loci for inbred and congenic strains. (continued
Locus
H52
Chr
Allele
H54
H61
HX
HY
X
Y
Strain
Stock
number
B6By.C-H52 Fgf5go/J
000795
BALB/cByJ
001026
C57BL/6ByJ
001139
B6.Cg-Sgk3fz H54 Mlphln/+ H54 +/J
000112
C57BR/cdJ
000667
C57BL/6J
000664
B6.C-H61b Me1a/(HW23)By
000137
BALB/cByJ
001026
C57BL/6ByJ
001139
C57BL/6ByJ
001139
BALB/cByJ
001026
A/J
000646
Congenics
Donor strain
Backcrosses (N)
BALB/cBy
11
C57BR/cdJ
11
BALB/cBy
15
b
C57BL/6J
000664
*H46 and H47, formerly designated H4, are linked (Davis and Roopenian, 1990).
Minor histocompatibility loci have been identified for H51, H52, and H54, but allele names have not
been assigned. The congenic strain and the donor strain (both designated by ) share an allele that differs
from the allele in the background strain (designated by). (Bailey DW and Bunker HP, 1972)
See footnote for .
For H61, the allele name in C57BL/6ByJ has not been assigned. This allele, however, differs from the b
allele in BALB/cByJ.
References
Bailey DW, Bunker HP. 1972. Located histocompatibility genes. Mouse News Lett. 47:18.
Davis AP, Roopenian DC. 1990. Complexity at the mouse minor histocompatibility locus H-4.
Immunogenetics. 31:712.
Fischer Lindahl K. 1997. On naming H2 haplotypes: functional significance of MHC class 1b
alleles. Immunogenetics. 46: 5362.
Kumanovics A, Madan A, Qin S, Rowen L, Hood L, Fischer Llindahl K. 2002. Quod erat
faciendum: sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice. Immunogenetics.
54:479489.
Shen F-W, Chorney MJ, Boyse EA. 1982. Further polymorphism of the T1a locus defined by
monoclonal TL antibodies. Immunogenetics. 15: 573578.
329
Appendix G: Equivalencies of Human Age to Life

Phases of Mice
Kevin Flurkey, Joanne M. Currer, David E. Harrison
Mice have virtually the same organs and tissues as humans, despite the considerable difference
in shape and size. Not surprisingly, the developmental, maturational, and aging schedule for
these organs and tissues also has the same sequence, although the timing is very different. In
this appendix we provide comparisons of the developmental, maturational, and aging rates as
well as age equivalencies between mice and humans.
Age equivalencies and relative rates of development

The relative rates of pre- and post-natal development, maturation, and aging in mice and
humans differ greatly at different life history stages. In a detailed study of prenatal age
equivalencies, Otis and Brent (1950) compared 147 anatomical markers of development (such
as appearance of the first somites, anterior limb buds, and first intestinal villi) in mice and
humans. Ages ranged from 1 day post conception (dpc) in both species to 16.5 dpc in mice and
to the equivalent, 85 dpc, in humans. Their analysis suggests that gestation can be divided into
three phases that are developmentally equivalent between mice and humans. Within each phase,
the ratio of developmental rates (the time it takes for each marker to appear) between mice and
humans is remarkably consistent; however, between phases, this ratio differs dramatically.
Conception to implantation. Pre-implantation cleavage occurs at about the same rate in mice
and humans. Implantation occurs at 4.5 dpc in mice and 6 dpc in humans.
Implantation through formation of most organs (4.5 to 14.5 dpc in mice; 6 to 45 dpc in
humans). This is the phase when almost all the organs are formed. During this phase,
developmental markers are expressed about four times faster in mice than in humans. At the
end of this phase, an abrupt change occurs as development shifts to a phase characterized
more by cell proliferation.
Formation of organs through organ differentiation. Otis and
Parturition as a developmental marker
Brent (1950) reported data only for the first two days after this
Often developmental timing is anchored to
third phase begins (14.5 to 16.5 dpc in mice, equivalent to about
birthbirth completes gestation and initiates
postnatal development. However, among
45 to 85 dpc in humans). The phase continues, however, as
mammalian species, the developmental stage of
tissues and organs that are necessary for independent life grow
the fetus at birth varies considerably. For
and complete their differentiation. In mice, this phase continues
example, in contrast to humans, mice are blind,
even after birthuntil about day 12 postnatal, which is
deaf, and hairless when they are born. It is not
developmentally equivalent to birth in humans. During organ
until mice are about 12 days old that they are
developmentally comparable to humans at birth.
differentiation, developmental markers appear about 1520
times earlier in mice than in humans.
Following completion of generalized tissue differentiation at the end of tissue expansion,
subsequent maturational markers consist almost entirely of markers that are dependent on
maturation of the gonads and sex hormones. Laboratory mice are sexually mature at about 30
37 days of age. If we use 12 years as an age at which most humans are capable of reproducing
(National Institutes of Health, 2008), the maturational equivalency rate is about 200 times faster
in mice than humans (based on 1234 days of age in mice, 012 years of age in humans).
After sexual maturation, few biologically timed events occur at precise ages; age-related change
for almost all the biomarkers of aging (collagen cross-linking and wound healing, for example)
is more progressive and continuous than for developmental markers. If we consider the age at
which females can no longer reproduce (around 450 days for genetically mixed populations of
mice [Klebanov et al., 2001] and 50 years for humans) and maximum lifespan as representative
markers, mice age about 30 times faster than humans throughout adulthood.
Table G.1 provides a summary of the above information.
330 Appendixes
Table G1. Comparison of developmental and aging rates between mice and humans.
Age range
Developmental or
aging stage
Conception to implantation
Mice
Humans
Relative rate of
development or aging in
mice compared to humans
0 to 4 days post
conception (dpc)
0 to 5 dpc
Starts about the same.
Implantation through
formation of most organs
4.5 to 14.5 dpc
5 to 45 dpc
Increases to about 4 times

faster in mice.
Formation of organs through

organ differentiation
14.5 dpc to 12 days

old (postnatal)
45 dpc to birth*
Increases to about 15 to 20
times faster in mice.
Organ differentiation to
sexual maturity
12 to about 34 days
old
Birth to about 12
years old
Increases to about 200 times

faster in mice.
Sexual maturity through

adulthood
34 days old and

older
12 years old and

older
Diminishes to about 30 times

faster in mice.
*Human gestation is about 266 days.
Life phases of adult mice

Following sexual maturity, we have very few age-specific milestones to help us characterize
stages of aging. But for some types of research, such as pathology studies and aging and
lifespan studies, we identify three stages of adult maturation and aging.
Mature adult: 36 months of age

Mature adulthood refers to a period when mice are mature but not yet affected by senescence.
Although mice are sexually mature by 35 days, relatively rapid maturational growth continues
for most biological processes and structures until about 90 days. Thus, the youngest mice in the
mature adult group should be at least three months old. The upper age limit is six months,
because after that age mice might exhibit some age-related change. (As an example, female
mice are retired from breeding at eight months because litter size diminishes.) However, if, for a
specific biomarker, measurements are known to be stable through adulthood until 12 months,
adult mice as old as 12 months may be used as the normal control.
Middle age: 1015 months of age

Middle age refers to a period during which senescent changes can be detected for some, but not
all, biomarkers of aging. For the middle-aged group, mice should be at least 10 months old.
Senescence processes that begin in younger adults (for example, collagen cross linking and
accumulation of activated/memory T cells) often can be detected by then. The upper age limit
for the middle-aged group is typically 15 months because, at this age, most biomarkers still have
not changed to their full extent and some have not yet started changing.
Old age: 18 monthsdeath

Old age refers to a period when senescent changes can be detected in almost all biomarkers in
all animals. For studies of senescence, for the old-aged group, mice should be at least 18 months
old. The upper limit is 2226 months, depending on the timing of the onset of disease for a
specific genotype. Past that age, even in robust F1 hybrids, undetected disease in a large subset
of the population can produce misleading results.
In cross-sectional studies, thorough necropsies are absolutely essential to determine the presence
of a concurrent disease that might interfere with results. It is important to note that, in crosssectional studies, the upper boundary for the old group should be adjusted for each genotype
based on relative survivorship and age-specific incidence of disease. A general guideline for the
upper age limit for biomarker studies in any genotype is the age at 8590% survivorship.
Of course, mice older than 26 months can be used to study terminal processes of senescence and
age-related pathology.
Appendix G: Equivalencies of Human Age to Life Phases of Mice 331
Comparison of life phases between mice and humans

Using a survival curve for C57BL/6J (000664) mice, Figure G.1 compares the life phases of this
genotype with those of humans.
Figure G.1. Life phases for C57BL/6J mice, human equivalencies, and maturational
comparisons.
C57BL/6J survivorship
data are based on a large
cohort of mice (150 males
and 150 females).
Comparison of life phases
is based on decades of
work on maturation and
aging by D. E. Harrison,
The Jackson Laboratory.
(Modified from Flurkey et
al., 2007).
Genotype differences among mice

The guidelines presented in this appendix are similar for most inbred strains and F1 hybrids.
However, it is important that researchers recognize strain variation. For details about specific
strains of mice, refer to the Mouse Phenome Database (MPD) at www.jax.org/phenome.
References
Flurkey K, Currer JM, Harrison DE. 2007. The Mouse in Aging Research, in The Mouse in
Biomedical Research, 2nd Edition. Fox JG et al. (eds). American College Laboratory Animal
Medicine. American College Laboratory Animal Medicine. Academic Press. pp. 637672.
Klebanov S, Flurkey K, Roderick TH, Archer J, Astle CM, Chen J, Harrison DE. 2001.
Heritability of life span in mice and its implication for direct and indirect selection for
longevity. Genetics. 110:209218.
National Institute of Child Health and Human Development. 2008. What is puberty?
www.nichd.nih.gov/health/topics/Puberty.cfm (accessed June 24, 2008).
Otis EM, Brent R. 1954. Equivalent ages in mouse and human embryos. Anat Rec. 120:3563.
333
Appendix H: Transfer of a Mutant or Variant Allele

to a New Genetic Background by Phenotypic
Selection
Creating congenic mice is straightforward when a genetic marker is available. However,
researchers often wish to create a congenic strain when a mutant or variant allele is identifiable
only by phenotype. This is typically the case for spontaneous mutants or for strain differences
that segregate as a single locus (which indicates that a single gene is involved). Techniques to
create congenic strains based strictly on phenotypic selection have been used since the 1940s
(Table H.1). These techniques also make it possible to transfer mutations with a lethal or
infertile phenotype. Note that these procedures are for the actual backcrossing and development
of the strain. Once the mutation has been transferred to the new background, the new strain is
maintainedand controls are chosenusing the same strategies provided in Table 3.8,
Expansion and maintenance breeding schemes for models with single-locus mutations.
Table H.1. Using phenotypic selection to create a congenic mouse.
For this type of mutant
or variant allele
use this breeding scheme.
Comments
A dominant allele (M)
Backcross matings using heterozygotes:

1. Backcross a heterozygote (M/+) to the inbred
recipient strain (+/+).
Offspring: (M/+), (+/+)
2. Repeat step 1 for generations N2N10.
3. To expand the line or maintain the allele on this
background, see Table 3.8.
This breeding pattern can continue

indefinitely.
With sibling mating, the line should be
refreshed occasionally by backcrossing
to the inbred recipient strain to prevent
substrain divergence.
This is the same scheme used to transfer
an allele or gene that can be genotyped.
A recessive allele (m)

when the homozygote
is viable and fertile
Backcross-intercross (sometimes called crossintercross) matings using homozygotes:

1. Backcross a homozygote (m/m) to the inbred
Offspring: (m/+)
2. Intercross heterozygote (m/+) offspring.
Offspring: (m/m), (m/+), (+/+)
3. Select homozygous (m/m) offspring.
4. Repeat steps 13 until N10.
5. After N10, either incross siblings or backcross to
the inbred recipient strain.
OR
To expand the line or maintain the allele on this
With sibling mating, the line should be

refreshed occasionally by backcrossing
to the recipient inbred strain to prevent
substrain divergence.
A recessive allele (m)

that produces sterility
or is lethal in
homozygotes
Backcross-intercross (sometimes called crossintercross) matings using heterozygotes:

1. Backcross a heterozygote (m/+) to the inbred
Offspring: (m/+), (+/+)
2. Intercross siblings (test mating).
Offspring: (m/m), (m/+), (+/+)
3. Identify breeding pairs that produced (m/m)
mutants. These are heterozygote carriers (m/+).
4. Repeat steps 13 until N10.
5. To expand the line or maintain the allele on this
In the test mating intercross, for

mutations that are fully penetrant, 1 of 4
sibling matings will produce mutant
offspring.
Ovarian transplants may be used to
propagate the strain once the mutation
has been moved to the recipient inbred
strain after N7 (to ensure
histocompatibility).
335
Appendix I: Using a Balanced Stock to Carry a

Recessive Mutation That Is Sterile or Lethal,
Including Embryonic Lethal
Stocks carrying recessive mutations that cause sterility or lethality, including embryonic
lethality, are a challenge to maintain and expand. Today, researchers often use direct genotyping
and, occasionally, ovarian transplants into histocompatible hosts. These are good strategies for
producing a maximal quantity of mutant offspring. However, when a genetic probe is
unavailable, researchers still use a breeding method based on classical genetics. This method
using a balanced stock of double heterozygotesincorporates a marker gene (coat color, for
example) that is so closely linked (or balanced) with the mutant gene that they rarely recombine.
A major disadvantage of using a balanced stock is the time and effort it takes to produce it
initially. But once a balanced stock is available, it provides a way to carry a mutation and
generate mutants and controls that can be even more efficient than direct genotyping. Table I.1
describes the marker and double heterozygote options available with a balanced stock.
Table I.1. Balanced stocks: marker and double heterozygote breeding options.
To
distinguish
carriers from
non-carriers
by sight to
efficiently
propagate the
strain
when the
marker allele is
maintain the balanced

stock using this
breeding strategy
recessive
Double heterozygotes in
repulsion
dominant
coupling
distinguish
mutants by
sight before
the mutant
phenotype is
expressed
recessive
coupling
Implications regarding
identification of offspring
The mice used to set up new

breeding pairs (double
heterozygotes in repulsion) will not
express either the marker or the
mutation. (See Figure I.1.)
heterozygotes in coupling) will
express the marker but not the
mutation. (See Figure I.2.)
heterozygotes in coupling) will not
express either the marker or the
mutationcarriers and noncarriers cannot be distinguished.
(See Figure I.3.)
ma = recessive marker allele; Ma = dominant marker allele; r = recessive mutant allele.
A note about conventions

In this appendix, we chose to represent linked dihybrid genotypes
using vertical lines for each genotype so that we could more
clearly specify the allelic composition at each locus. The
commonly used graphic and typographic conventions are shown at
the right. The examples are for mice with linked genotypes ma/+
and r/+.
Coupling
Repulsion
OR
OR
ma r/+ +
ma +/+ r
336 Appendixes
Offspring of double heterozygotes in repulsion with a

recessive marker: new breeders that express neither the
marker nor the mutant phenotype
Figure I.1 illustrates the results of breeding double heterozygotes in repulsion with a recessive
marker allele. The offspring that are double heterozygotes in repulsion are normal appearing.
They do not express either the marker or the mutant phenotype, but they are expected to carry
both recessive alleles. They are used to create the next generation and are also used as controls,
but they cannot be distinguished by sight from the offspring that express the mutant phenotype
until the mutant phenotype appears.
Figure I.1. Illustration of balanced stock with double heterozygotes in repulsionrecessive
marker allele.
ma = recessive marker allele; r = recessive mutant allele.
The double heterozygotes in repulsion will be produced at a frequency that is dependent on the
linkage between the marker gene and the gene of interest. For example, if the genes are 7 cM
apart, 93% of the mice that express neither the marker nor the recessive phenotype will be
double heterozygotes in repulsion. When these mice are bred, 86% (0.93 x 0.93) of the matings
will produce the expected phenotypic ratios in the offspring (Green, 1966). Only the
heterozygotes in repulsion from these breeding pairs should be used to propagate the line. (It is
important to note that the few wild-type animals that result from crossovers should not be used
for breeding.)
Appendix I: Using a Balanced Stock to Carry a Recessive Mutation 337
Offspring of double heterozygotes in coupling with a

dominant marker: new breeders that express the marker
phenotype but not the mutant phenotype
Figure I.2 illustrates the results of breeding double heterozygotes in coupling when the marker
allele is dominant. The offspring that are double heterozygotes in coupling express the dominant
marker phenotype. They do not express the recessive mutant phenotype, but they carry a
recessive allele. These offspring are used to create the next generation and are also used as
controls, but they cannot be distinguished by sight from the offspring that express the mutant
phenotype until the mutant phenotype appears.
Figure I.2. Illustration of balanced stock with double heterozygotes in couplingdominant
marker allele.
Ma = dominant marker allele; r = recessive mutant allele.
338 Appendixes
Offspring of double heterozygotes in coupling with a

recessive marker: mutant mice that express the marker
phenotype before expression of the mutant phenotype
Figure I.3 illustrates the results of breeding double heterozygotes in coupling when the marker
allele is recessive. The offspring that express the marker phenotype also express the mutant
phenotype. These mutant mice can be identified as soon as the marker phenotype appears,
which could be well before the mutant phenotype appears. The offspring that are double
heterozygotes in coupling do not express either the marker or mutant phenotypes. They are
carriers of both recessive alleles, but they cannot be distinguished by sight from the wild-type
offspring. Although either of these genotypes can be used as controls, only the double
heterozygotes in coupling can be used to propagate the strain. These mice must be identified by
test mating. Breeder pairs that do not produce a mouse with the marker phenotype within the
first 13 offspring should be discarded.
Figure I.3. Illustration of balanced stock with double heterozygotes in couplingrecessive
marker allele.
ma = recessive marker allele; r = recessive mutant allele.
Example of balanced stock: BKS.Cg-Dock7m +/+ Leprdb

(000642)
An example of a strain of JAX Mice maintained as a balanced stock is BKS.Cg-Dock7 m +/+
Leprdb/J (000642), in which the Dock7m allele is balanced with the Leprdb diabetes mutant allele
on Chr 4. Leprdb homozygotes are sterile, and a balanced stock provides a way to breed mutant
mice. We distribute both double heterozygotes in repulsion and double heterozygotes in
coupling. Breed the heterozygotes in repulsion to produce the greatest number of carriers of the
mutation. Breed the heterozygotes in coupling to produce mutant mice that can be identified by
the marker before the disease phenotype appears. Figure I.4 illustrates the implications of
breeding each genotype.
Appendix I: Using a Balanced Stock to Carry a Recessive Mutation 339
db
Figure I.4. BKS.Cg-Dock7 +/+ Lepr (000642): implications of breeding double

heterozygotes in repulsion and double heterozygotes in coupling.
References
Green EL. 1966. Breeding Systems, in Biology of the Laboratory Mouse, 2nd Edition. Green
E (ed) Dover Publications, Inc. NY. pp. 122.
341
Appendix J: Cryopreservation
Cryopreservation is the freezing of biological tissues and organs at temperatures less than -80 C
(-112 F) for the purpose of preservation and live recovery. Cryopreservation technology is a
critical colony management tool used for assisted reproductive techniques (ARTs),
minimization of genetic drift, and preservation of a strain or stock of mice, either to free up
colony shelf space or to provide a way to restore a
line in the event of a disaster.
Our Cryopreservation Laboratory provides services
for internal and external investigators. We also
present courses and seminars on cryopreservation,
both at our campus and at other institutions. This
appendix provides an overview of the
cryopreservation process and our cryopreservation
activities.
Overview of cryopreservation
procedures
Where to get information about

cryopreservation at The Jackson
Laboratory
JAX Services:
Telephone:
1-800-422-6423 (North America)
Email:
[email protected]
Web:
www.jax.org/jaxservices/
cryopreservation-and-recovery
Our Cryopreservation Laboratory:
www.jax.org/cryo
Training:
www.jax.org/courses
Cryopreservation of sperm, ovaries, and embryos

requires specific protocols, which include
specifications for the cryoprotectant media, time and
temperature requirements, and techniques and
procedures for tissue collection, freezing, and thawing. All cryopreservation protocols must be
followed very precisely to help assure recovery of live tissue. For details of our
cryopreservation program at The Jackson Laboratory, visit our Cryopreservation Laboratory
website at www.jax.org/cryo.
Sperm
Although researchers have been cryopreserving sperm for many years, fertilization rates using
thawed sperm have been quite low and inconsistent, especially for several popular strains of
inbred mice such as C57BL/6J (000664) and FVB/NJ (001800). Now, however, researchers at
The Jackson Laboratory have developed a patented technique that has significantly improved
fertilization rates to 50 percent or greater for these and other strains (JAX NOTES, 2006,
2008).
Cryopreservation of sperm is most often used for
single mutations on common inbred backgrounds,
most transgenics, and strains developed using
homologous recombination.
Freezing techniques
The epididymides and vas deferentia are removed
from the mouse and placed in cryoprotectant
medium. Sperm are released into the medium and
then frozen.
Sperm cryopreservation is now a viable

alternative at The Jackson Laboratory.
Historically, the use of sperm
cryopreservation was limited by poor
recovery rates. Researchers at The
Jackson Laboratory are funded to study
ways to improve cryopreservation methods.
In the spring of 2006, we developed patent
pending techniques that greatly improve the
recovery of frozen sperm for strains for
which recovery was poor (Ostermeier et al.,
2008). This advancement enhances the
application of sperm cryopreservation as a
colony management tool.
Thawing techniques
Frozen samples are thawed rapidly by removing them
from liquid nitrogen storage and placing them into a
warm water bath until all ice crystals are melted (approximately two minutes). Immediately,
morphology and motility are evaluated. Thawed sperm should be used as soon as possible for in
vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI).
342 Appendixes
Considerations
Progeny will be heterozygotes or a mix of heterozygotes and wild-type.
Yield from cryopreserved sperm is high107 sperm per male.
Recovery of cryopreserved sperm from F1 and outbred strains is excellent; recovery from
inbred strains is much better with improved techniques.
Ovaries
Cryopreservation of ovaries is an alternative when embryo freezing cannot be used or is not cost
effective. It also is a way to preserve the genotype of a female when you are not ready to breed
her or do not have sperm available for IVF or ICSI.
It takes longer to produce live mice from frozen ovaries than from frozen sperm or embryos.
This is because the female must recover for one to two weeks after the ovarian transplant before
being set up for mating. Then time must be allowed for her to become pregnant.
Cryopreservation of ovaries is most often used for mice with single mutations on a common
inbred background, most transgenics, and strains developed using homologous recombination.
Freezing techniques
Ovaries are removed and placed in a Petri dish containing medium. Each ovary is divided into
two to four segments. The segments are transferred to cryoprotectant solution and then into
cryotubes. Ovaries are then cooled and frozen.
Thawing techniques
The protocol for thawing frozen ovaries or ovary segments involves rehydrating in fresh
medium. Following thawing, the ovarian tissue can be used immediately in ovarian
transplantation or for IVF.
Considerations
Progeny will be heterozygotes or a mix of heterozygotes and wild-type.
Cryopreservation of ovaries does not preserve Chr Y.
Yield from cryopreserved ovaries is lowapproximately 2050 live born per ovarian donor.
Reliability of recovery of cryopreserved ovaries is questionable.
For ovary transplantation, recipient females must be histocompatible with the ovary donor.
Embryos
For many years at The Jackson Laboratory, we used the method of Wittingham, Liebo and
Mazur (1972), for which embryos are frozen in cryovials using dimethyl sulfoxide (DMSO) as
a cryoprotectant. Since 2002, we have used the method of Renard and Babinet (1984), which
uses semen straws for storage and propylene glycol (PrOH) as the cryoprotectant. Using the
PrOH method, we can cryopreserve 2-cell embryos, pack straws more densely in the freezer,
and, due to the chemistry of PrOH, use a less-expensive controlled rate freezer. This method has
one major disadvantage: because of the reduced thermal mass, straws must be handled with care
to avoid inadvertent warming and damage.
Cryopreservation of embryos is useful when preservation of the entire genome is necessary,
such as for strain preservation or for preservation of multiple, unlinked loci.
Appendix J: Cryopreservation 343
Freezing technique
Oocytes are removed from super-ovulated females and fertilized in vitro. Embryos are screened
carefully for abnormalities. Then they are loaded into medium-filled straws and frozen.
Thawing technique
Embryos are thawed and transferred into the oviducts of pseudopregnant recipients.
Considerations
Cryopreservation of embryos is an inexpensive, simple, reliable, technique.
Compared to other techniques, the yield of live pups per donor is relatively lowless than 15
live born per oocyte donor (seven per oviduct).
Advantages of cryopreservation
Cryopreservation has several distinct advantages for colony
managers.
Purchasing cryopreserved embryos rather
than live mice
Colony management issues

Cryopreserve a strain to free up colony shelf space. Balance the
cost of cryopreservation and storage against the cost of
maintaining the live strain and the risk of losing the strain.
Cryopreserve a rescued stock or a rare stock you cannot afford
to lose.
Cryopreserve a stock for backup to insure against catastrophic
lossfrom genetic or pathogenic contamination or natural
disaster.
For any of these applications, storing additional frozen tissue offsite provides extra security.
Sometimes, purchase of cryopreserved embryos

is a preferable alternative to shipment of live
mice. This strategy is as applicable to
collaborators sharing mice as it is to researchers
purchasing mice from a supplier.
Frozen tissue generally is not subject to the same
importation restrictions as live animals are. The
frozen embryos are germ free. Also, shipping
costs are less. Of course, the researcher must
have the appropriate facilities and expertise to
thaw and implant the embryos successfully.
Genetic issues
Cryopreserve a strain to minimize genetic drift. By refreshing your breeding stock with
cryopreserved embryos every 10 generations, you effectively reduce the number of
generations in the breeding lineage and greatly minimize genetic drift.
Cryopreserve a transgenic strain after you have established that the transgene is in the animal
and working and, again, after you have completed any additional genetic manipulations. If
you subsequently lose the transgene through breeding, you can restore the stock with the
appropriate frozen embryos.
Cryopreserve stocks that must be maintained with complex breeding schemes. Because
complex breeding schemes increase the chance for breeding errors, cryopreserved embryos
are valuable insurance against losing the strain or stock.
344 Appendixes
Cryopreservation resources at The Jackson Laboratory

The Cryopreservation Laboratory
The Jackson Laboratory has maintained a successful cryopreservation programcryopreserving
and reconstituting strainsfor more than two decades. We have cryopreserved more than 3,000
lines as sperm, ovaries, or embryos. We recover more than 400 lines per year. Our
cryopreservation laboratory comprises a group of researchers dedicated to improving
cryopreservation techniques and training the scientific community in those techniques. For more
information, visit www.jax.org/cryo.
Cryopreservation facilities
At The Jackson Laboratory we store cryopreserved stocks in liquid nitrogen (-196 C [-320.8 F])
in a secure facility on our campus. We also have backup storage at a remote site.
Cryopreservation-based JAX Services

Features of all of our cryopreservation
services. We
Store frozen material in multiple tanks at two
locations.
Incorporate numerous quality controls,
including test thaws of control embryos.
Continuously monitor all tanks with an alarm
system and we regularly monitor visually.
Provide an annual report detailing the number
of straws and balance of storage time
remaining on your contract.
Offer three options at the end of the contract
period. You can
- pay for additional storage,
- instruct us to destroy the embryos, or
- release the embryos to The Jackson
Laboratory and authorize us to store and
distribute them.
To meet specific needs of colony managers, both within and

outside The Jackson Laboratory, we bundle cryopreservation
services in many different configurations, customized to meet
program objectives. Scheduling is an important component of
these services. The length of time it takes to recover a frozen
stock of mice depends on which tissues are cryopreserved, the
availability of frozen material, and the yield and viability of the
embryos produced. For most recovery projects, live mice can
typically be recovered within 15 weeks of order placement.
We can also deploy teams of reproductive specialists to your
facility to cryopreserve large numbers of strains. This service is
ideally suited for institutions or investigators with large
rederivation projects or substantial backlogs of strains that must
be cryopreserved. On site, our teams can routinely cryopreserve
120 strains or more in a week.
For an overview of our JAX Services related to
cryopreservation, refer to Chapter 18, JAX Services. Or
contact us as indicated on the first page of this appendix.
Cryopreservation training programs

At The Jackson Laboratory, we provide cryopreservation training using several different
strategies. Cryopreservation is a component of our Colony Management Workshop, which we
offer multiple times each year. We also offer workshops, both at The Jackson Laboratory and at
other institutions, specifically tailored to the techniques of cryopreservation and associated
ARTs. Topics are tailored to the audience, but options include the following: cryopreservation
strategies, mouse reproductive biology, basic cryobiology, sperm cryo (lecture and lab), in vitro
fertilization (lecture, lab, troubleshooting), slow-rate freezing (lecture and lab), repository
operations, and embryo vitrification (lecture and lab). For information about cryopreservation
training, visit our courses and conferences website at www.jax.org/courses.
Appendix J: Cryopreservation 345
Other sources of information about cryopreservation

Davisson MG, Taft RA. 2006. Strategies for managing an ever increasing mutant mouse
repository. Brain Res. 1091:225257.
Byers SL, Payson SJ, Taft RA. 2005. Performance of ten inbred mouse strains following
assisted reproductive technologies (ARTs). Theriogenology. 65:17161726.
Sztein JM, McGregor TE, Bedigian HJ, Mobraaten LE. 1999. Transgenic mouse strain rescue
by frozen ovaries. Lab Anim Sci. 49:99100.
Sztein JM, Sweet H, Farley J, Mobraaten LE. 1998. Cropreservation and orthotopic
transplantation of mouse ovaries: new approach in gamete banking. Biol Reprod. 58:1071
1074.
Taft RA, Davisson M, Wiles MV. 2006. Know thy mouse. Trends Genet. 22:659653.
References
Ostermeier GC, Wiles MV, Farley JS, Taft RA. 2008. Conserving, distributing and managing
genetically modified mouse lines by sperm cryopreservation. PLoS ONE. 3(7):e2792.
doi:10.1371/journal.pone.0002792.
Renard JP, Babinet C. 1984. High survival of mouse embryos after rapid freezing and thawing
inside plastic straws with 1-2 propanediol as cryoprotectant. J Exp Zool. 230:443448.
Whittingham DG, Leibo SP, Mazur P. 1972. Survival of mouse embryos frozen to -196
degrees and -269 degrees C. Science. 178:411414.
JAX NOTES. 2006. Reliable new sperm cryopreservation service developed at The Jackson
Laboratory. JAX NOTES. 504:12.
JAX NOTES. 2008. New sperm cryopreservation milestone: 1,000 strains cryopreserved and
successfully recovered. JAX NOTES. 508:3.
347
Appendix K: Donating or Submitting a Strain of

Mice to The Jackson Laboratory
The Jackson Laboratory is committedand publicly fundedto distribute strains of mice
developed by researchers at The Jackson Laboratory and elsewhere. We have accepted
thousands of strains of mice that were donated by investigators and that are currently maintained
live or cryopreserved. Due to funding constraints, the number of strains our Repository can
accept in a year are limited. To supplement our strain donation program, we also offer a strain
distribution program. This appendix provides overviews of both programs.
Strain donation
Following submission and approval of a strain donation from a researcher, we rederive the
strain to produce SPF mice at The Jackson Laboratory and then house and distribute mice from
our facilitywith no cost to the investigator who donated the strain. If the donating investigator
elects, we will provide up to three rederived breeder pairs to the donator (presuming that mice
are available), also at no charge. Strain donation provides a real cost savings to donating
researchers, who can free themselves from the time and expense of maintaining a colony and
shipping mice to colleagues. (These costs can be especially bothersome for strains not being
actively used for research.)
Strain donation has two other important benefits for donating
researchers:
It provides a contingency source of the strain.
It fulfills NIH obligations for investigators to share mice.
Responsibilities of a donating investigator

All donating investigators submitting a strain to The Jackson
Laboratory have specific responsibilities to the scientific
community and The Jackson Laboratory. These responsibilities
are described in the document, Information for Donating
Investigators, available online at
www.jax.org/grc/strain_submission_form. We strongly
recommend that donating investigators review this document
thoroughly before submitting a strain to us for review.
Selection criteria
The stringent importation policy of The Jackson

Laboratory: a major component of both
programs.
Donated or sponsored strains are subject to the
same rigorous importation procedures as all strains
of mice that enter The Jackson Laboratory. We
quarantine and rederive all incoming mice. We
quarantine the SPF progeny until weaning, and we
release pups only after they pass pathological
evaluation by our Animal Health organization.
For further details on our animal health program
and importation procedure, please refer to Chapter
7, Animal HealthPreventing, Identifying and
Eradicating Microbial Contamination. Or visit our
Animal Health website at
www.jax.org/jaxmice/genetichealth or our
importation website at
www.jax.org/imr/importhome.
All strain donations must be approved by our Genetic Resources Committee (GRC), comprising
at least 10 scientists with extensive expertise in many areas of biomedical research. Committee
members use the following evaluation guidelines for each donated strain:
Importance of its current use for research (based on publication history and current demand).
Importance of its anticipated or potential future use.
Difficulty of maintaining it relative to its scientific value.
Difficulty of re-creating the strain relative to the time and effort required for its importation
and preservation.
In the case of a potentially valuable mutant strain with low current demand, existence and
reliability of other resources that would ensure its survival.
348 Appendixes
Where to learn more

For full program details, visit www.jax.org/grc. You also can call Tech Support at 1-800-4226423 (North America) or 1-207-288-5845 (International). Or email us at [email protected].
What to do if you want to expedite the donation process or if we

decline the submission
Sometimes our scheduling and funding priorities delay importation and distribution of a new
strain or preclude us from accepting a new strain. In either case, donating investigators can take
advantage of our Sponsored Strain Distribution program. A program summary follows.
Sponsored Strain Distribution

Our Sponsored Strain Distribution program is one of our JAX Services. It represents a way for
The Jackson Laboratory to share the cost of distributing novel mouse strains with the
investigators who developed the strains. Our program fulfills the requirements of the official
NIH policy on sharing of model organisms for
Registering a mutation
Program commitments include the following:

One function of the Mutant Mouse Resource
group at The Jackson Laboratory is to register
Rederivation and cryopreservation of the
mutations discovered or developed by
strain; development of an archive.
investigators. Even if researchers dont want The
Adaptation or refinement of existing
Jackson Laboratory to distribute a mouse strain,
they might want to register the mutation. To do so,
genotyping protocols followed by posting on
email [email protected].
our website (www.jax.org).
Development of a strain data sheet for our
JAX Mice Database.
Submission of strain information to the Mouse Genome Informatics (MGI) databases
(www.informatics.jax.org).
Promotion of the strain to the international research community via an email campaign and
inclusion in JAX Mice literature.
Selection criteria
Candidate strains must meet the following criteria:
Details of the phenotype or construction of the strain or both must have been published in a
peer-reviewed journal.
A functional allele-specific, PCR-based assay must be available.
The strain must have a practicable fertility rate.
The submitter must have the permission of the strains creator or owner to donate the strain.
Where to learn more

For details about Sponsored Strain Distribution, visit
www.jax.org/jaxservices/sponsoreddistribution. You also can call our JAX Services
representatives at 1-800-422-6423 (North America) or 1-207-288-6294 (International). Or email
us at [email protected].
349
Appendix L: Simplifying Power Analysis to

Determine Sample Size
Kevin Flurkey, Joanne M. Currer, David E. Harrison
Power analysis is the quantitative way to determine the optimal number of mice for an
experiment. Its use has become more widespread because the National Institutes of Health and
other funding agencies now require formal justification for the number of mice proposed for an
experiment.
This appendix provides background information on power analysis and a computational shortcut
that simplifies its application.
Definitions of precision and power

Any experiment that requires a statistical test involves a three-way trade-off among sample size,
precision, and power. Precision refers to the minimum difference between two groups that an
experimenter considers to be important. Power is the likelihood of detecting that difference.
With power analysis, you can determine the minimal number of mice (sample size) you will
need in order to have a reasonable chance (power) of identifying a given difference (precision)
between experimental groups.
How to calculate sample size using our computational

shortcut
The basic steps to determine sample size are as follows:
1. Choose the probabilities of a type I error (a false positive) and a type II error (a false
negative) that are acceptable to you.
2. Choose whether you will conduct a two-tailed (bidirectional) test or a one-tailed
(unidirectional) test.
3. With your choices from Steps 1 and 2, use our computational tool to solve the power analysis
equation for sample size (n).
4. For a small sample size (n " 25 mice), make a final adjustment to n.
Below are the details for each step.
1. Choose the probabilities of type I and type II errors.

Type I errors
Type I errors are false positives. They occur when a statistical test indicates that two groups
differ, even though there is no real difference. " is the probability of a type I error.
The conventionally accepted level for " is 0.05. When a larger value, such as 0.10, is used for
", results are generally considered suggestive, but not definitive. Smaller values of " may be
used when the cost of a false positive is particularly high.
Type II errors
Type II errors are false negatives. They occur when a real difference between two groups is not
detected (i.e., the statistical test generates a false negative result). ! is the probability of a type II
error. The power of a test (i.e., the chance of detecting a given difference) is stated by the
formula 1-!.
350 Appendixes
Typically, ! values of 0.10 or 0.20 are used. The greater tolerance for type II errors, compared
to type I errors, reflects a general view that errors of omission are less serious than errors of
commission. If a negative finding (i.e., a finding of no difference between the groups) is
particularly important for the conclusions of a study, a ! value of 0.10, or even 0.05, should be
used. Whenever a finding of no difference between the groups is important, written results
should include a statement of the precision of the test at a given power (for example, In the
present experiment a difference between the groups of at least 2 gm in body weight would have
been detected 90% of the time.).
Can both error types occur for a single statistical test?

If a statistical test indicates that the means of the groups differ, the potential for only a type I
error exists. If a statistical test does not indicate that the means of the groups differ, the potential
for only a type II error exists. Thus, type I and type II errors cannot occur at the same time.
However, when determining an appropriate sample size, power analysis must take into account
the potential for either error type. (At the planning stage of the experiment, you do not know the
results, and it is the results that determine whether you are vulnerable to type I or type II errors.)
2. Choose whether you will conduct a two-tailed or a one-tailed test.

Two-tailed test
For a two-tailed test, the direction of the difference between the mean of the treatment group
and the mean of the control group is not specified a priori. Either a positive or a negative
difference can be accepted as significant.
One-tailed test
For a one-tailed test, the direction of the difference is set by the researcher before the
experiment is run. Only a single direction is tested, and any difference in the opposite direction
will not be accepted as significant. One-tailed tests require a smaller sample size for a given
power.
How do error types relate to the directionality of the test?

For a type I error, the researcher can designate a priori whether a test will be one- or two-tailed.
If no designation is made, a two-tailed test is assumed. For a type II error, only one-tailed tests
are possible.
Appendix L: Simplifying Power Analysis to Determine Sample Size 351
3. Solve the power analysis equation for sample size n.

a. Using Figure L.1, select the two-tailed or one-tailed version of the power analysis
equation.
Figure L.1. Power analysis equations.
352 Appendixes
b. Use Table L.1our computational toolto select the multiplier.

Table L.1 provides the multipliers that incorporate the standard Z scores for specific " and !
values. Panel A is for two-tailed tests; Panel B is for one-tailed tests. The " and ! values (in
bold) and the standardized scores (in parentheses) are listed across the top row and down the left
column. The intersecting cells represent the multipliers for those specific values.
Table L.1. Multipliers for various combinations of " and !
Panel A. Two-tailed test: multipliers for results of (Z + Z )
"
", (Z )
"
!, (Z )
!
0.50, (0.0)
0.20, (0.842)
0.10, (1.283)
0.05, (1.645)
0.10,
(1.645)
0.05,
(1.96)
0.01,
(2.576)
0.001,
(3.30)
0.0001,
(3.8)
2.7
6.2
8.6
10.8
3.8
7.9
10.5
13.0
6.6
11.7
14.9
17.8
10.9
17.2
21.0
24.5
14.4
21.6
25.8
29.6
Panel B. One-tailed test: multipliers for results of (Z2 + Z )

"
", (Z2 )
!, (Z )
0.50, (0.0)
0.20, (0.842)
0.10, (1.283)
0.05, (1.645)
"
0.10,
(1.283)
0.05,
(1.645)
0.01,
(2.326)
0.001,
(3.09)
0.0001,
(3.7)
1.6
4.5
6.6
8.6
2.7
6.2
8.6
10.8
5.4
10.0
13.0
15.8
9.5
15.5
19.1
22.4
13.7
20.6
24.8
28.6
These tables adapted from Snedecor GW and Cochran GW. (1980), Statistical Methods, 7th ed. Table
6.14.1, p. 104. The Iowa State University Press, Ames, IA.
c. Use the multiplier, substitute your # value and your s value (estimate of $ ), and solve
the power analysis equation. Round any fractional result to the next highest integer.
n = multiplier " (2s2 /# 2 )
The total number of mice in the study is 2n (the treatment group plus the control group).
4. Make final adjustments for a small sample size.

When the sample size per group is small (less than 25), add a correction factor to n. For
" = 0.10 or 0.05, the sample size should be n + 1. For " = 0.01, the sample size should be n + 2.
The correction factor is the same for both two-tailed and one-tailed tests.
Appendix L: Simplifying Power Analysis to Determine Sample Size 353
Example of a calculation for a two-tailed test

The problem: We need to determine the number of mice per group (n) required for a study. Our
criteria are as follows:
We decided that the minimum difference that we consider important (%#%) is equal to the
standard deviation (s) of our outcome variable. For our example, both %#% and s equal 5.
We chose the probability of a type I error (") to be 0.05.
We chose the probability of a type II error (!) to be 0.20 (power equals 80% probability).
The solution:
n = ("# + " $ ) 2 (2s2 /% 2 ) = multiplier & (2s2 /% 2 )
1. Using Table L.1, Panel A, we selected the probability

value of " (0.05) from the top row and ! (0.20) from
the left column. The intersecting cell contains the
value of the multiplier (Z + Z )2.
!
2. We substituted our %#% and s values and completed
the calculation.
(" 0.05 + " 0.20 ) 2 = multiplier = 7.9
3. We made the adjustment for a small sample size.
n adjusted = 16 + 1 = 17 mice
"
n = 7.9 " (2(5 2 ) /5 2 )

n = 15.8
n = 16
This result can be generalized: For a two-tailed comparison of two groups, when the minimum
!
difference considered important equals the standard deviation,
if you want an 80% chance of
detecting the difference, you need 17 mice per group.
Note: For a one-tailed test, we would have first specified the direction of the hypothesis we
were testing. Then we would have used (Z2 + Z )2 as the multiplier. The solution would
be 6.2 * (2(52)/52) = 12.4; n adjusted = 13 + 1 = 14 mice.
"
Additional considerations when comparing more than 2 groups

The formulae for calculating sample size that we present here are appropriate only for the
comparison of two groups; power analysis is more complex for other experimental designs.
However, these formulae may be used for any experimental design that can be divided into pairwise comparisons. To do so, you should adjust the Z value for the number of comparisons
before calculating the multiplier. For example, if your experimental design can be partitioned
into four, two-tailed comparisons of two groups each, a Bonferroni adjustment would give " =
0.05 / 4 = 0.0125. Z would be the standardized score for " = 0.0125, which is 2.50 (obtained
from the standard normal distribution).
"
"
References
Flurkey K, Currer JM, Harrison DE. 2007. Mouse Models in Aging Research, in The Mouse
in Biomedical Research, Vol. III, Normative Biology, Husbandry, and Models. 2nd Edition, Fox
JG et al. (eds). American College of Laboratory Animal Medicine Series; Academic Press,
Elsevier, Burlington, MA. pp. 637672.
Snedecor GW and Cochran GW. 1980. Statistical Methods, 7th Edition. The Iowa State
University Press, Ames, IA.
355
Appendix M: Courses and Educational Programs

Clarence Cook Little founded The Jackson
Laboratory in 1929. Since 1924, Little had been
Where to get more information
running student programs on the current site of The
Upcoming courses and conferences at
Jackson Laboratory, and in 1931 he organized the
www.jax.org/courseseducation
first formal summer student program, thus
Conferences we will be attending:
establishing a powerful link between our research and
www.jax.org/booth/index
education initiatives. Today, in conjunction with our
Mailing list signup form:
research programs, we offer numerous courses and
www.jax.org/courses/signup_form
educational programs here at our campus in Bar
Harbor and at partnering institutions around the world. Following is a brief overview of our
programs.
Postdoctoral opportunities
Postdoctoral opportunities at The Jackson Laboratory provide research experience under the
tutelage of a faculty member. Postdoctoral associates also participate in seminars, meetings,
courses, and workshops; apply for fellowship grants; present results to in-house interest groups;
and publish the results of their research in peer reviewed journals. Our staff works closely with
our postdoctoral associates, which normally number around 50, to ensure that their research
experience at The Jackson Laboratory is as productive and as successful as possible. For details,
visit www.jax.org/research/opportunities/postdoc.
The Jackson Laboratory also offers a special
postdoctoral training program for veterinarians. This
three-year program offers mentor-based training in
normal mammalian development and in animal
models of human disease. For details, visit
www.jax.org/research/opportunities/vet.
Courses and conferences
Postdocs rate our program at The

Jackson Laboratory
On an annual basis TheScientist.com
conducts an international survey to
determine which research institutions and
universities provide the best experience for
postdoctoral associates. In 2008, The
Jackson Laboratory was ranked #9 among
U. S. research institutions (Scheff, 2008).
The Courses and Conferences Program seeks to

promote both research and resource missions of The Jackson Laboratory by offering a wide
array of courses, conferences, and workshops designed to educate and train members of the
scientific community in the use of the laboratory mouse as a platform for discovery research in
biomedicine. The Office of Courses and Conferences develops and administers programs that
bring large numbers of outside investigators to the Laboratory each year, enabling collaboration
and productive discourse between Jackson Laboratory scientific staff and the global research
community. The Office also oversees and otherwise administers traveling workshops designed
to train scientists how to more efficiently use the scientific resources provided by The
Laboratory.
The Jackson Laboratory is a thought leader in the development and application of mouse models
for research on human disease, and has historically served as a gathering place for scientists
from around the world. Currently, The Jackson Laboratory is recognized as one of the only
institutions of its kind to offer a courses and workshops program focusing on the use of the
laboratory mouse and related resources in basic and translational research.
In addition to programs hosted on-site in Bar Harbor, the Office of Courses and Conferences
administers a wide range of highly focused practical workshops at participating institutions
around the world. These hands-on workshops are specifically designed to promote the use of
mouse resources by making training more accessible to investigators and their staff who may
not be able to travel to Bar Harbor.
356 Appendixes
Following are highlights of several of our most popular, regularly held courses and conferences.
For more information about courses and conferences, visit www.jax.org/courses.
Short Course on Medical and Experimental Mammalian Genetics
The two-week Short Course on Medical and Experimental Mammalian Genetics (the Short
Course) has been held at The Jackson Laboratory every summer since 1960. The course was
organized by Drs. Victor McKusick and John
Fuller as a collaboration between The Jackson
A few words about one of the originators of
Laboratory and Johns Hopkins University. The
the Short Course, Dr. Victor A. McKusick
initial goal was to improve genetics education in
Dr. Victor A. McKusick, one of the co-founders of
the Short Course, was a recipient of the National
medical schools (Ledger, 1999). Over the years,
Medal of Science in 2002. In 2008 he was
the objective has broadened to include
awarded the prestigious Japan Prize for Medical
presentation to the public of the latest
Genetics and Genomics for his role in the
developments in both experimental animal and
establishment and development of the field of
human genetics.
medical genetics.
Speakers include faculty members from The
Jackson Laboratory and Johns Hopkins
University as well as prominent scientists from
other institutions throughout the world. The
Short Course continues to be one of our most
highly regarded courses.
We are proud of the long and productive

relationship we have had with Dr. McKusick, and
in the important role he has played in helping us
educate the medical community and investigators
about the latest directions and discoveries in
Short Course on Experimental Models of Human Cancer

The Jackson Laboratory offers a variety of other residential short courses that are disease
focused and designed for advanced predoctoral and postdoctoral students as well as established
investigators. A typical example is The Short Course on Experimental Models of Human
Cancer, which focuses on the mouse as an experimental model for translational cancer research.
Over a period of eight days, students are exposed to a mix of formal lectures on genetics,
genetic tools, translational models for cancer research, stem cells, and epigenetics. Hands-on
workshops and tutorials include genome informatics; mouse colony management; necropsy,
gross pathology tumor histopathology, and in vivo imaging.
The course is held in a retreat-like setting and is limited to 35 participants to ensure a supportive
learning atmosphere with exceptional interaction between students and faculty. Course
participants and faculty reside at the historic Highseas Conference Center in dormitory style
housing, consisting of shared bedrooms and bathrooms. Highseas overlooks Frenchman Bay on
the rocky coast of Maine and is adjacent to beautiful Acadia National Park. Meals are prepared
by our resident chef.
Colony Management: Principles and Practices and other practical workshops
We offer many hands-on workshops designed to train scientists in the practical aspects of using
the laboratory mouse and related resources in their research. Colony Management: Principles
and Practices is one of our most popular workshops and is offered several times throughout the
year, both at our Bar Harbor facility and at other institutions. This workshop provides training in
the theory and practice of maintaining mouse colonies for production and research. Topics
include genetics of the laboratory mouse, nomenclature, animal health, genetic quality control,
breeding strategies, general husbandry, cryopreservation, and disaster prevention.
Appendix M: Courses and Educational Programs 357
Educational programs
Educational programs at The Jackson Laboratory are tailored to scientists at various levels of
their careerfrom talented high school students investigating genetic diseases to experienced
researchers defining the cutting edge of genomic research. Programs include the following:
Summer student program
The Jackson Laboratory summer student program is one of the most significant ways in which
we immerse high school and undergraduate students in scientific research and the
responsibilities of independent work.
Our training department works with high school and university
administrators to solicit applications and select students who can
most benefit from this unique opportunity of independent
research under the mentorship of a research scientist. Although
participants learn about techniques and fundamentals of biology,
the emphasis of the program is on methods of discovery and
communication of new knowledge, not mastery of established
facts. At the end of the program, students present their results at
the annual Summer Student Symposium, attended by their
mentors, peers, parents, and The Jackson Laboratory
community.
The summer student program is about much more than research.
Students spend between eight to ten weeks in Bar Harbor, where
they reside together dormitory style at Highseas, a seaside
Georgian retreat located on campus and overlooking beautiful
Frenchman Bay. An important component of the summer
student program experience is the opportunity for intellectual
and social interaction between other students and Faculty. The
program is renowned for the opportunities it provides to
exceptional science students and currently claims at least two
Nobel Laureates among its alumni.
For details about the program, visit
www.jax.org/education/summerstudent.
The success of our summer student program

The Jackson Laboratory summer student program
is one of the accomplishments about which we are
most proud. Since its inception in 1931, more than
2,000 students have participated in the program.
Several students have done quite well.
Two graduates of our program, David Baltimore
and Howard M. Temin, were awarded the Nobel
Prize in Medicine or Physiology for their
discoveries concerning the interaction between
tumor viruses and the genetic material of the cell.
In Dr. Baltimores Nobel Prize autobiography, he
states that his interest in biology began when he
attended our summer student program as a high
school student in 1952 (Baltimore, 1976). Dr.
Temin writes in his autobiographical entry that his
specific interest in biological research was focused
by several summers he spent as part of our
summer program, between 1949 and 1952 and
again in 1955 (Temin, 1976).
But it isnt just Nobel Prize winners who have
benefited from our Summer Student Program. We
are especially proud of our program graduates who
have returned home and opened doors to
possibilities they did not even know existed before
their summer in Bar Harbor.
College academic year program

Our college academic year program is a way for undergraduate students to spend an academic
year working full-time on an independent research project under the sponsorship of a faculty
member of The Jackson Laboratory. Some participants are previous summer students who want
to continue their research programs. Others want wet lab experience that is not a part of their
normal undergraduate curriculum. Others are participants in educational programs that require
specific research experience. Academic credit is provided in accordance with the policy of the
students college or university.
For more information, visit www.jax.org/education/academicyear.
358 Appendixes
Predoctoral opportunities
The Jackson Laboratory participates in a graduate program in conjunction with the Graduate
School of Biomedical Sciences (GSBS) at The University of Maine. The program consists of six
tracks: cell and molecular biology, functional genomics/interdisciplinary studies, neurobiology,
cell and molecular biology, toxicology, and biomedical engineering.
For more information, visit www.jax.org/education/predoc.
Other academic programs
Master of Science in Teaching program, for secondary science and mathematics teachers
participating in the University of Maine Center of Science and Mathematics Education
Research. For more information, visit www.jax.org/education/mst.
High school internship, for local Maine high school students. For more information, visit
www.jax.org/education/hs-internship.
References
Baltimore D. 1976. Nobel Prize autobiography. http://nobelprize.org/nobel_prizes/medicine/
laureates/1975/baltimore-autobio.html (accessed May 22, 2008).
Ledger K. 1999. And so to Maine. Hopkins Medical News. http://hopkinsmedicine.org/hmn/
S99/annals.html (accessed May 23, 2008.)
Scheff J 2008. Best places to work 2008, Postdocs. TheScientist.com. www.thescientist.com/2008/3/1/53/1 (accessed May 22, 2008).
Temin HM. 1976. Nobel Prize autobiography. http://nobelprize.org/nobel_prizes/medicine/
laureates/1975/temin-autobio.html (accessed May 22, 2008).
359
Appendix N: Sources of Information about

Laboratory Mice
Following are a list of web addresses for information accessible online and a list of print
resources that researchers at The Jackson Laboratory have found particularly useful.
Information available at The Jackson Laboratory website:

www.jax.org
The Jackson Laboratory website (www.jax.org) provides a wide variety of information related
to laboratory mice, research conducted using them, and the relationship of this research to
human health. Following is a list of some of the information available at the time this book was
printed. We have included direct web address for your convenience. We regularly evaluate and
update information, so we recommend browsing www.jax.org frequently.
Web-based information related specifically to JAX Mice.
JAX Mice database
www.jax.org.jaxmice/query
JAX Mice and Services
www.jax.org/jaxmice
Courses and educational programs
www.jax.org/courseseduation/index
Animal health and genetic quality
www.jax.org/jaxmice/genetichealth
Our repositories
www.jax.org/jaxmice/findmice/repository
Research being conduced by our faculty
Relevance of our research to human health
www.jax.org/advances/index
New discoveries and news about The Jackson

Laboratory; registration for email notification of
updates (RSS feed) and JAX enews.
www.jax.org/news/index
Printed material, PDF files, and email newsletters related specifically to JAX Mice, all
available at www.jax.org/jaxmice/literature.
Catalogs and general literature:

Most Popular JAX Mice Strains Catalog
Complete 20072009 JAX Mice Catalog
JAX Services June 2008May 2009 Catalog
20072009 Price List (domestic)

20072009 Price List (international)
Resource manuals (in-depth educational guides on our mouse models and other tools:
Autoimmune disease
Infectious disease
Breeding strategies
Neurobiology
Cancer
Research tools
Cardiovascular
Sensorineural
Genetic background
Type 2 diabetes and obesity
Posters and calendar:
Choosing immunodeficient JAX Mice
JAX Mice coat colors
2009 Courses and Conferences calendar
14-day pups (appearance at 314 days old)
Divergence of C57BL6 substrains
Email newsletter subscriptions:
JAX Mice News email biweekly newsletter
JAX NOTES email quarterly newsletter
DIO (diet-induced obesity) weekly
Special J offers (limited offers for JAX
newsletter
Mice)
360 Appendixes
For more information
Mouse Genome Informatics (MGI)
Web: www.informatics.jax.org
Email: [email protected]
Phone: 1-207-288-6445
Customer Service
Web: www.jax.org/jaxmice/orders
Phone: 1-800-422-6423 (United States)
Technical Support
Web: www.jax.org/jaxmice/micetech
JAX Services
Web: www.jax.org/jaxservices
General online resources and print resources

Online books and other information related to laboratory mice in general, available at
On-line books:
Biology of the Laboratory Mouse. 1968. Green EL, ed.
Mouse Genetics, Concepts and Applications. 1995.
Silver L.
The Anatomy of the Laboratory Mouse. Cook M. 1965.
The Coat Colors of Mice, A Model for Mammalian
Gene Action and Interaction. 1979. Silvers WK.
Origins of Inbred Mice. 1978. Morse HC III, ed.
(More Resources menu option)
Festings characteristics of inbred mice and rats
www.informatics.jax.org/external
/festing/search_form.cgi
Poster of Genealogies of mouse inbred strains
www.informatics.jax.org/mgihome
/genealogy
Print resources
Guide for the Care and Use of Laboratory Animals. National Resource Council. 1996.
National Academy Press. Washington DC.
The Laboratory Mouse. Hedrich HJ (ed). 2004. Elsevier, London.
The Laboratory Mouse. Vol. 8. Laboratory Animal Pocket References. Suckow M,
Danneman P, Brayton C. 2000. CRC Press. Boca Raton FL.
The Mouse in Biomedical Research, 2nd edition. Fox JG, et al. (eds). 2007. American
College of Laboratory Animal Medicine Series. Academic Press. NY.
Ordering JAX Mice

Web: www.jax.org/jaxmice/orders

361
Appendix O: General Biological Information about

Laboratory Mice
Diploid chromosome number
40
Adult weight (females and males)
2040 g
Newborn weight
0.751.5 g
Food consumption
1.5 g/10 g body weight (~36 g/day)
Water consumption
1.5 ml/10 g body weight (~36 ml/day)
Rectal temperature
3639 C
Heart rate
310800 bpm
Blood volume
0.60.8 ml/10 g body weight
Weaning age
1828 days
Sexual maturity
2860 days
Estrous cycle
45 days
Gestation
1821 days
Litter size
212 pups
Post-partum estrus
Fertile
Reproductive lifespan (female)
Terminates at 612 months
Reproductive lifespan (male)
Terminates at 1214 months
Lifespan
1.53 years
Several places in this handbook provide more specific detail:

Table 4.1, Reproductive performance for selected strains of JAX Mice, page 138.
Table 13.1, Reproductive characteristics for most inbred strains of laboratory mice, page
242.
Appendix G, Equivalencies of Human Age to Life Phases of Mice, page 329.
363
Index
1
129 strains
use of with embryonic stem (ES) cells, 47
129 substrains
genes and uses, 303
nomenclature, 291, 292
parental categories, 291
related ES cell lines, 291, 293
129B6F1, 54
129P1/ReJ, 78, 292
129P1/ReJ-Lama2dy/J, 292
129P3/J, 30, 79, 292
129S1/SvImJ, 80, 292, 293
129S1/Sv-Oca2+ Tyr+ KitlSl-J/J, 292, 293
129S8/SvEv-Gpi1c Hprtb-m2/J, 292
129T1/Sv-Oca2+ Tyrc-ch Dnd1Ter /J, 292
129T2/SvEms, 292
129T2/SvEmsJ, 292
129X1/SvJ, 81, 292, 293
4
4-way cross. See also multi-way cross.
research example
drug intervention study, 44
genetic correlations and lifespan
inheritance, 44
A
A (allele), 22
a (gene), 307, 308
A (strain)
development of, 3
A substrains
genes and uses, 303
origins of, 296
A/HeJ, 82, 154
A/J, 35, 83, 153, 154
A/WySnJ, 84
Acadsdel-J acyl-Coenzyme A dehydrogenase,
short chain deletion allele
strains with, 88
additive, definition of, 11
ae, 307, 308
age equivalencies
mouse and human, 329
developmental rates, 329
aggression in mice
confusion with dominance behavior, 212
strategies to alleviate, 212
symptoms of, 212
aging research
drug study, 44
female reproduction, 37
lifespan genetics, 37
lifespan inheritance, 44
type 2 diabetes, 53
where to get information about, 159

aging service (JAX Services), 278, 280
agouti protein, 22
air flow in mouse room and cages, 205
air quality and odors in mouse room
effect on breeding performance, 243
AKR substrains
genes and uses, 303
AKR/J, 58, 85, 153
albino locus, 22
allele
mode of inheritance of, 12
mutant, 11
simultaneously dominant and recessive?, 12
variant, 11
wild-type, 11
allelic relationships
dominant, 11
recessive, 11
semi-dominant, 11
allergies, animal. See laboratory animal
allergies.
alopecia areata surgical model (JAX Services),
280
ALR/LtJ, 58
ALR/LtJ-mtNOD/ShiLtDvs/Mx, 58
Anatomy of the Laboratory Mouse, The
MGI website address for online version, 174
angiogenesis research
example, 64
animal bites, 261
prevention and management of at The
Jackson Laboratory, 262
animal care
sources of information about, 214
animal caretakers. See vivarium staff.
animal husbandry, 201
Apoetm1Unc
strains with, 86
ash, in feed, 224
assisted reproductive techniques (ARTs), 250,
251
at, 307, 308
atherosclerosis research
example, 53, 64
autoclaving, 220. See also feed,
decontamination of.
effect on pellet clumping, 221
effect on pellet hardness, 220
autoimmunity research
automatic watering system. See watering
system, automatic.
aw, 307, 308
AXB, 154
axenic colonies, 181
ay, 307, 308
364 Index
B
B10.O20, 66
B6.129 congenic strains
popularity of, 54
B6.129P2-Apoetm1Unc/J, 86
B6.129P2-Il10tm1Cgn/J, 180
B6.129S2-Igh-6tm1Cgn/J, 155
B6.C3-6T, 72
B6.Cg-m +/+ Leprdb/J
example of strain background effect, 153
B6.V- Lepob/J
B6129PF2/J, 157
B6129SF2/J, 157
B6D2F1/J, 87
B6EiC3Sn a/A-Ts(1716)65Dn, 72
backcross, definition of, 27
backcrossing
comparison with intercrossing, 55
effects on homozygosity and residual
heterozygosity, 55
backcrossintercross
breeding scheme for producing congenic
mice, 333
background effects, 45
in congenic strains, 56
on expression of mutation, 50, 153
Bailey, Donald
development of recombinant inbred (RI)
strain panel, 5
influence on field of gene mapping, 5
balanced stock, 51
breeding options with, 335
double heterozygotes
in coupling, 335, 337, 338
in repulsion, 335, 336
using to carry a sterile, lethal, or embryonic
lethal recessive mutation, 335
example of, 338
BALB/c substrains
genes and uses, 304
origins of, 297
BALB/cByJ, 88
BALB/cHeA, 66
BALB/cJ, 35, 89, 155, 187, 248
barometric pressure in mouse room
bedding. See cage bedding.
behavioral genetics research
example, 69
bioinformatics, 165. See also MGI website.
combined cross analysis, 19
comparative genomics, 19
definition and overview of, 166
genome-wide haplotype association, 19
interval-specific haplotype analysis, 19
resources at Mouse Genome Informatics
(MGI) and The Jackson Laboratory, 165
use in gene mapping, 18, 19
biological information for laboratory mice
general summary, 361
biological products
risks related to zoonotic disease, 261
Biology of the Laboratory Mouse
example of use as a balanced stock, 338
BKS.V- Lepob/J
blindness. See also Pde6brd1.
Pde6brd1 retinal degeneration allele in CBA
substrains, 29
Bmp5se short ear allele
strains with, 131
breeding
strategies, 241
factors that can affect, 242, 243
femalemale ratio, 245
reproductive characteristics that can
affect, 242
to optimize colony production, 244
tips to improve breeding behavior,
244
when to
cull a litter, 244
foster pups, 244
replace
breeding pairs, 244
individual female breeders, 244
individual male breeders, 244
set up breeding, 244
terminology, 27
breeding colonies
confirming phenotypes and genotypes in,
250
expansion of, 30
issues when inbreeding heterogeneous mice,
246
maintaining without expanding, 247
minimizing genetic drift in, 250
preventing genetic contamination in, 250
refreshing, 30
sizing for a research program, 246
troubleshooting, 252
breeding records
comparison with suppliers data, 245
use for colony management, 245
breeding service (JAX Services), 278
brown locus, 22
BTBR, 35
BTBR T+ tf/J, 90
Btkxid X linked immunodeficiency allele
strains with, 104, 304
BUB/BnJ, 91
Burgess-Herbert, S, 19
burnout, as option for contaminated colony, 184
BXA, 154
BXD RI panel, 64
Index 365
C
C3H
development of, 3
C3H substrains
genes and uses, 304
origins of, 299
C3H/HeJ, 49, 92, 153, 248
chromosomal inversion in, 72
C3H/HeOuJ, 93
C3H/HeSnJ, 94
C3HeB/FeJ, 94
C57BL substrains
genes and uses, 305
origins of, 300
C57BL/10J, 97, 154
C57BL/10SnJ, 98
C57BL/6ByJ, 95
C57BL/6J, 7, 29, 33, 35, 54, 96, 153, 154, 211,
248
Nnt, 194
C57BL/6J-Chr#A/J/NaJ strain panel, 69
C57BL/6J-Ghrhrlit/J, 30
C57BLKS/J, 99, 153
C57BR/cdJ, 100
C57L/J, 58, 101
C58/J, 102
cage bedding, 206
corn cob, 206
cotton, 206
hardwood shavings, 206
paper (cellulose), 206
softwood shavings, 206
used at The Jackson Laboratory, 206
cage changing, 208
as opportunity to monitor animals, 208
at The Jackson Laboratory, 208
minimizing escapes, 208, 209
preventing the spread of pathogens, 208
transferring mice, 208
cage location
caging, 202
space requirements for, 203
types of
conventional, 202
microisolator, 202
portable ventilated, 202
ventilated, 202
cancer research
colon
example, 66
heritability in F1 hybrids
example, 41
candidate genes, testing, 20
carbohydrates, in feed, 224
cardiovascular biology research
CAST/EiJ, 103
castaneus, M. m., 10
Castle, William
research using mice, 2
CBA
development of, 3
CBA substrains
genes and uses, 304
origins of, 298
CBA/CaHN-Btkxid/J, 104
CBA/CaH-T(14;15)6Ca/J, 103, 157
CBA/CaJ, 29, 105, 157
CBA/J, 29, 106
CByJ.RBF-Rb(8.12)5Bnr/J, 107
CcS/Dem, 66
Cdh23ahl age related hearing loss 1 allele
strains with, 78, 79, 81, 83, 84, 88, 91, 96,
99, 100, 101, 102, 108, 109, 110, 111,
115, 116, 117, 121, 126, 303, 304, 305,
306
CE/J, 108
centimorgan (cM)
definition of, 17
chemically defined diet, 218
chimeras, germline, 47
choosing a mouse strain for research. See
selecting a mouse strain for research.
chromosomal aberration strains, 70
breeding strategies for, 70
controls for, 71
nomenclature for, 71
research example
Down syndrome, 72
inversion, 72
types of
Chromosome Y aberrations, 70
insertions, 70
inversions, 70
reciprocal translocations, 70
Robertsonian, 70
trisomies, 70
uses of, 70
chromosomal inversion
in C3H/HeJ, 72
chromosome substitution (CS) strain panels, 67
developing, 67
H2 haplotypes for, 317
overview, 60
research example
pubertal timing, 69
uses of, 68
variations, 68
chromosome substitution (CS) strains
JAX Mice, website address for list of, 151
Chromosome Y aberrations, 70
closed formula diet, 218
366 Index
coat color
as genotyping marker, 16
biology of, 21
genes and alleles, 307
albino locus, 22
for commonly used JAX Mice, 309
Myo5a locus, 22
names and symbols, 307
nonagouti locus, 22
pink-eyed dilution locus, 22
related biological systems, relative
dominance, 308
tyrosine-related protein locus, 22
genetics of, 20
uses of as marker, 21
Coat Colors of Mice, The. A Model for
Mammalian Gene Action and Interaction
coisogenic strains
selecting controls for, 157
coisogenic strains, definition of, 27
Coleman, Douglas
research on diabetes and obesity, 6
Collaborative Cross, The, 5, 20, 64
college academic year program
collets (feed), 219
colony management, 177
colony management software
advantages of, 234, 235
considerations for, 234
The Jackson Laboratorys Colony
Management System (JAX-CMS), 233,
235
Colony Management Workshop
complementation testing, 20
complex trait, 12
Complex Trait Consortium, The, 64
compound evaluation services (JAX Services),
279
conferences at The Jackson Laboratory. See
educational programs at The Jackson
Laboratory.
congenic strains, 54
considerations for use, 56
controls for, 57
creating
using phenotypic selection, 333
developing, 54
using phenotyping, 56
effect of passenger genes in, 56
incipient, 54
minor histocompatibility loci for, 321
origin of, 4
research example
gallstones, 58

speed congenics
development of, 56
speed congenic development service
(JAX Services), 280
value of, 56
uses of, 54
conplastic strains, 54, 56
controls for, 57
development of, 56
research example
free radical protection, 58
consomic strains. See also chromosome
substitution (CS) strain panels.
contact sentinel mice, 183
control mice
choosing, 156
purchasing and housing, 157
selecting
for mutation carried on a mixed
background, 157
for mutation carried on an inbred strain,
157
copy number variation (CNV), 33
definition of, 33
in inbred strains, 33
minimizing at The Jackson Laboratory, 33
relevance to humans, 33
coupling
double heterozygotes in a balanced stock,
335
courses at The Jackson Laboratory. See
Laboratory.
Cre-lox System
considerations when using, 49
example of, 47
research example, 53
crossintercross
breeding scheme for producing congenic
mice, 333
cryopreservation, 341
advantages of, 343
as backup strategy, 184, 192, 193
as colony management tool, 343
as part of Genetic Stability Program at The
for emergencies related to loss of animals,
247, 256
JAX Services related to, 341, 344
of embryos, 342
as alternatives to live mice, 343
of foundation stocks at The Jackson
Laboratory, 196
of ovaries, 342
of sperm, 341
to minimize genetic drift, 343
Index 367
cryopreservation (continued)
training programs provided by The Jackson
Laboratory, 344
where to get more details, 345
cryopreservation (JAX Services), 278, 279
cryopreservation team (JAX Services), 279
cryopreserved stocks at The Jackson
Laboratory, 197
cryostorage and recovery services (JAX
Services), 279
custom (homozygous embryo) cryopreservation
service (JAX Services), 279
Customer Service at The Jackson Laboratory
contact information, 271
CZECHII/Ei, 213
CZECHII/EiJ, 108
D
Davisson, Muriel, 6
DBA, 2
DBA substrains
genes and uses, 305
origins of, 301
DBA/1J, 109
DBA/1LacJ, 110
DBA/2J, 35, 111, 187
decontamination of feed, 220
autoclaving, 220
comparison of methods for, 221
irradiation, 221
methods used at The Jackson Laboratory,
226
dedicated supply of mice
dedicated supply service (JAX Services),
278
delayed implantation, 242
developmental rates
mouse and human equivalencies, 329
diabetes. See type 1 diabetes. See type 2
diabetes.
diet. See feed.
diet-induced obesity (DIO) (JAX Services),
280
dilute locus, 22
dirty bedding sentinel mice, 183
disaster planning. See emergency planning.
Disc1del disrupted in schizophrenia 1, deletion
allele
strains with, 78, 79, 80, 81, 90, 116, 303
disease
possible impact on breeding, 245
DNA, extracted
as alternative to live mice, 158
domesticus, M. m., 10
dominant, definition of, 11
donating a mouse strain to The Jackson
Laboratory, 347
Down syndrome research
example, 72
drug studies
example, 44
use of recombinant strain panels for, 154

DW/J Mlphln Pou1f1dw/J, 155
Dysf im inflammatory myopathy allele
Dysf prmd progressive muscular dystrophy allele
E
ear punching for mouse identification, 230
codes used at The Jackson Laboratory, 231
ear tags for mouse identification, 230
Ednrbs piebald allele
Laboratory, 355
college academic year program, 357
Colony Management Workshop, 356
high school internship, 358
Master of Science in teaching program, 358
postdoctoral opportunities, 358
Short Course on Experimental Models of
Human Cancer, 356
Short Course on Medical and Experimental
Mammalian Genetics, 356
summer student program, 357
Eicher, Eva, 15
embryo flushing, 251
embryo transfer, 251
embryonic lethal mutation
carrying in a balanced stock, 335
embryonic stem (ES) cells
cell lines
relationship with 129 substrains, 291, 293
Stevens, Leroy, 6
use of in 129 strains, 47
embryos
cryopreservation of, 342
as alternatives to live mice, 343
emergency planning, 255
components of, 256
for loss of employees, 257
for pandemics, 257
for redeployment of mouse rooms, 257
insurance, 256
issues related to animals, 256
to minimize effects of disaster, 256
to minimize loss of data, 257
ENU (N-ethyl-N-nitrosourea) mutagenesis
mutations induced with, 46
environment, colony
issues when ultra-clean, 180
environmental enrichment for mice, 211
use of exercise wheels, 211
368 Index
environmental factors that can affect breeding,

243
air quality and odors, 243
barometric pressure, 243
bedding and nesting material, 243
diet, 243
handling of mice, 243
lighting, 243
location of cages, 243
temperature and humidity, 243
epistasis, 12
masking, 13
Eppig, Janan, 6
essential amino acids, in feed, 224
estrous cycle, 242
estrus
suppressing, 248
exclusion list of infectious agents at The
extrusions (collets), 219
F
F1 and F2 hybrids
comparison with multi-strain crosses, 42
F1 hybrids, 38
availability from The Jackson Laboratory, 40
heterosis in, 38
histocompatibility of, 155
abbreviations, 34
reciprocal, 38
research example
cancer heritability, 41
uses of, 38
transplantation studies, 39
F2 hybrids, 38, 39
availability from The Jackson Laboratory, 40
comparison with recombinant strain panels,
61
hybrid vigor in, 39
abbreviations, 34
possibility of multiple coat colors, 274
research example
cancer heritability, 41
uses of, 39
fat and fatty acids, in feed, 223
fatal mutation
maintaining with a balanced stock, 51
feed
decontamination of, 220
autoclaving, 220
comparison of methods for, 221
irradiation, 221
methods used at The Jackson Laboratory,
226
diet types, 218

chemically-defined, 218
closed formula, 218
fixed formula, 218
natural, 218
open formula, 218
purified, 218
variable formula, 218
nutritional composition of, 222
ash, 224
carbohydrates, 224
essential amino acids, 224
fat and fatty acids, 223
fiber, 224
minerals, 225
phytoestrogens
concern about, 224
protein, 223
vitamins, 224
physical forms of, 219
extrusions (collets), 219
gel, 220
ground, 219
pellets, 219
quality control for, 225
quantity that normal mice eat daily, 209
storage of, 222
fertility rate, 242
Festings characteristics of inbred mice
website address for, 151
fiber, in feed, 224
fire, recovery from at The Jackson Laboratory,
258
fixed formula diet, 218
FLP-FRT system
example of, 48
food and water, 217
fostering a litter, 249
foundation stocks at The Jackson Laboratory,
196
Fv1b Friend virus susceptibility 1, b allele
FVB substrains
genes and uses, 305
FVB/NJ, 112
G
gallstone research
example, 58
Galton, Francis
genetics research, 1
GBASE, 6
gel diets, 220
gene
vs. allele, 12
vs. locus, 13
Index 369
Gene Expression Database (GXD), 168, 171

gene expression services (JAX Services), 280
gene mapping, 5, 17
definition of, 17
example of, 19
from locus to gene, 20
from strain difference to a locus, 15
genotyping methods, 18
interference from chromosomal inversion, 72
purpose of, 17
recombinant inbred (RI) strain panel
The Collaborative Cross, 64
strategies for, 18
use of bioinformatics with, 18
wild-derived strains, 37
gene mapping services (JAX Services), 280
Gene Ontology (GO), 169
generation time, 242
genetic analysis & research services (JAX
Services), 280
genetic architecture
vocabulary of, 11
genetic background
possible impact on breeding, 245
genetic contamination
definition of, 192
examples of, 192
identifying, 194
managing an event, 198
preventing, 33, 192, 210, 250
at The Jackson Laboratory, 33, 210
when introducing new mice, 238
genetic correlations research
example, 44
genetic drift, 32
and homozygosity, 193
breeding strategies to minimize, 51
definition of, 193
examples of, 193
identifying, 194
difficulty in, 194
with genotyping, 194
minimizing effects of, 193, 246, 250
in inbred strains at The Jackson
Laboratory, 32
minimizing impact on interpretation of
results, 33
rate of in inbred strains, 32
relationship to residual heterozygosity, 193
genetic integrity programs at The Jackson
Laboratory, 197, 199
Genetic Quality Control Program, 197
Genetic Stability Program, 199
genetic quality control, 191. See also genetic
contamination. See also genetic drift.
genetic integrity programs, 197
Genetic Quality Control Program, 197

Genetic Stability Program, 199
Genetic Quality Control program at The
Jackson Laboratory, 197, 199
monitoring criteria, 198
Genetic Stability Program at The Jackson
Laboratory, 199
genetic traits
quantitative, 2
relationship to human traits, 2
simple, 2
genetically engineered mice
controls for, 49, 50
example of, 47
Cre-lox System, 47
FLP-FRT system, 48
RNA-mediated interference (RNAi)
system, 48
T cell receptor (TCR) transgenic mice, 47
germline chimeras, 47
strain background considerations for, 50
genetically engineered strains, 45, 46
breeding schemes for, 49, 50
genetics of the mouse, basic
allele, multiple modes of inheritance, 12
basic inbred strain comparison experiment,
the, 14
coat color. See coat color.
dominance vs. masking epistasis, 13
F2 vs. N2 cross, 18
fine mapping, 18
gene mapping, 17, 18
candidate genes, 20
complementation testing, 20
genotyping methods, 18
use of bioinformatics, 18
gene vs. allele, 12
gene vs. locus, 13
genotyping, 16
linkage analysis, 15
recombinant strain panels, 18
segregation, 13
simple vs. complex inheritance, 14
genome, 11
genome scanning services (JAX Services), 280
genome tagged mice, 68
research example
behavioral genetics, 69
genotype, 11
genotyping
common methods of, 16
biochemical markers (isoenzymes), 16
coat color, 16
immunological markers, 16
microsatellite markers, 16
simple sequence length polymorphisms
(SSLPs), 16
single nucleotide polymorphisms (SNPs),
16
definition of, 16
370 Index
genotyping (continued)
gene mapping, 18
to identify genetic contamination and genetic
drift, 194
uses of, 16
genotyping JAX Mice, 250
germline chimeras, 47
gestation length, 242
Gluchos1C57BL/6J glucose homeostasis QTL 1
Gnat2cpfl3 cone photoreceptor function loss 3
allele
strains with, 80
GpnmbR150X iris pigment dispersion allele
Gpr98frings G protein-coupled receptor 98, frings
allele
strains with, 91
Green, Margaret
archiving data on mouse genetics, 6
Gria4spkw1 glutamate receptor, ionotropic,
AMPA4 (alpha 4), spike wave discharge 1
allele
strains with, 92
ground diets, 219
H
H2 haplotypes, 313
allelic designations for standard strains, 313
for conplastic strains, 317
for consomic strains, 317
for F1 hybrids, 315
for H2 congenic strains, 318
for inbred strains, 314
for recombinant congenic strains, 316
for recombinant inbred strains, 315
haplotype
definition of, 19
haplotype block analysis, 19
harem mating, 245
Hc0 hemolytic complement, deficient allele
strains with, 82, 83, 84, 85, 108, 111, 112,
114, 119, 121, 124, 129, 135, 136, 303,
305, 306
health reports for JAX Mice, 189
health, animal, 179
containment and eradication plan, 188
exclusion list of unacceptable microbial
agents, 184
notification procedures, 188
preventive measures, 185
barrier levels, 185
monitoring, 186
mouse room activity, 186
quarantine and importation, 186
sick and injured animal program, 187,

270
developing a plan to maintain, 180
containment and eradication of infection,
184
burnout, 184
exclusion list of unacceptable microbial
agents, 180
monitoring, 182
frequency of, 182
general appearance of mice, 183
interpretation of results, 183
involvement of technicians, 182
sampling considerations, 182
test animals for, 182
test types, 183
histopathology, 183
microbiologic culture, 183
parisitology, 183
PCR (polymerase chain reaction),
183
serology, 183
preventive measures, 181
Helicobacter, 180, 181, 185
hematology research
hematpoiesis
relationship to bone marrow transplants, 6
hemizygous, 11
heritability of a phenotype, 49
heterosis
in F1 hybrids, 38
heterozygosity
minimizing in inbred strains at The Jackson
Laboratory, 32
heterozygous, 11
hf hepatic fusion allele
strains with, 117
hid hair interior defect allele
strains with, 85
high school internship
histocompatibility
hybrid resistance, 39
issues related to strain selection, 155
major histocompatibility. See H2 haplotypes.
minor histocompatibility. See minor
histocompatibility.
histology services (JAX Services), 281
Hld hippocampal lamination defect allele
strains with, 88, 89, 304
homologous recombination, 47
homozygosity, 31
differences between backcrossing vs.
intercrossing, 55
effects of backcrossing on, 55
relationship with genetic drift, 193
homozygous, 11
hotspots, recombinational, 17
Hrhr hairless allele
strains with, 113
HRS/J, 113
Index 371
human health
advances in the 20th century, 1
expectations in the 21st century, 1
human health, concerns related to exposure to
mice
animal bites, 261
laboratory animal allergies (LAAs), 260
working with mice, 259
zoonotic disease, 261
humanized mice, 47
humidity in mouse room and cages, 205
hybrid resistance, 39
hysterectomy derivation, 251
I
I/LnJ, 114
identification methods for mice. See mouse
identification methods.
IL-10 knockouts, 180
Il2rgtm1Wjl interleukin 2 receptor, targeted
mutation 1 allele
strains with, 120
ILAR (Institute for Laboratory Animal
Research), 26
immunodefiency research
immunology research
importation of new mice, 186
in silico mapping, 29
in vitro fertilization, 251
in vivo services (JAX Services), 279
In(6)1J (inversion)
strains with, 92
inbred strain
definition of, 27
inbred strain panels, 29
inbred strains
basic comparison experiment, the, 14
books about, 152
characteristics and value of, 14, 29
chromosomal aberrations in, 70. See also
chromosomal aberration strains.
commonly used
genes and uses, 303
crosses made from, 28
development of, 28
differences from substrains, 29
effects of domestication on, 29
Festings characteristics of
genetic contamination of, 33
genetic drift in, 32
rate of, 32
genetically engineered, 46
heterozygosity of, 31
individual strains not representative of mice
in general, 29
induced random mutations in, 45, 46
maintenance breeding strategies for, 30

avoiding inadvertent creation of subline,
30
forced heterozygosity in, 30
minor histocompatibility loci for, 321
abbreviations used in F1 and F2 names,
34
when mutation is designated, 49
origins of substrains, 295
A strains, 296
BALB/c strains, 297
C3H strains, 299
C57BL strains, 300
CBA strains, 298
DBA strains, 301
overview, 28
research advantages of, 3
research example
drug study, 35
strain panel, 35
residual heterozygosity in, 31
selecting for research, 153
single locus mutations
strains with
breeding schemes for, 50
controls for, 50
single locus mutations in, 45
spontaneous mutations in, 45, 46
use as an RC strain panel, 65
value to genetics research, 1, 7, 28
inbred substrains. See also inbred strains.
definition of, 27, 28
development of, 28
inbreeding
effects of, 30
value of, 2
incipient congenic strain. See also congenic
strains.
definition of, 54
incross, definition of, 27
induced mutations. See mutations, induced
infectious agents
excluded from The Jackson Laboratory, 184
infectious disease research
inflammation research
example, 64
inflammatory bowel disease
disappearance in ultra-clean environment,
180
inhibitor of DNA binding 1 (Id2), 64
insertions (chromosomal), 70
Institute for Laboratory Animal Research
(ILAR), 26
intercross, definition of, 27
intercrossing
comparison with backcrossing, 55
International Mouse Strain Resource (IMSR)
database, 169, 172
website address for, 150, 172
372 Index

intracytoplasmic sperm injection (ICSI), 251
introducing new mice into a colony, 237
determining their readiness for research, 238,
239
helping them use an automatic watering
system, 240
managing transportation stress in, 238
precautions for wild-derived mice, 239
preventive measures when, 181
protecting against loss of phenotypic
expression, 238
protecting colony from genetic
contamination, 238
protecting colony from new pathogens, 238
use of quarantine, 238
use of rederivation, 238
what we do at The Jackson Laboratory, 240
inversions (chromosomal), 70
irradiation, 221. See also feed, decontamination
of.
IVF embryo cryopreservation service (JAX
Services), 279
J
Jackson Aging Center, The, 154
Jackson Laboratory, The
website (www.jax.org)
information about, 150, 171
Jackson LabWest, The, 283
JAX Mice
coat color genes and alleles for, 309
diet at The Jackson Laboratory
duplicating to maintain a phenotype, 274
health reports for, 189
licensing fees for, 275
ordering, 271
from Bar Harbor vs. Sacramento, 274
from Europe or Asia, 272
pregnant mice, 273
reducing the lead time of, 272
setting up a delivery schedule for, 272
popular strains
characteristics of, 77
reproductive performance of, 138
registering interest in a new strain, 275
shipping methods for, 272
strain database
datasheet overview, 153
strain lists, 150
technical support and literature
when a shipment arrives
determining research readiness of, 274
genotyping, 274
possibility of multiple coat colors with F2
hybrids, 274
what to do if there is a problem, 273
what to do immediately, 273
when phenotypes differ from published

descriptions, 274
JAX Mice Database
datasheet overview, 153
overview of, 173
JAX Services, 277
aging service, 278, 280
alopecia areata surgical model, 280
available at The Jackson LabWest, 283
breeding service, 278
compound evaluation services, 279
cryopreservation team, 279
cryorecovery services, 279
custom (homozygous embryo)
cryopreservation service, 279
dedicated supply service, 278
diet-induced obesity (DIO) service, 280
gene expression services, 280
gene mapping services, 280
genetic analysis & research services, 280
genome scanning services, 280
histology services, 281
in vivo services, 279
IVF embryo cryopreservation service, 279
mouse DNA resource, 281
phenotyping and efficacy testing, 279
phenotyping services, 279
QTL mapping service, 280
speed congenic development service, 280
speed expansion service, 278
speed rederivation with sperm
sperm cryopreservation & recovery, 279
sponsored strain distribution, 278
standard rederivation, 278
strain rescue service, 278
STZ-induced diabetes service, 280
surgical and histological services, 281
surgical and tissue collection services, 281
VCD-induced model of menopause, 281
JAX-CMS Colony Management System, 233,
235
JF1/Ms, 115
K
KK/HlJ, 115
knockin mice, 46
knockout mice, 46
know your mice program
Index 373
L
laboratory animal allergies (LAAs), 260
possible interaction with animal bites, 261
research conducted on at The Jackson
Laboratory, 262
resources for information about, 263
laboratory mice
biological information, general 361
breeding terminology for, 27
genetic characteristics of
number of base pairs, 10
number of centimorgans, 10
number of chromosomes, 10
number of genes, 10
genetic makeup of, 10
nomenclature for
general information about, 26
origins of, 10
overview of, 25
terminology for, 27
where to get information about, 7, 23, 359
LDL receptor (Ldlr)
Lee-Boot Effect, 248
Leprdb-5J
used to study role of leptin, 53
leptin, 6, 53
lethal mutation
carrying in a balanced stock, 335
licensing fees for JAX Mice, 275
light intensity in mouse room, 205
light period in mouse room, 205
lighting in mouse room
line (of mice), definition of, 27
linkage analysis, 15
linkage groups, 15
lipoprotein receptor
literature about JAX Mice
Lith1 and Lith2 loci, 58
Lith9PERA/EiJ lithogenic gene 9, PERA/EiJ allele;
strains with, 126
litter fostering, 249
litter size, 242
Little, Clarence Cook (CC)
founder of The Jackson Laboratory, 3
his research using mice, 2
legacy of, 7
reasoning about inbreeding, 2
role in developing DBA strain, 2, 21
study of coat color genetics, 21
live mice, alternatives to, 158
locus symbol, new
submitting, 26
LP/J, 116
lung cancer loci (Sluc), 66
lung cancer research
example, 66
M
MA/MyJ, 117
mammalian phenotype (MP) ontology, 168
mapping. See gene mapping.
Master of Science in Teaching program
maternal effects research
type 2 diabetes, 41
McKusick, Victor, 356
MclrE-tob tobacco darkening allele
strains with, 128
Mdmg1BALB/cBy mandibular morphogenesis 1
allele
melanocyte, 21
melanocyte stimulating hormone (!MSH), 21
Mendel, Gregor
genetics research, 1
Mendelian inheritance, 14
metabolic syndrome research
metabolism research
MGI website
address of, 150, 166
databases accessible from, 171
Gene Expression Database (GXD), 171
International Mouse Strain Resource
(IMSR), 172
Mouse Genome Database (MGD), 171
Mouse Tumor Biology (MTB) Database,
172
MouseCyc Database, 172
related literature about, 174
examples of use, 170
functionality of
Explore MGI, 167
Expression (Gene Expression Database
[GXD]), 168
Function (Functional Annotation Using
the Gene Ontology [GO]), 169
Genes (Genes, Genome Features &
Maps), 168
menu bar, 170
nomenclature information, 170
online books, 170
Orthology (Mammalian Orthology), 169
Pathways (Biochemical [metabolic]
Pathways), 169
Phenotypes (Phenotypes, Alleles &
Disease Models), 168
Quick Search, 167
Strains/SNPs (Strains, SNPs &
Polymorphisms), 169
Tumors (Mouse Tumor Biology [MTB]
Database), 169
getting help for, 166
introduction to, 166
online books available at, 174
overview of, 150, 167
precursors of, 6
374 Index
mice
life phases of, 330
equivalencies with humans, 330
age, 331
developmental rates, 329
genotype differences among, 331
mature adult, 330
middle age, 330
old age, 330
microchips for mouse identification, 230
microsatellite markers, 16
minerals, in feed, 225
minor histocompatibility loci
for inbred and congenic strains, 321
mitochondrial congenics, 54
Mlphln melanophilin, leaden allele
strains with, 101
MMTVstrains with, 304
mode of inheritance, 11
of a phenotype, 15
mode of inheritance of a phenotype, 49
modifier genes
relationship to single-locus mutations, 45
MOLF/EiJ, 117
molossinus, M. m., 10
mouse allergens, 207, 260. See also laboratory
animal allergies.
Mus m1 (mouse urinary protein), 260
strategies to minimize effects of in mouse
room, 207
mouse colony staff. See vivarium staff.
mouse colony structure at The Jackson
Laboratory, 195
cryopreserved stocks, 197
production colonies, 196
repository colonies, 196
research colonies, 197
mouse DNA resource (JAX Services), 281
Mouse Genetics, Concepts and Applications
Mouse Genome Database (MGD), 171
Mouse Genome Informatics. See MGI website.
mouse hepatitis virus (MHV), 182, 183, 184,
244
mouse identification methods, 230
ear punch, 230
ear tags, 230
microchips, 230
tattoos, 230
toe clipping, 230
ear punch codes, 231
Mouse Mutant Resource (MMR)
Mouse Phenome Database (MPD), 19, 29, 35,
42, 77, 173, 242, 331
example of use, 151
mouse room
cleaning, 210
day-to-day activities in, 207

entry to and exit from, 207
environment, 205
preventing genetic contamination in, 210
providing water in, 209
traffic patterns in, 207
mouse strain, new
registration of, 26
Mouse Tumor Biology (MTB) database, 169,
172
MouseCyc database, 169, 172
MRL/MpJ, 118
MSM/Ms, 118
multi-strain crosses, 42
advantages of, 42
comparison with F1 and F2 hybrids, 42, 43
development of, 42, 43
research example
genetic correlations and lifespan
inheritance, 44
Mus m1 (mouse urinary protein), 260
musculus, M. m., 10
mutant allele, transferring using phenotypic
selection, 333
mutant mice
importing into and distributing from The
repository at The Jackson Laboratory, 186
mutation rate in mice, 32
mutations
carrying on a mixed background
carrying on an inbred background
effects of strain background on expression
of, 50
fatal or sterile
maintaining with balanced stocks, 51
induced, 45
new
registering at The Jackson Laboratory,
26, 348
random, 46
research example
LDL receptor, 53
spontaneous, 45
inbred strains with, 46
JAX Mice carrying
Mouse Mutant Resource (MMR) at The
Index 375
mutations, spontaneous (continued)

programs to identify at The Jackson
Laboratory
phenotypic deviant search, 46
research example
type 1 diabetes, 53
targeted, 46
transgenic, 46
Myo5a, 22, 307, 308
Myo5a+, 307, 308
Myo5ad, 307, 308
N
National Institute on Aging (NIA) Interventions
Testing Program (ITP), 44
natural diet, 218
nesting material
N-ethyl-N-nitrosourea. See ENU (N-ethyl-Nnitrosourea) mutagenesis.
Neu1a neuraminidase, a variant
strains with, 133
neurobiology research
neuromuscular biology research
NntC57BL/6J nicotinamide nucleotide
transhydrogenase, C57BL/6J allele
effect of, 29
role in glucose clearance, 194
NOD substrains
genes and uses, 306
NOD.CB17-Prkdcscid/J, 119, 156
NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ, 47, 120
NOD/LtJ, 245
NOD/ShiLtJ, 53, 58, 121, 156
NOD/ShiLtJ-Leprdb-5J/LtJ, 53
noise in mouse room, 205
nomenclature
chromosomal aberration strains, 71
chromosome substitution (CS) strain panels,
69
congenic strains, 57
conplastic strains, 57
F1 hybrids, 40
F2 hybrids, 40
general information about, 26
inbred strain abbreviations, 34, 287
inbred strains, 34
when to designate mutation, 49
multi-strain crosses, 43
quick reference, 285
recombinant congenic (RC) strain panels, 66
recombinant inbred (RI) strain panels, 64
strains with single locus mutations, 52
symbols and abbreviations used in, 288
where to get detailed information about, 26,
285
wild-derived inbred strains, 37
NON/ShiLtJ, 41, 122
nonagouti locus, 22
NONcNZO10/LtJ, 123, 238
NOR/LtJ, 156
novel mouse strains
help with locating or creating, 150
nutritional composition of feed. See feed,
nutritional composition of.
NZB substrains
genes and uses, 306
NZB/BlNJ, 124, 240
NZO/HlLt, 67
NZO/HlLtJ, 41
NZW/LacJ, 125
O
O20 (mouse strain), 66
obesity research
example, 67
Obq3AKR/J obesity QTL 3 allele
strains with, 85
Obq3C57L/J obesity QTL3 allele
strains with, 101
Obq4AKR/J obesity QTL 4 allele
strains with, 85
Obq4C57L/J obesity QTL4 allele
strains with, 101
Oca2, 22, 307, 308
Oca2p, 307, 308
online books
available at Mouse Genome Informatics
(MGI) website, 150
Online Mendelian Inheritance in Man
(OMIM), 168, 173
ontology, mammalian phenotype (MP), 168
open formula diet, 218
ordering JAX Mice. See JAX Mice, ordering.
organs, frozen
Origins of Inbred Mice
outbred stocks
comparison to other crosses, 42
outcross, definition of, 27
ovarian transplantation, 251
ovaries, cryopreservation of, 342
ovulation rate, 242
P
P/J, 126
pair mating, 245
pandemics, 257. See also emergency planning.
passenger genes, 56
Pasteurella, 181, 185
pathogen exclusion list at The Jackson
Laboratory, 184
pathogen protection
disinfecting shipping containers before
unpacking new mice, 238
when introducing new mice into a colony,
238
376 Index
PctpR120H phosphatidylcholine transfer protein,

R120H allele
Pde6brd1 retinal degeneration 1 allele, 29, 49
strains with, 91, 92, 93, 94, 106, 112, 117,
122, 126, 127, 132, 135, 136, 304, 305,
306
pedigreed expansion stocks (PES) at The
pedigreed numbering system used at The
pellets, 219
clumping
relationship to autoclaving, 221, 226
hardness
relationship to autoclaving, 220, 226
penetrance, 14
PERA/EiJ, 126
pharmacology research
phenotype, 11
degree of penetrance, 14
dominance of, 13
loss of
due to environment, 155, 274
due to microbiologic environment, 238
when introducing new mice, 238
when rederiving mice, 238
mode of inheritance, 15
penetrance of, 13
segregation of, 13
whether monogenic or polygenic, 15
phenotypic selection
using to transfer mutant or variant allele, 333
phenotypic traits
complex, 12
linked, 15
quantitative, 12
simple, 12
phenotyping and efficacy testing (JAX
Services), 279
phenotyping services (JAX Services), 279
phytoestrogens, in feed
concern about, 224
pink-eyed dilution locus, 22
pinworms, 180
PL/J, 127
Pneumocystis, 180, 184, 185, 187
Poli d polymerase (DNA directed), iota,
deficient allele
strains with, 78, 79, 81, 303
polymorphic, 11
postdoctoral opportunities
post-partum estrus, 242
power analysis
using to determine sample size, 349
example using our computational tool,
353
precision
related to power analysis, 349
pregnancy
confirming with palpation, 248

timing of, 248
Lee-Boot Effect, 248
strain differences in, 248
Whitten Effect, 248
vaginal plug as confirmation of mating, 247
pregnant mice
ordering, 273
Prkdcscid severe combined immunodeficiency
allele
production colonies at The Jackson Laboratory,
196
production stocks at The Jackson Laboratory,
196
SNP genotyping of, 198
protein, extracted
protein, in feed, 223
Pseudomonas, 180, 185, 187
pseudopregnancy, 251
purified diet, 218
PWK/PhJ, 128
Q
QTL mapping service (JAX Services), 280
quality control
for feed, 225
quantitative trait, 12
quarantine
when introducing new mice, 186, 238
R
Rb(1.3)1Bnr (Robertsonian translocation)
strains with, 128
strains with, 128
RBF/DnJ, 128
Rd3rd3 retinal degeneration 3 allele
strains with, 128
recessive, definition of, 11
reciprocal F1 hybrids, 38. See also F1 hybrids.
reciprocal translocations, 70
recombinant congenic (RC) strain panels, 60, 65
development of, 65
research example
colon cancer, 66
lung cancer, 66
type 2 diabetes, 67
use of inbred strains in, 65
recombinant congenic (RC) strains
recombinant inbred (RI) strain panels, 60, 62
development of, 4, 62
Index 377
recombinant inbred (RI) strain panels

(continued)
research example
acute phase proteins, 64
angiogenesis, 64
The Collaborative Cross, 64
uses of, 62
variations, 63
recombinant inbred (RI) strains
JAX Mice, website address for, 151
recombinant strain panels
advantages of, 59
chromosome substitution (CS), 60
comparison with F2 hybrids, 61
comparisons among, 60
congenic (RC), 60
overview of, 59
recombinant inbred (RI), 60
uses of, 18, 154
recordkeeping, 229. See also colony
management software.
at The Jackson Laboratory
production and repository colonies, 233
research colonies, 233
day-to-day
recommendations for, 232
The Jackson Laboratorys Colony
Management System (JAX-CMS), 233,
235
refreshing a breeding colony, 30
registering a new mouse strain, 26
registering a new mutation, 26, 348
registering interest in a new strain of JAX
Mice, 275
repository colonies at The Jackson Laboratory,
196
repository strains at The Jackson Laboratory
SNP genotyping, 198
reproductive biology research
reproductive characteristics of mice, 242
delayed implantation, 242
estrous cycle, 242
fertility rate, 242
generation time, 242
gestation length, 242
litter size, 242
ovulation rate, 242
post-partum estrus, 242
reproductive lifespan
female, 242
male, 242
seasonal breeding fluctuations, 242
sexual maturity, 242
time between litters, 242
total litters, 242
weaning age, 242
reproductive development research
example, 69
reproductive lifespan
female, 242
male, 242
reproductive performance
of popular JAX Mice, 138
reproductive techniques, 247
assisted reproductive techniques (ARTs),
250
standard, 247
repulsion
double heterozygotes in a balanced stock,
335
research areas
aging, 159
autoimmunity, including type 1 diabetes,
159
cancer, 160
cardiovascular biology, 160
hematology, 160
immunodeficiency, 161
immunology, 161
individual faculty websites at The
infectious disease, 161
metabolic syndrome, 163
metabolism, 161
neurobiology, 161
neuromuscular biology, 161
obesity, 163
pharmacology, 162
reproductive biology, 163
sensorineural biology, 161
type 1 diabetes, 159
type 2 diabetes, 163
research colonies
maintaining without expanding, 247
sizing, 246
research colonies at The Jackson Laboratory,
197
residual heterozygosity, 31
effects of backcrossing on, 55
relationship to genetic drift, 193
RF/J, 129
RIIIS/J, 130
Rmcf s sensitive to MCF virus allele
strains with, 85, 100, 101, 102, 105, 109,
129, 131, 132, 135
RNA, extracted
RNA-mediated interference (RNAi) system,
examples of, 48
Robertsonian aberrations, 70
Roderick, Thomas, 6
Russell, Elizabeth Tibby
research on hematopoiesis, 6
S
S0 generation
in multi-strain crosses, 42
S1 generation
in multi-strain crosses, 42
378 Index
Salmonella, 261, 262

sample size
using power analysis to determine, 349
SEA/GnJ, 131
segregating inbred strains
segregating phenotype, 13
segregation, genetic, 13
selecting a mouse strain for research, 149
general sources of information for, 150
issues related to
control mice, 156
environment, 155
histocompatibility, 155
transplantation studies, 155
using recombinant strain panels, 154
value of input from animal caretakers and
technicians, 156
semi-dominant, definition of, 11
Sendai, 183
sensorineural biology research
sentinel mice, dirty bedding and contact, 183
sexual maturity, age at, 242
shipping containers
disinfecting before unpacking mice, 238
shipping methods for JAX Mice, 272
Short Course on Experimental Models of
Human Cancer
Short Course on Medical and Experimental
Mammalian Genetics
Shultz, Leonard, 47
sick and injured animal program
simple sequence length polymorphisms
(SSLPs), 16
simple trait, 12
single locus mutations
relationship to modifier genes, 45
controls for, 50, 51
single nucleotide polymorphisms (SNPs), 16
SJL substrains
genes and uses, 306
SJL/J, 132, 155, 245
SM/J, 133
Snell, George, 3
development of congenic strains, 4
influence on tissue transplantation, 4
winning the Nobel Prize, 4
SNPs (single nucleotide polymorphisms)
genotyping, 198
Soat1ald adrenocortical lipid depletion allele
speed congenics
development of, 56
speed congenic development service (JAX

Services), 280
value of, 56
speed expansion service (JAX Services), 278
speed rederivation with sperm cryopreservation
service (JAX Services), 278
sperm cryopreservation & recovery (JAX
Services), 279
sperm, cryopreservation of, 341
SPF colonies
SPF environment
need for, 155
relationship to loss of phenotype, 155
sponsored strain distribution (JAX Services),
278, 348
spontaneous mutations. See mutations,
spontaneous
SPRET/EiJ, 134
ST/bJ, 135
staff, mouse colony. See vivarium staff.
standard rederivation (JAX Services), 278
standard reproductive techniques, 247
Staphylococcus, 180, 185, 186
sterile mutation
carrying in a balanced stock, 51, 335
Stevens, Leroy
research on teratomas, 6
STOCK, 27
comparison to substrain, 30
stock, definition of, 27
strain background effects. See background
effects.
strain donation to The Jackson Laboratory, 347
importation procedures, 347
selection criteria used for, 347
strain panels
chromosome substitution (CS), 67
inbred, 29
recombinant. See recombinant strain panels.
recombinant congenic (RC), 65
recombinant inbred (RI), 62
research example using, 35
strain rescue service (JAX Services), 278
strain, definition of, 27
stress in mice
effects of, 211
identification of, 211
strategies to alleviate, 211
Strong, Leonell
role in developing inbred strains, 2
STS/A, 66
STZ-induced diabetes service (JAX Services),
280
subline
inadvertent creation of, 30
submitting a mouse strain to The Jackson
Laboratory for distribution, 347
summer student program
superovulation, 251
Index 379
supplier of mice
selecting, 158
surgical and histological services (JAX
Services), 281
surgical and tissue collection services (JAX
Services), 281
susceptibility to colon cancer loci (Scc-1, -2, -3,
-4), 66
SWR substrains
genes and uses, 306
SWR/J, 136
T
T cell receptor (TCR) transgenic mice, 47
T(14;15)6Ca (reciprocal translocation)
strains with, 103
T+ brachyury
strains with, 90
targeted mutant mice, 46
JAX Mice, website address for, 150
with homologous recombination, 46, 47
tattoos for mouse identification, 230
Technical Support from The Jackson Laboratory
temperature and humidity in mouse room
temperature in mouse room and cages, 205
tetanus, 261
tf tufted allele
strains with, 90
Thy1a thymus cell antigen1 theta, a variant
allele
time between litters, 242
tissue transplantation studies, 155
tissues, frozen
Tlr4Lps-d toll-like receptor 4, defective LPS
response allele, 49
strains with, 92, 304, 305
Tnfrsf13cBcmd1-A/WySnJ B-cell maturation defect 1
allele
strains with, 84
toe clipping for mouse identification, 230
total litters per female, 242
training and career development, vivarium staff,
266
transgenic mice, 46, 47
creation of, 47
transgenic strains
JAX Mice, website for, 150
loss of transgene expression in, 49
transplantation
effect of Y antigen on, 29
transplantation studies
use of F1 hybrids in, 39
transportation stress in mice
recognizing and managing, 238
trio mating, 245

trisomies, 70
type 1 diabetes research
example, 53, 58
type 2 diabetes research
example, 53, 67
juvenile risk factors, 41
maternal effects, 41
Tyr, 22, 307
relationship to albinism, 13
Tyr+, 307
Tyrc, 307
Tyrc-ch, 307
Tyrc-e, 307
tyrosinase, 21, 22
Tyrp1, 22, 307, 308
Tyrp1+, 307, 308
Tyrp1b, 307, 308
Tyrp1B-lt, 307, 308
Tyrpisa iris stromal atrophy allele
V
vaginal plugs, 247
variable formula diet, 218
variant allele, transferring using phenotypic
selection, 333
VCD-induced model of menopause (JAX
Services), 281
vitamins, in feed, 224
vivarium staff
at The Jackson Laboratory
communication with, 270
know your mice program, 270
sick and injured animal program, 270
training and development, 266
career advancement, 269
management training, 267
new hire training, 266
technician training, 267
tuition reimbursement, 269
effective communication with, 269
training and career development, 266
value of
input regarding strain selection, 156
reputation to organization, 265
W
water
delivery systems for
automatic, 204
helping mice learn to use, 240
bottles, 204
cleanliness of, 226
plastic bags, 204
used at The Jackson Laboratory, 204, 226
380 Index
water (continued)
preparing, 209
quantity that normal mice drink daily, 209
standards for, 226
treatment of, 226
weaning age, 242
Whitten Effect, 248
Wicked High Cholesterol (WHC) mouse, 53
wild mice
concerns about bites from, 261
risk of zonotic disease from, 261
wild-derived inbred strains, 36
aggression in, 213
breeding of, 213
caring for, 213
development of, 36
hints for unpacking, 239
husbandry of, 36
origin of, 36
research example
life history traits, 37
mapping and lifespan study, 37
what to do when a shipment arrives, 213
WSB/EiJ, 137
www.jax.org
databases accessible from, 171
information about, 150
Z
zoonotic disease, 261
relationship to biological products, 261
relationship to laboratory mice, 261
resources for information about, 263
610 Main Street, Bar Harbor, Maine 04609

Tel: 1-207-288-5845 Online: www.jax.org

JAX Handbook On Genetically Standardized Mice

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What is The Jackson Laboratory and what is its mission?

What is The Jackson Laboratory and what is its mission?

What are some of the services provided by The Jackson Laboratory?

What are some of the services provided by The Jackson Laboratory?

The Jackson Laboratory

The Jackson Laboratory Handbook

A note to our readers from the

About The Jackson Laboratory

The Jackson Laboratory Handbook

The Jackson Laboratory Handbook on Genetically Standardized Mice

Registered trademarks of The Jackson Laboratory: JAX

Section I: Introduction ...........................................................................

Section II: Using Mice in Research

The Jackson Laboratory Handbook on Genetically Standardized Mice

viii Table of Contents

Chapter 4: Characteristics of Popular Strains of JAX Mice, Including

Section III: Bioinformatics

Section IV: Colony Management

The Jackson Laboratory Handbook on Genetically Standardized Mice

Monitoring procedures to identify the presence of unacceptable agents ..182

Chapter 8: Genetic Quality ControlPreventing Genetic Contamination and

The Jackson Laboratory Handbook on Genetically Standardized Mice

Breeding schemes ........................................................................................................246

Chapter 14: Emergency Planning ............................................................................. 255

The Jackson Laboratory Handbook on Genetically Standardized Mice

xii Table of Contents

Section V: Ordering JAX Mice and JAX Services

Chapter 17: Ordering JAX Mice and JAX ServicesContact Information

Chapter 18: JAX Services .......................................................................................... 277

Appendix D: Commonly-Used Inbred Strains and Substrains of JAX Mice

The Jackson Laboratory Handbook on Genetically Standardized Mice

The organization of The Handbook

Conventions used in the Handbook

Chapter 1: Why the Mouse?

1.A. From inbred sweet peas to mice

1.A.2. Galtons work with peas

The Jackson Laboratory Handbook on Genetically Standardized Mice

1.A.3. Application of Mendels and Galtons theories to mammals

However, most human traits and geneticallybased diseases are quantitativerelated to

1.B. From mice to inbred mice

Clarence Cook Little was one of the early researchers interested

1.B.2. Littles and Strongs development of inbred mice

Chapter 1: Why the Mouse? 3

1.C. From inbred mice to JAX Mice

1.C.2. Littles vision for The Jackson

1.D. JAX Mice and The Jackson

Why geneticists love mice

Many important scientific discoveries related to genetics have

1.D.1. George Snell and congenic strain development

1.D.1.b. Snells legacy: organ transplantation, the congenic mouseand

Chapter 1: Why the Mouse? 5

1.D.2.b. Baileys insight into preserving recombinations in a panel of

1.D.2.c. The reinvigoration of the recombinant inbred strain

The Jackson Laboratory Handbook on Genetically Standardized Mice

1.D.3. The inbred mouse and further seminal research at The

1.D.3.a. A few of the biomedical research breakthroughs at The Jackson

Chapter 1: Why the Mouse? 7

1.D.3.c. JAX Mice

1.E. It is still about the inbred mouse