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M E T H O D S I N M O L E C U L A R M E D I C I N E™

Congenital Heart
Disease
Molecular Diagnostics

Edited by

Mary Kearns-Jonker
Transplantation Biology Research Lab
Division of Cardiothoracic Surgery
Children's Hospital of Los Angeles
Los Angeles, CA
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Congenital heart disease : molecular diagnostics / edited by Mary Kearns-Jonker.

p. ; cm. -- (Methods in molecular medicine ; 126)
Includes bibliographical references and index.
ISBN 1-58829-375-0 (alk. paper)
1. Congenital heart disease--Molecular diagnosis. 2. Congenital heart
disease--Genetic aspects. 3. Heart--Diseases--Molecular diagnosis.
4. Heart--Diseases--Genetic aspects. 5. Molecular diagnosis.
I. Kearns-Jonker, Mary. II. Series.
[DNLM: 1. Heart Defects, Congenital--diagnosis. 2. Diagnostic
Techniques, Cardiovascular. 3. Heart Defects, Congenital--genetics.
4. Molecular Biology--methods. WG 220 C7543 2006]
RC687.C666 2006
616.1'042--dc22 2005026174
Preface
The Methods in Molecular Medicine™ series is noted for providing clini-
cians, research scientists, and interested individuals with detailed experimental
procedures that are written by leading experts in the field. Congenital Heart
Disease: Molecular Diagnostics introduces a series of techniques that are cur-
rently used to identify the molecular basis for cardiovascular disease. New
knowledge gained from the application of molecular genetics to medicine has
had a significant impact in biomedical research. The chapters in this book
update the reader on new developments in the field and introduce the technol-
ogy currently used to define the molecular genetic basis for congenital malfor-
mations of the heart, cardiomyopathies, cardiac tumors, and arrythmias in
human patients. In addition, the limitations to identifying patients with con-
genital heart disease using this information during both pre- and postnatal
periods is discussed in this volume. The experimental techniques are presented
in sufficient detail to ensure that the procedures can be reproduced in any labo-
ratory, irrespective of the level of experience of the investigators. The notes
section included at the end of each chapter provides valuable insight for
troubleshooting, experimental design, and data analysis that come from the
benefit of the expertise of the authors who are all renowned and well-
respected in the field. It is my hope that Congenital Heart Disease: Molecular
Diagnostics will be a valuable resource for medical personnel, researchers,
patients, and their families.
I would like to express my gratitude to the authors of this volume for their
enthusiasm for the work and thoughtful input into each chapter. I would also
like to thank the series editor, Professor John Walker, for his guidance and
endless patience during the preparation of this volume.
This book is dedicated to my mom, Lillian Kearns, and to my family for
their continuous love and support.
Mary Kearns-Jonker

v
Contents
Preface .............................................................................................................. v
Contributors ..................................................................................................... ix

1 Introduction
D. Woodrow Benson ............................................................................. 1
2 Genetics of Cardiac Septation Defects
and Their Pre-Implantation Diagnosis
Deborah A. McDermott, Craig T. Basson, and Cathy J. Hatcher ....... 19
3 Molecular and Genetic Aspects
of DiGeorge/Velocardiofacial Syndrome
Deborah A. Driscoll ............................................................................ 43
4 Mutation Screening for the Genes Causing Cardiac Arrhythmias
Jeffrey A. Towbin ................................................................................ 57
5 Mutation Analysis of the FBN1 Gene
in Patients With Marfan Syndrome
Paul Coucke, Petra Van Acker, and Anne De Paepe .......................... 81
6 Mutation Analysis of PTPN11
in Noonan Syndrome by WAVE
Navaratnam Elanko and Steve Jeffery ................................................ 97
7 Williams–Beuren Syndrome Diagnosis
Using Fluorescence In Situ Hybridization
Lucy R. Osborne, Ann M. Joseph-George, and Stephen W. Scherer ... 113
8 Congenital Heart Disease: Molecular Diagnostics
of Supravalvular Aortic Stenosis
May Tassabehji and Zsolt Urban ...................................................... 129
9 “Chip”ping Away at Heart Failure
J. David Barrans and Choong-Chin Liew .......................................... 157
10 Molecular Diagnostics of Catecholaminergic Polymorphic
Ventricular Tachycardia Using Denaturing High-Performance
Liquid Chromatography and Sequencing
Alex V. Postma, Zahurul A. Bhuiyan, and Hennie Bikker ................ 171
11 Mutation Detection in Tumor Suppressor Genes
Using Archival Tissue Specimens
Aristotelis Astrinidis and Elizabeth Petri Henske ............................. 185

vii
viii Contents

12 Friedreich Ataxia: Detection of GAA Repeat Expansions

and Frataxin Point Mutations
Massimo Pandolfo ............................................................................. 197
13 The Cardiovascular Manifestations
of Alagille Syndrome and JAG1 Mutations
Elizabeth Goldmuntz, Elizabeth Moore, and Nancy B. Spinner ...... 217
14 Array Analysis Applied to Malformed Hearts:
Molecular Dissection of Tetralogy of Fallot
Silke Sperling .................................................................................... 233
15 DNA Mutation Analysis in Heterotaxy
Stephanie M. Ware ........................................................................... 247
16 Use of Denaturing High-Performance Liquid Chromatography
to Detect Mutations in Pediatric Cardiomyopathies
Amy J. Sehnert .................................................................................. 257
Index ............................................................................................................ 271
Contributors
ARISTOTELIS ASTRINIDIS • Department of Medical Oncology, Fox Chase
Cancer Center, Philadelphia, PA
J. DAVID BARRANS • Department of Medicine, Brigham and Women’s
Hospital, Boston, MA
CRAIG T. BASSON • Greenberg Cardiology Division, Department
of Medicine, Weill Medical College of Cornell University, New York, NY
D. WOODROW BENSON • Division of Cardiology, Department of Pediatrics,
Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
ZAHURUL A. BHUIYAN • Department of Clinical Genetics, Academic Medical
Center, Amsterdam, The Netherlands
HENNIE BIKKER • Department of Clinical Genetics, Academic Medical
Center, Amsterdam, The Netherlands
PAUL COUCKE • Department of Medical Genetics, Ghent University Hospital,
Ghent, Belgium
ANNE DE PAEPE • Department of Medical Genetics, Ghent University
Hospital, Ghent, Belgium
DEBORAH A. DRISCOLL • Division of Reproductive Genetics, Department
of Obstetrics and Gynecology, University of Pennsylvania Medical
Center, Philadelphia, PA
NAVARATNAM ELANKO • Genetics Unit, St. George’s Hospital, London,
United Kingdom
ELIZABETH GOLDMUNTZ • The Division of Cardiology, Abramson Research
Center, The Children’s Hospital of Philadelphia, Philadelphia, PA
CATHY J. HATCHER • Greenberg Cardiology Division, Department of
Medicine, Weill Medical College of Cornell University, New York, NY
ELIZABETH PETRI HENSKE • Department of Medical Oncology, Fox Chase
Cancer Center, Philadelphia, PA
STEVE JEFFERY • Division of Medical Genetics, Department of Clinical
Developmental Sciences, St. George’s University of London, London,
United Kingdom
ANN M. JOSEPH-GEORGE • Genetics and Genomic Biology, The Hospital
for Sick Children, Toronto, Ontario, Canada
MARY K EARNS-JONKER • Transplantation Biology Research Lab, Division
of Cardiothoracic Surgery, Children's Hospital of Los Angeles,
Los Angeles, CA

ix
x Contributors

CHOONG-CHIN LIEW • Department of Medicine, Brigham and Women’s

Hospital, Boston, MA
DEBORAH A. MCDERMOTT • Greenberg Cardiology Division, Department
of Medicine, Weill Medical College of Cornell University, New York, NY
E LIZABETH MOORE • Division of Human Genetics, The Children’s Hospital
of Philadelphia, Abramson Research Center, Philadelphia, PA
LUCY R. OSBORNE • Department of Medicine, The University of Toronto,
Toronto, Ontario, Canada
MASSIMO PANDOLFO • Service de Neurologie, Université Libre de Bruxelles-
Hôpital Erasme, Bruxelles, Belgium
ALEX V. POSTMA • Experimental and Molecular Cardiology Group,
Academic Medical Center, Amsterdam, The Netherlands
STEPHEN W. SCHERER • Genetics and Genomic Biology, The Hospital
for Sick Children, Toronto, Ontario, Canada
AMY J. SEHNERT • Department of Pediatrics, University of California
at San Francisco, Pediatric Heart Center, San Francisco, CA;
CardioDX Inc., Palo Alto, CA
SILKE SPERLING • Department of Vertebrate Genomics, Max Planck Institute
for Molecular Genetics, Berlin, Germany
NANCY B. SPINNER • The Division of Human Genetics, The Children’s
Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA
MAY T ASSABEHJI • Academic Unit of Medical Genetics, The University
of Manchester, St Mary’s Hospital, Manchester, United Kingdom
JEFFREY A. TOWBIN • Pediatric Cardiology, Texas Children’s Hospital,
Houston, TX
ZSOLT URBAN • Departments of Pediatrics and Genetics, Washington
University School of Medicine, St. Louis, MO
PETRA V AN ACKER • Department of Medical Genetics, Ghent University
Hospital, Ghent, Belgium
STEPHANIE M. WARE • Divisions of Molecular Cardiovascular Biology
and Human Genetics, Department of Pediatrics, Cincinnati Children's
Hospital Medical Center, Cincinnati, OH
Introduction 1

1
Introduction

D. Woodrow Benson

Summary
This chapter introduces the book by providing a summary of the detailed technical informa-
tion regarding the materials, reagents, and experimental procedures presented in each chapter.
Key Words: Pediatric heart disease; cardiovascular disease in the young; congenital heart
disease; cardiovascular genetics; heterotaxy syndrome; vasculopathy.

1. Introduction
The close of the 20th century marked the beginning of the era of molecular
medicine, which gave birth to the field of cardiovascular genetics. Insight into
the genetic basis of cardiovascular disease is having a transforming effect on
this field of medicine, long dominated by biophysical models of disease thought
to result largely from environmental effects. Major genetic effects, caused by
chromosomal and single-gene defects, have been identified from studies of
humans affected with cardiovascular disease at young ages. Identification of
disease-causing human gene mutations has provided the means to study the
pathogenesis of these conditions in model systems and has supplied new tools
for the developmental biologist.
Because of these human genetic discoveries, genetic techniques have
become important for scientists, geneticists, and physicians. This book, Con-
genital Heart Disease: Molecular Diagnostics, contributes a compilation of
laboratory tools and provides the latest information on the use of molecular
genetics for the diagnosis of cardiovascular disease. Each chapter provides
detailed technical information regarding the materials, reagents, and experi-
mental procedures necessary to identify genetic alteration associated with spe-
cific disease phenotypes. A wide variety of techniques for detecting single-gene
defects, analyzing cytogenetic abnormalities, and gene expression studies using
microarray techniques are presented. The techniques are applied to diverse
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

1
2 Benson

phenotypes, including congenital cardiac malformations, cardiomyopathies,

cardiac tumors, and cardiac arrhythmias.

2. Genetics of Cardiac Septation Defects and Their Pre-Implantation

Diagnosis
Major advances in the understanding of the underlying genetic basis of car-
diac septation defects has provided insight into the molecular basis of cardiac
development (1). At the same time, advances in ultrasound technology has
made possible precise prenatal diagnosis of both syndromic and nonsyndromic
forms of these cardiac malformations, which may, in some instances, be ame-
nable to fetal intervention. In addition, improved therapeutic strategies during
the last several decades have dramatically increased the number of individuals
living to reproductive age, raising the possibility that, as these individuals have
their own families, clinicians are likely to see an increase in familial clustering
of cardiac malformations.
In Chapter 2, by McDermott et al., an overview of genes whose mutation is
known to cause atrial and/or ventricular septal defects is provided. This is a
rapidly increasing list, and, at present, genetic testing for most of the genes
implicated in septal defects is available only on a research basis. It is to be
expected that, as pointed out in many chapters in this book, advances in tech-
nology and improved understanding to the genotype–phenotype correlations
will ameliorate this problem somewhat.
However, even with advances in technology, it is impractical to screen all
septation defect-associated genes in any given patient, and, as the list increases,
this will be an increasingly challenging problem. Rather than focusing on the
debate about the technology best used to screen for mutations in a particular
gene (e.g., denaturing high-performance liquid chromatography [DHPLC],
denaturing gel electrophoresis, single-strand conformational polymorphism
analysis, or automated sequencing), emphasis in this chapter is on the biologi-
cal processes underlying different genetically determined septation defects. The
idea being that such understanding may appropriately inform the choice of
genes to be screened for mutations on a patient-by-patient basis; the methods
used to prioritize genes selected for mutation analysis should rely on a thor-
ough understanding of the phenotypes, expression patterns, and functional
developmental defects associated with mutations in each gene.
Chapter 2 also includes discussion regarding the use of molecular genetic
techniques in concert with in vitro fertilization. Before identification of genes
whose mutations cause septation defects, couples interested in prenatal diag-
nosis for cardiac malformations were limited to genetic counseling and general
recurrence risk assessments, ultrasound imagining, or testing for chromosomal
causes of cardiac malformations in conjunction with amniocentesis or chori-
Introduction 3

onic villus sampling. With the identification of single genes responsible for
cardiac malformations, the ability to offer pre-implantation genetic diagnosis
in combination with in vitro fertilization is now a potential option for some
couples that prefer earlier diagnosis.

3. Molecular and Genetic Aspects of DiGeorge/Velocardiofacial

Syndrome
The deletion 22q11.2 syndrome (del22q11; OMIM 188400, 192430), which
includes DiGeorge syndrome, Shprintzen syndrome, velocardiofacial syn-
drome, conotruncal anomaly face syndrome, and CATCH-22, results from a
heterozygous, submicroscopic deletion on chromosome 22q11.2 at the
DiGeorge chromosomal region (2–5). Although approx 90% of del22q11 cases
are said to occur sporadically, family occurrence has been well-documented
since the syndrome was first recognized nearly 40 yr ago (6–8). The associated
phenotype is variable, and more than 150 manifestations have been acknowl-
edged by the advocacy group, Velo-Cardio-Facial Syndrome Educational
Foundation (9). Common manifestations can be broadly grouped as cardiovas-
cular abnormalities, dysmorphic facial features, speech problems, and learning
problems (10–12).
Cardiovascular malformations are common in patients with del22q11. In
reviewing the three largest groups of patients reported to date (N = 810) in
which cardiac phenotypes were analyzed, the most common types were tetral-
ogy of Fallot (TOF; 22–35%), interrupted aortic arch (15–19%), ventricular
septal defect (13–18%), truncus arteriosus (7–12%), and vascular ring (5%)
(13–15). Overall, cardiovascular malformations have been reported to be
present in approx 75% of individuals with del22q11 (13–15), and infant
patients frequently come to medical attention because of symptoms caused by
heart disease. However, the prevalence is much lower in pediatric patients
diagnosed after 6 mo (38%) and in adult patients (~30%), suggesting that the
prevalence figure of 75% is likely an overestimation resulting from ascertain-
ment bias caused by selecting sporadic cases presenting with cardiovascular
malformations (8,15–18).
As pointed out in Chapter 3, by Driscoll, fluorescence in situ hybridization
(FISH) with commercially available probes is a sensitive test for detecting the
22q11.2 deletion. The deletion detection rate varies with the type of cardiac
defect and the extent of extracardiac anomalies. Identifying individuals with
the deletion is important for ascertaining individuals who are at risk for related
health and learning problems, so that diagnosis, management, and treatment
can be implemented early. Further, diagnosis of the deletion will allow for
identification of additional family members who may be at risk for learning
disabilities, who also may benefit from appropriate intervention strategies.
4 Benson

Finally, identifying family members with the deletion allows more accurate
risk counseling and reproductive decision making. Risk counseling for
del22q11 will become more advanced as more is learned about the phenotype;
for example, recent investigation suggests that individuals with del22q11 may
have poorer outcomes after cardiac surgery (19).

4. Mutation Screening for the Genes Causing Cardiac Arrhythmias

This chapter details our current understanding of the clinical and molecular
genetic aspects of cardiac arrhythmias as well as the methodology for mutation
analysis of the causative genes. Information regarding the molecular genetic
basis of these important clinical problems has accumulated at an explosive
pace since the initial report of linkage of long QT syndrome in 1991 (20).
Subsequent reports have identified the molecular genetic basis of a number of
arrhythmia phenotypes, including atrioventricular block (21), idiopathic ven-
tricular fibrillation or Brugada syndrome (22), atrial fibrillation (23,24), sick
sinus syndrome (25), ventricular preexcitation (26), and polymorphic ventricu-
lar tachycardia (27–30), using genetic linkage analysis and candidate gene
approaches. Mutations in ion channels, referred to as channelopathies, have
been identified most often.
Mutation analysis of genes causing arrhythmia disorders has been greatly
assisted by the development of rapid, high-technology and high-throughput
methods. The methodology presented in Chapter 4, by Towbin, includes
DHPLC and DNA sequencing. The methodological approaches are important
because not only are a larger number of genes associated with cardiac
arrhythmias, but also because most of the mutations are private (i.e., only seen
in one family). This creates a challenge for mutation analysis. A test,
FAMILION, is available on a fee-for-service basis from Genaissance Pharma-
ceuticals (http://www.familion.com/). Identification of cardiac arrhythmia-
causing mutations will become increasingly important in the future, as therapies
become gene specific (31).

5. The Molecular Genetics of Marfan Syndrome

Marfan syndrome (MFS; OMIM 154700) is a disorder of connective tissue,
which affects mainly the skeleton, the cardiovascular system, and the eyes.
MFS shows autosomal-dominant transmission, with a prevalence of approx 1
in 10,000 people. The phenotype is pleiotropic and characterized by tall stat-
ure, arachnodactyly, lens subluxation, mitral valve prolapse, and aortic root
dilation with a high risk of aortic aneurysm and dissection, which may result in
aortic rupture and sudden death.
Genetic linkage of MFS to chromosome 15, where the fibrillin (FBN)1 gene
is encoded (32) was followed by identification of mutations in FBN1 in indi-
Introduction 5

viduals with MFS (33). Subsequently, more than 600 mutations in the FBN1
gene have been identified (34), and the list of known phenotypic effects result-
ing from these mutations has been extended. FBN1 is a major component of
extracellular matrix structures known as microfibrils, on which elastin (ELN)
seems to be deposited. It has been widely thought that the loss of tissue integ-
rity (e.g., lens and aorta) associated with MFS is the consequence of altered
microfibril structural integrity, i.e., the presence of a population of abnormal
molecules alters the entire fibril structure (a dominant-negative effect; refs. 35
and 36).
FBN1 has a pattern of structural motifs, also common to FBN2 and FBN3,
that includes more than 40 calcium-binding, epidermal growth factor precur-
sor-like units arranged in similarly sized blocks, separated by modules known
as eight cysteine-binding or transforming growth factor (TGF)-β-binding do-
mains. Recently, it was proposed that the loss of the FBN1 protein by any of
several mechanisms and the subsequent effect on the pool of TGF-β may be
more relevant in the development of MFS than mechanisms previously pro-
posed in the dominant-negative disease model (37). The possibility that FBN
haploinsufficiency is a significant factor in the pathogenesis of MFS suggests
that strategies aimed at boosting protein expression may warrant consideration.
The contribution by Coucke et al. (Chapter 5) provides methods for muta-
tion analysis of FBN1 by both DHPLC and direct sequencing of genomic DNA
and complementary DNA (cDNA) isolated from peripheral blood leukocytes
or skin fibroblasts. Identification of FBN1 mutations can be important for con-
firming the diagnosis of MFS and for characterizing genetic risk, and may play
a key role in management of patients with MFS.

6. Mutation Analysis of PTPN11 in Noonan Syndrome by WAVE

Analysis
Noonan syndrome (NS; MIM 163950) is an autosomal-dominant disorder
characterized by dysmorphic facial features, short stature, cardiac defects, and
skeletal malformations (38,39). Linkage to chromosome 12q24 (NS1) and
genetic heterogeneity were established (40,41) before PTPN11, the gene
encoding the src-homology region 2-domain phosphatase-2 (SHP-2), which is
a nonreceptor-type protein tyrosine phosphatase, was identified as the NS1 dis-
ease gene (42). Heterozygous PTPN11 mutations are present in approx 50% of
NS cases (43). PTPN11 mutations are found more often among familial cases
than among sporadic cases. Genotype–phenotype analysis revealed that pul-
monic stenosis was more prevalent among the patients with NS who had
PTPN11 mutations than it was in the group without PTPN11 mutations (70.6%
vs 46.2%), whereas hypertrophic cardiomyopathy was less prevalent among
those with PTPN11 mutations (5.9 vs 26.2%; p < 0.001).
6 Benson

PTPN11 mutations causing NS are heterozygous missense mutations that

alter amino acid residues located in or around the N-SH2 and phosphotyrosine
phosphatase domains, which interact to switch the protein between its inactive
and active conformations. An energetics-based structural analysis of SHP-2
mutants indicated that NS-causing mutations might result in a shift of the equi-
librium favoring the active conformation, suggesting that the mutations are
gain-of-function changes and that the pathogenesis of NS arises from exces-
sive SHP-2 activity (42). This possibility was confirmed by demonstrating an
increase in phosphatase activity of the two most common mutants (44).
Although studies are underway to identify additional NS genes, the identifi-
cation of PTPN11 mutations is already exhibiting clinical usefulness. Chapter
6, by Elanko and Jeffrey, details the methodology for polymerase chain reac-
tion amplification and WAVE DHPLC analysis for all coding exons for the
gene PTPN11, which is mutated in approx 50% of cases of NS. Although DNA
sequencing is initially required to determine the mutation(s) detected by
WAVE (sequencing methods are not described), each mutation has its own
DHPLC signature, and experienced operators can determine known mutations on
this basis. The new Navigator™ software has made this process more reliable.

7. Williams–Beuren Syndrome
Williams–Beuren syndrome (WBS; MIM 194050) and autosomal-dominant
familial supravalvar aortic stenosis (SVAS; MIM 185500) are related disor-
ders (45–47). The cardiovascular malformations of both conditions are thought
to result from haploinsufficiency of ELN. The cardiovascular manifestations
of these elastinopathies, often referred to as arteriopathies, typically include
SVAS, branch pulmonary artery hypoplasia, coronary artery stenosis, and
coarctation of the aorta. Aortic or mitral valve defects have been identified in
10 to 20% of cases (48,49), and isolated pulmonary valve stenosis has been
reported (48).
WBS is a developmental disorder affecting approx 1 in 20,000 live births
(50). Individuals with this syndrome, which is usually sporadic, exhibit char-
acteristic physical and behavioral features. Affected individuals have a distinc-
tive elfin-like facial appearance and mild-to-moderate mental retardation;
however, they typically have relatively good verbal skills and characteristic
personality traits. Cardiovascular abnormalities occur in approx 75% of
affected individuals (49).
WBS is caused by a hemizygous chromosomal microdeletion (~1.5 Mb) at
chromosome 7q11.23; ELN is one of the 24 genes assigned to the deleted WBS
critical region, and virtually all (98–99%) people with typical features of WBS
have a deletion of the ELN gene (46). This observation, coupled with the
coincident distribution of ELN expression and cardiovascular malformations
Introduction 7

suggest that ELN haploinsufficiency may contribute to the pathogenesis of the

characteristic cardiovascular anomalies. Other genomic rearrangements of this
region have also been described (51), and a partial deletion of the WBS region
also resulting in ELN haploinsufficiency has been identified in a small group
of patients with a phenotype intermediate to WBS and SVAS (52).
FISH of either metaphase or interphase nuclei can be used to detect all of
these chromosomal rearrangements, providing the ability to test this segment
of chromosome 7 in individuals with a suspected diagnosis of WBS. Chapter 7,
by Osborne et al., outlines performance of an initial screen using commercially
available FISH probes. Karyotyping (performed in parallel or subsequent to
the standard diagnostic FISH test) and targeted FISH analyses could then be
used to detect macroscopic changes, such as translocations or smaller dele-
tions/inversions, respectively. Each type of analysis varies in the number of
probes used and the cell stage analyzed after hybridization.

8. Congenital Heart Disease: Molecular Diagnostics of Supravalvular

Aortic Stenosis
Mutation or deletion of the ELN gene results in ELN haploinsufficiency,
which has been established as the cause of autosomal-dominant SVAS, which,
as discussed in Chapter 7, is related to WBS. In addition, ELN, whose mutation
also results in the connective tissue disorder autosomal-dominant cutis laxa,
has been implicated as a susceptibility gene for hypertension and intracranial
aneurysms. Chapter 8, by Tassabehji and Urban, describes methodology to
identify point mutations, chromosomal deletions and translocation involving
the ELN gene.

9. “Chip”ping Away at Heart Failure

Cardiomyopathy refers to cardiac dysfunction of unknown cause; the World
Health Organization has defined clinical subtypes that include dilated, hyper-
trophic, restrictive, arrhythmogenic, and unclassified (which includes mito-
chondrial problems) (53). Through use of genetic linkage analysis, positional
cloning, and candidate gene analyses, disease-causing mutations have been
identified in nearly 30 genes from diverse functional categories (reviewed in
refs. 54–56). However, in most human cases of cardiomyopathy, the cause is
still unknown. Although the cardiomyopathies share common clinical end-
points, e.g., heart failure, the molecular mechanisms contributing to the under-
lying pathogenesis are quite varied (57,58).
In the past decade, there has been increasing interest in analyzing profile
similarities of global gene expressions using microarray technology to identify
candidate genes contributing to disease pathogenesis (59). For example, analy-
sis of the expression profiles of colorectal cancers led to identification of a
8 Benson

novel gene subsequently identified as playing a role in regulating cell growth

(60). Chapter 9, by Barrans and Liew, reviews the technical approaches to
microarray studies and describes their experience with a custom-made, cardio-
vascular-based cDNA microarray, termed the CardioChip, in characterizing
gene expression in end-stage cardiomyopathies relative to gene expression as-
sociated with normal heart function (61).

10. Molecular Diagnostics of Catecholaminergic Polymorphic

Ventricular Tachycardia
Polymorphic ventricular tachycardia is a term used to describe a beat-to-
beat alternating QRS axis and morphology during ventricular tachycardia. The
duration is usually nonsustained, with a slower rate than torsade de pointes.
Catecholaminergic polymorphic ventricular tachycardia (CPVT) has the added
feature of being induced by adrenergic stimulation. CPVT is an important clini-
cal problem with a high mortality rate, of up to 50% by the age of 30 yr.
Recently, the molecular diagnostics of this disease have become increasingly
important because disease-causing mutations have been identified in approx
60% of CPVT patients.
In Chapter 10, by Postma et al., the molecular diagnostics are presented for
three genes whose mutations are known to cause polymorphic ventricular
tachycardia: the cardiac ryanodine receptor 2 (27,28), the calsequestrin 2 gene
(29), and an inward-rectifying potassium channel gene (62–64). Genetic diag-
nosis of this clinical problem is likely to become increasingly important both
in selecting gene-specific therapies and to augment early diagnosis and subse-
quent preventive strategies.

11. Mutation Detection in Tumor Suppressor Genes Using Archival

Tissue Specimens
Tuberous sclerosis complex (TSC; OMIM 191090 and 191100) is a neuro-
cutaneous syndrome characterized by seizures, mental retardation, and benign
tumors of many organs, including the heart. Rhabdomyoma, the most common
cardiac tumor discovered in the perinatal period, is a signature finding of TSC
(65). TSC is caused by mutations in the TSC1 and TSC2 tumor suppressor
genes (reviewed in ref. 66); TSC is inherited as an autosomal-dominant trait,
but 60 to 70% of cases are sporadic and represent new mutations. The absence
of obvious mutational hot spots in TSC1 or TSC2 and their relatively large size
(21 and 41 coding exons, respectively) make the screening for mutations chal-
lenging. Because rhabdomyomas often spontaneously regress during early
childhood, the usual clinical approach avoids surgical intervention. Conse-
quently, access to tissue (particularly fresh tissue) is very limited, and rela-
tively little is known about the pathogenesis of rhabdomyoma. Importantly,
Introduction 9

the contribution by Astrinidis and Henske presents methodology for mutation

detection using paraffin-embedded tissue.

12. Friedreich Ataxia

Friedreich ataxia (FRDA; OMIM 229300), named for the physician who
first described it nearly 150 yr ago, is an autosomal-recessive disease that
involves the nervous system and the heart (reviewed in refs. 67 and 68). The
disease phenotype is characterized by degenerative neurological disorder
(ataxia) and hypertrophic cardiomyopathy; males and females are equally
affected (69). Although rare, FRDA is the most prevalent inherited ataxia,
affecting approx 1 in 50,000 people in the United States. In most affected indi-
viduals, symptom onset occurs in the first two decades of life, and, usually, the
neurological symptoms dominate the clinical picture. However, the cardi-
omyopathy is observed in all patients, and, in 70% of patients, cardiomyopathy
develops into a life-threatening condition. Rarely, initial disease manifesta-
tions are caused by cardiomyopathy.
The disease gene was mapped to chromosome 9q13, where a 210 amino-
acid protein called frataxin is encoded (70,71). The most common mutation,
present in 95% of cases, is the expansion of a GAA triplet-repeat polymor-
phism localized within an Alu sequence (FRDA-Alu) in the first intron of the
FRDA gene (72). Because of a founder effect of the main responsible mutation,
the disease usually affects individuals of European, North African, Middle
Eastern, and Indian origin. Truncating or missense mutations in FRDA have
been identified (73).
The GAA expansion in FRDA-Alu impairs transcription and reduces frataxin
levels (72). Frataxin is involved in the control of mitochondrial iron metabo-
lism (74), and it is thought to be involved in the iron–sulphur cluster biogen-
esis (75). Whatever the exact primary role of frataxin might be, its deficiency
leads to potentially harmful oxidative injury associated with excessive iron
deposits in mitochondria. Current therapeutic attempts use antioxidant strate-
gies, and such efforts are likely to be enhanced by the availability of animal
models of the disease (76). The promise of effective therapy is a rationale for
genetic diagnosis. As outlined in Chapter 12, by Pandolfo, the diagnostic
molecular test for FRDA is aimed at detecting the common mutation, the GAA
triplet repeats in the first intron of the FRDA gene. Methods are also given for
sequence analysis in individuals suspected of having point mutations.

13. The Cardiovascular Manifestations of Alagille Syndrome and JAG1

Mutations
It has been longer than 30 yr since the original descriptions of Alagille syn-
drome as an autosomal-dominant disorder characterized by hepatic, cardiac,
10 Benson

ocular, skeletal, and facial abnormalities (77,78). The varied cardiovascular

malformations with high penetrance were established early on. The recogni-
tion of abnormal karyotypes in 5 to 10% of patients resulted in the identifica-
tion of a locus on chromosome 20, which eventually lead to the identification
of JAG1 as the Alagille syndrome disease gene.
Specific types of cardiovascular malformation are a cardinal feature of
Alagille syndrome (79). More than 90% of patients with Alagille syndrome
have a cardiovascular anomaly, ranging from mild peripheral pulmonary
stenosis to TOF with pulmonary atresia. Although right-sided defects are
most common, left-sided cardiac abnormalities and septal defects are also
present. A correlation between the type and location of the JAG1 mutation,
cardiac phenotype, and other manifestations has not been identified (80–83).
For the investigator pursuing genetic causes of cardiovascular disease in the
young, JAG1 deserves consideration even in the absence of extracardiac
manifestations.
As pointed out in Chapter 13, by Goldmuntz et al., identifying JAG1 muta-
tions is challenging because of the size of JAG1 (26 exons) and the type of the
mutations, which include whole-gene deletions in 3 to 7% of cases. For this
reason, methods include mutation detection by conformation-sensitive gel elec-
trophoresis using genomic DNA, direct cDNA sequencing, and FISH to iden-
tify whole-gene deletions.

14. Array Analysis Applied to Malformed Hearts: Molecular Dissection

of Tetralogy of Fallot
TOF (OMIM 187500) is the most common type of cyanotic congenital heart
disease; it is estimated to occur in 3.3 per 10,000 live births and accounts for
6.8% of all congenital heart disease (84). Genetic causes of TOF are being
increasingly recognized. For example, approx 15% of patients with TOF have
a deletion of chromosome 22q11 (85), and nearly 7% of TOF patients have
trisomy 21 (Down syndrome) (86). Heterozygous mutations in the transcrip-
tion factor, NKX2.5, have been identified in approx 4% of TOF patients
(87,88). TOF patients with Alagille syndrome have mutations in JAG1 (81,89).
Recently, mutations in the ZFPM2 gene were identified in sporadic cases of
TOF (90). Despite these advances, the genetic cause of TOF is unknown in
approx 70% of cases. Identification of specific genetic causes for TOF will
allow for improved family counseling and provide insight into the develop-
mental mechanisms that result in the TOF phenotype.
Microarray technology as a method for large-scale gene expression analysis
is being increasingly used in the field of cardiovascular research. Chapter 14,
by Sperling, summarizes the application of arrays to study gene expression
profiles of congenital heart diseases, in particular the molecular portrait of TOF.
Introduction 11

The sections of this chapter correspond to the several distinct steps of

microarray experiments. A general introduction to the method, information on
the selection of arrays, and preparation of labeled cDNA samples are given in
Chapter 14. A specific focus of Chapter 14 is experimental design and data
analysis.

15. DNA Mutational Analysis in Heterotaxy

Heterotaxy refers to a complex of multiple malformations with various situs
abnormalities, primarily of the heart, lung, and spleen, as well as midline
defects involving the gut and kidney, which, together, suggest a defect in left–
right patterning. Heterotaxy is characterized by complex cardiac malforma-
tions; in addition to dextrocardia, the cardiac phenotype includes total
anomalous pulmonary venous return, atrioventricular septal defect, pulmonary
stenosis, double-outlet right ventricle, and systemic vein anomalies. Most cases
of heterotaxy seem to occur sporadically; however, pedigree analysis of famil-
ial situs abnormalities have suggested both autosomal and X-linked transmis-
sion, supporting the idea that heterotaxy is genetically heterogeneous (91).
Defining the developmental basis of left–right patterning has been daunting
because of the large number of genes involved and the different roles that these
genes play across species. However, human genetic studies in individuals with
heterotaxy syndromes, complemented by mechanistic studies in animal mod-
els, are illuminating the molecular basis for this complex phenotype.
Chapter 15, by Ware, provides methods for analysis of four genes whose
mutations have been identified in human heterotaxy (92–97). ZIC3, a zinc-
finger transcription factor, causes X-linked heterotaxy. Epidermal growth fac-
tor-CFC, ACVR2B, and LEFTYA are all members of a TGF-β signal
transduction pathway that is critical for proper left–right development. Point
mutations have been identified in each of these genes using polymerase chain
reaction-based mutation analysis strategies.

16. Use of DHPLC to Detect Mutations in Pediatric Cardiomyopathies

Cardiomyopathy, referring to cardiac dysfunction of unknown cause, is an
important form of cardiovascular disease in the young. To date, the most com-
mon forms of dilated, hypertrophic, and restrictive cardiomyopathy, and of
arrhythmogenic right ventricular dysplasia have been caused by heterozygous
mutations in sarcomeric or cytoskeletal genes, and, in this way, exhibit overlap
with neuromuscular disorders (reviewed in refs. 54, 56, and 98–100). How-
ever, recent reports have identified mutations in genes with diverse other func-
tions, such as regulation of cell energy status (26) and transcriptional regulation
(101). As the list of genes whose mutations cause cardiomyopathy continues to
grow, we can expect the diversity of gene functions to expand.
12 Benson

Despite this exciting progress, the genetic basis of many cases of pediatric
cardiomyopathy remains unknown (idiopathic). Chapter 16, by Sehnert, is
timely because identification of the genetic basis of cardiomyopathy continues
to be primarily a research effort. To detect genetic variations (polymorphisms
and mutations) in human DNA samples, a variety of methods are needed. Chap-
ter 16 focuses on the use of DHPLC as a high-throughput method for mutation
analysis.

Conclusion
This publication, a compilation of laboratory tools, is timely, because the
genetic insights into cardiovascular disease, having moved from the bedside to
the bench, now move from the bench back to the bedside. Consequently, it can
be anticipated that the approaches outlined in this book will continue to move
from the research laboratory to the clinical laboratory.

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Introduction 17

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Genetics of Cardiac Septation Defects 19

2
Genetics of Cardiac Septation Defects and Their
Pre-Implantation Diagnosis

Deborah A. McDermott, Craig T. Basson, and Cathy J. Hatcher

Summary
Cardiac septation defects are among the most common birth defects in humans. The fre-
quency of these defects reflects the complexity of cardiogenesis, which involves such pro-
cesses as cell proliferation, migration, differentiation, and morphogenetic interactions.
Major advances in the understanding of the underlying genetic etiologies of cardiac septa-
tion defects have provided insight into the genetic pathways involved. These genetic factors are
most often transcription factors involved in the early stages of cardiogenesis. The ability to
modify these genes in animal models is providing a better understanding of the role of these
genes in common pathways leading to diverse forms of cardiac defects. Ultimately, our under-
standing of these basic processes should lead to molecular-based treatment and prevention
options for those individuals most at risk for such birth defects.
Key Words: Heart; congenital; genetics; septation defect; transcription factor.

1. Introduction
Congenital heart malformations (CHMs) occur in more than 0.5 to 1% of
live births (1) and are among the most common birth defects in newborns.
Atrial septal defects (ASDs) and ventricular septal defects (VSDs) account for
the greatest proportion of CHMs (2). Serial echocardiography of large new-
born populations has revealed that VSDs are present at birth in approx 5% of
all newborns (3), but most VSDs close spontaneously before adolescence (4).
In recent years, our understanding of the etiology of certain CHMs has
increased significantly. Great strides have been made in the identification of
genes responsible for both syndromic and nonsyndromic forms of CHM, and
their role in cardiogenesis. By identifying human gene mutations associated
with syndromes affecting cardiac chamber septation, in vitro and in vivo mod-

From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

19
20 McDermott et al.

els of abnormal cardiogenesis can be created, and investigators can define

genetic interactions that regulate cardiogenesis.
To understand how gene mutations cause syndromic and nonsyndromic
forms of septal defects, one must delineate the process of septal formation dur-
ing cardiogenesis. Cardiogenesis requires a complex series of events, includ-
ing proliferation, migration, differentiation, and morphogenetic interactions
involving cells from several embryonic origins. The susceptibility of the heart
to developmental anomalies reflects the complexity of these embryonic pro-
cesses. Among the most sensitive cardiac structures are the atrial and ventricu-
lar septa. Separation of the four cardiac chambers involves more than mere
formation of simple partitions between the chambers. After formation of the
primary heart tube, this linear tube loops to the right, creating inflow and out-
flow limbs. The primitive chambers become recognizable by the constrictions
that demarcate the sinus venosus, common atrial chamber, atrioventricular
(AV) canal, ventricular chamber, and conotruncus. Initially, endocardial cush-
ions form within the common AV junction. Simultaneously, the myocardium
of the atrial and ventricular chambers develop trabeculations of endocardium-
covered myocardium that extend into the lumen of the heart tube. Ultimately,
all of the septa fuse with the AV cushions, and these cushions divide the AV
canal into left and right canals. Although many genes that regulate septogenesis
remain to be identified, several genes have been shown to play key roles in
septation.
Historically, recurrence risk assessment for CHM in individuals and their
relatives was based on epidemiological data (5,6). As the genetic bases for
many types of CHMs are elucidated, genetic counseling for such families is
increasingly refined and effective. The ability to offer genetic testing will aid
in identifying those at-risk individuals who may present with normal cardiac
evaluations but who may be susceptible to complications later in life, or for
having children with more severe presentations of disease. A detailed three-
generation family history is useful in the evaluation of the individual with a
CHM. Additionally, a peripheral blood karyotype is warranted in those indi-
viduals with multiple congenital anomalies.
CHMs can be detected and diagnosed prenatally, and, in some instances,
may be amenable to fetal intervention (7). Furthermore, vast improvements in
the surgical and medical management of individuals with CHMs during the
last several decades has dramatically increased the number of adults living
with CHMs (4). ASDs, which occur more commonly in women than men, are
among the most common CHMs to be identified in the adult CHM patient (4).
Because these individuals have their own families, clinicians are likely to see
an increase in clusters of familial CHMs.
Genetics of Cardiac Septation Defects 21

At present, genetic testing for the majority of the genes implicated in CHMs
is available only on a research basis (8). Continued research to better under-
stand the incidence, penetrance, and expressivity of mutations in these and
other genes involved in CHMs is critical before such tests warrant widespread
clinical application. In this chapter, we discuss syndromes that are character-
ized by the presence of ASDs and/or VSDs and their causative genes. We pro-
vide an overview of some of the better understood genes investigated to date,
but this overview is not a comprehensive list. Mendelian syndromes and chro-
mosomal etiologies with associated CHMs that can include septation defects
are listed in Table 1 (9–11). The number of genes associated with ASDs and
VSDs in patients is rapidly increasing.
Although the technology best used to screen for mutations (e.g., denaturing
high-performance liquid chromatography, denaturing gel electrophoresis,
single-strand conformational polymorphism analysis, and automated sequenc-
ing) can be legitimately debated, and largely reflects institutional and labora-
tory biases, we do not focus on this technical aspect. Instead, we focus on the
biological processes underlying different genetically determined septation
defects so that such understanding may appropriately inform the choice of
genes to be screened for mutations in any given patient. From the perspective
of routine clinical testing, it is already impractical to screen all septation defect-
associated genes in any given patient, and the selection of genes to be screened
by the clinician evaluating the patient to undergo testing will be an increas-
ingly challenging problem. Thus, the methods used to make this selection should
rely on a thorough understanding of the phenotypes, expression patterns, and
functional developmental defects associated with mutations in each gene.
1.1. Holt–Oram Syndrome: TBX5
Holt–Oram syndrome (HOS) is an autosomal-dominant disorder character-
ized by structural and/or conductive heart deformities in the setting of upper-
limb radial ray anomalies (12). HOS is estimated to occur in approx 1 in
100,000 live births, and most individuals represent sporadic cases, i.e., new
mutations. There is significant phenotypic variability observed between
affected individuals even in a single family, suggesting a role for modifying
genetic factors. The limb findings associated with HOS are fully penetrant and
may be unilateral, bilateral/symmetric, or bilateral/asymmetric. A range of
upper-limb deformities (ULDs) with varying severity may be observed, such
as triphalangeal or absent thumb(s), severe limb hypoplasia, phocomelia,
abnormal forearm pronation and supination, possible sloping shoulders, and
restriction of shoulder joint movement. Polydactyly is not a feature of HOS.
Left-sided ULDs are often more severe than right-sided ULDs. In some affected
 22
Table 1
Mendelian and Chromosomal Forms of ASD, VSD, and AVSD
Gene (chromosomal
Disease location) OMIM or reference no. Clinical features, including CHMs

Autosomal-dominant conditions
Alagille syndrome JAG1 (20p12) 118450 Peripheral PS, ASD, TOF, deafness, decreased
number of intrahepatic bile ducts, posterior
embryotoxon, triangular facies
ASD with AV conduction NKX2.5 (5q34) 108900 ASD progressive AV block, TOF, VSD, tricuspid
defects valve anomalies
ASD2 GATA4 (8p23.1–p22) 607941 ASD, VSD, AVSD, PS, mitral and aortic valve
regurgitation
Autosomal-dominant ASD (5p) 10 Incomplete penetrance, aortic stenosis, atrial septal
aneurysm, persistent left superior vena cava
ASD1 (6p21.3) 108800 Autosomal-dominant ASD
AVSD (1p31–p21) 600309 Autosomal-dominant AVSD, incomplete
penetrance, and variable expressivity
AVSD2 CRELD1/CIRRIN 607170 Partial AVSD with heterotaxy
DiGeorge syndrome TBX1 (del22q11) 188400 VSD, right sided aortic arch, TOF, learning
disabilities, secondary palate clefts Mc
Holt–Oram syndrome TBX5 (12q24.1) 142900 Ostium secundum ASD, VSD, progressive heart
Der
block, upper-limb deformity
mot
Duane–Radial Ray syndrome SALL4 (20q13.13–q13.2) 607323 Radial ray abnormalities, Duane anomaly,
(Okihiro syndrome) sensorineural and/or conductive deafness, ASD
t
(infrequent), Hirschsprung disease, anal stenosis,
imperforate anus, renal abnormalities, fused
cervical vertebrae, hypoplasia of pectoral and
upper-limb musculature et
al.
 Ge
Noonan syndrome PTPN11 (12q24.1) 163950 PS, left ventricular hypertrophy, cardiac septal neti
defects, webbed neck, postnatal short stature, cs
characteristic facial features, cryptorchidism,
bleeding diathesis, vertebral anomalies
Autosomal-recessive conditions of
Ellis–van Creveld syndrome EVC (4p16), 225500 Common atrium, ASD, AVSD, short limbs, short Car
EVC2 (4p16) dia
ribs, postaxial polydactyly, dysplastic teeth and nails
Ivemark syndrome Not identified 208530 Asplenia or polysplenia, abnormal lobation of c
lungs, malposition and maldevelopment of
abdominal organs, ASD, VSD, AVSD, PS
McKusick–Kaufmann MKKS (20p12) 236700 Hydrometrocolpos, postaxial polydactyly, ASD, Sep
syndrome VSD, AVSD, common atrium tati
Smith–Lemli–Opitz DHCR7 (11q12–q13) 270400 ASD, VSD, AVSD, PDA, aortic coarctation, shorton
stature, failure to thrive, low cholesterol levels,
facial dysmorphism, abnormal male external
genitalia
TARP syndrome Xp11.23–q13.3 300442 Club foot, ASD, Robin sequence, persistent left Def
superior vena cava, lethal in infancy ects
Chromosomal etiologies

Chromosomal anomaly Clinical features

Down syndrome/trisomy 21 AVSD, common neonatal findings include hypotonia, flat facial profile, poor motor reflex, slanted
palpebral fissures, joint hyperflexibility, excess skin on posterior neck, transpalmar crease
Trisomy 13 AVSD, holoprosencephaly-type defects, severe mental defect, minor motor seizures, polydactyly,
rocker-bottom feet, mild microcephaly, single umbilical artery
(continued)
 24
Table 1 (continued)
Disease Clinical features
Trisomy 18 AVSD, clenched hand and overlapping fingers, polyhydramnios, single umbilical artery, hypertonic,
mental deficiency, short sternum, small nipples, inguinal or umbilical hernia, hypoplastic nails
3pdel AVSD, mental and growth retardation (prenatal onset), hypotonia, microcephaly, bilateral ptosis,
upper limb postaxial polydactyly
Turner syndrome (45,X) Bicuspid aortic valve, aortic coarctation, MVP, AVSD, short stature (female), congenital
lymphedema, broad chest with widely spaced nipples, ovarian dysgenesis, narrow convex nails
Interstitial dupl 19p VSD, urinary tract anomalies, renal anomalies, rocker-bottom feet, small thorax, mild hydrops fetalis,
nuchal edema
ASD, atrial septal defect; AV, atrioventricular; AVSD, AV septal defect; MVP, mitral valve prolapse; PDA, patent ductus arteriosis; PS, pulmonic
stenosis; TOF, Tetrology of Fallot; VSD, ventricular septal defect.

Mc
Der
mot
t

et
al.
Genetics of Cardiac Septation Defects 25

individuals, the ULD may involve only the carpal bones and be visible only on
X-ray. Initial clinical evaluation should, therefore, include posterior–anterior
hand X-rays of the affected individual’s parents to rule out any carpal bone
anomalies. This information, in the absence of mutational analysis, is critical
for offering accurate recurrence risk estimates for the family.
Heart defects in HOS are incompletely penetrant, occurring in approx 75%
of affected individuals (13). When they do occur, expressivity is highly vari-
able. The most typical CHMs associated with HOS are ostium secundum ASDs,
which may be associated with isomerism and can present as a common atrium.
Similarly, VSDs, particularly of the muscular trabeculated septum are frequent
manifestations (13,14). Such defects are often associated with abnormal ven-
tricular trabeculation. Numerous other complex CHMs have been associated
with HOS, but conotruncal anomalies and ostium primum ASDs are not cardi-
nal features of this syndrome. All individuals with HOS, regardless of the pres-
ence of a CHM, are at risk for cardiac conduction disease. Such conduction
disease can be progressive, resulting in complete heart block with or without
atrial fibrillation, and mandates routine electrocardiographic evaluation for all
individuals with HOS.
Mutations in TBX5, a member of the T-box transcription factor gene family,
cause HOS. This gene is located at chromosome 12q24.1 (14,15). The T-box
gene family is characterized by a highly conserved T-box DNA-binding
domain. Of the many TBX5 mutations identified to date, most are nonsense or
frameshift mutations, splice mutations, or chromosomal rearrangements that
are predicted to produce HOS through TBX5 haploinsufficiency. TBX5 mis-
sense mutations do occur, and, unlike TBX5 haploinsufficiency mutations, they
have been associated in large family studies with more significant organ bias
in their manifestations (13). Because such genotype–phenotype correlations
are only evident as statistically significant findings in population studies, they
are not useful in predicting the individual patient’s phenotype (13,16). Only a
single family potentially affected by HOS (17) has been shown not to be linked
to chromosome 12q24.1, and, thus, if any intergenic genetic heterogeneity
exists in HOS, it is very small.
The specific role of TBX5 in heart development is slowly being elucidated.
TBX5 has been shown to play a role in chamber specification (18) as well as in
inhibition of cardiomyocyte proliferation (19). Therefore, TBX5 may partici-
pate in cardiogenesis by regulating cell proliferation in specific cardiac
domains, resulting in the regional morphological features of the heart. Cre-
ation of a Tbx5 knockout mouse (20) has provided an in vivo method for iden-
tifying downstream targets of Tbx5. Although these embryos died early in
development, before cardiac looping, several observations were made before
their death. Failed development of posterior sinoatrial structures resulted in a
26 McDermott et al.

common atrium and a distorted right ventricle, thus, adding credence to the
hypothesis that Tbx5 plays a role in cardiac septation. In addition, expression
of several cardiac-specific genes, such as Mlc2v, Irx4, Hey2, ANF, Nkx2.5, and
Gata-4 were noted to be either decreased or absent in the Tbx5-null mice. How-
ever, only expressions of ANF and Cx40 were altered in heterozygous Tbx5
mice, which were also observed to have enlarged hearts with ASDs. Bruneau
et al. (20) further demonstrated that Tbx5 acts synergistically with Nkx2.5 to
transactivate expression of Cx40. Other biochemical studies have confirmed
this finding and have demonstrated a synergy between Tbx5 and Nkx2.5 to
transactivate expression of ANF (21,22). Recent data from Garg et al. (23)
suggests that Tbx5 also interacts with Gata-4. Identification of the downstream
targets and cofactors of TBX5 is helpful in understanding the role of this tran-
scription factor in cardiogenesis.
1.2. Familial ASDs With Progressive AV Block: NKX2.5
Schott et al. (24) identified mutations in NKX2.5 (a member of the highly
conserved NK homeobox transcription factor gene family) as the underlying
cause for an autosomal-dominant cardiac disorder characterized by ostium
secundum ASDs and postnatal progressive AV conduction defects. Unlike
individuals with HOS, these patients did not exhibit limb deformity (25). The
families in this cohort had members with various other CHMs, including VSD,
tetralogy of Fallot (TOF), subvalvular aortic stenosis, ventricular hypertrophy,
pulmonary atresia, and mitral valve malformations. In another case, Pauli et al.
(26) reported a patient with a distal 5q deletion, including the NKX2.5 locus
and who presented with an ASD, AV block, and ventricular myocardial
noncompaction.
Benson and colleagues (27) provided further evidence for a diverse role for
NKX2.5 mutations in a variety of forms of congenital heart disease, including
ASD, muscular VSD, VSD associated with TOF or double-outlet right ven-
tricle (DORV), tricuspid valve abnormalities, and familial cardiomyopathy.
Goldmuntz et al. (28) identified NKX2.5 mutations in nonsyndromic TOF and
estimated that NKX2.5 mutations account for at least 4% of such cases. In a
series of 114 prospectively enrolled individuals with TOF (in whom 22q11
deletions were excluded), they identified six individuals with NKX2.5 muta-
tions. The combination of right-sided aortic arch and pulmonary atresia were
more common in the mutation-positive group. The authors demonstrated that
reduced penetrance and variable expressivity were associated with these muta-
tions, and that AV conduction disease was not associated with mutations
located outside of the gene’s DNA-binding homeodomain.
NKX2.5 mutations are proposed to contribute to a small but significant pro-
portion of sporadic cases of ASD and hypoplastic left-heart syndrome (HLHS)
Genetics of Cardiac Septation Defects 27

(29). One hundred forty-six individuals with a diagnosis of secundum ASD

(n = 102), patent foramen ovale complicated by paradoxical embolism (n =
25), or HLHS (n = 19) were analyzed. Ten percent of the patients with ASD
or patent foramen ovale reported a family history of heart defects, and 4%
of the patients had AV block. A missense mutation, T178M, was identified
in an ASD family without AV block, and in one child in the family with
HLHS. A second previously reported disease-causing mutation, E21Q, was
also identified, but did not segregate with disease in a family with ASD,
leading one to question the significance of this variant. These findings also
highlight the difficulty in establishing whether unique sequence variants
found in isolated individuals with CHMs are truly responsible for disease
pathogenesis.
McElhinney et al. (30) reported NKX2.5 mutations in 3% of a population of
prospectively enrolled patients afflicted with the following CHMs: TOF,
secundum ASD (with and without AV block), truncus arteriosus, DORV, left
transposition of the great arteries, interrupted aortic arch, HLHS, and aortic
coarctation. Almost 90% of patients with NKX2.5 mutations in this group
reportedly had no family history of CHMs. Heterozygote status was confirmed
in some available parents, suggesting decreased penetrance of these mutations.
Interestingly, none of the 18 mutations, which consisted of missense muta-
tions, an in-frame deletion, and an insertion resulting in premature translation
termination, were localized to the homeodomain region. Thus, these studies
highlighted the importance of mutational analysis, suggesting NKX2.5 in
nonhomeodomain NKX2.5 regions.
Given the various cardiac phenotypes observed in the previously mentioned
families, the role of NKX2.5 in other forms of CHMs as well as cardiac mor-
phogenesis seems diverse. Although genotype–phenotype correlations have not
borne out, the variable expressivity among affected individuals may reflect
various interactions between NKX2.5 and other modifier genes. Located on
chromosome 5q35 (31), the NKX2.5 gene, the human homolog of Drosophila
gene, tinman, is a marker of the cardiac lineage and is expressed in atrial and
ventricular myocardium during development (32). Mutations in the Drosophila
gene, tinman, result in absence of the dorsal vessel, a relative of the vertebrate
heart (33). In vertebrates, NKX2.5 is an important regulator of cardiac-restricted
gene activity required during cardiogenesis; as demonstrated in mice deficient
in Nkx2.5, which died before looping of the linear heart tube (32). Biochemical
analysis of mutant proteins demonstrated NKX2.5 haploinsufficiency as a
cause of these cardiac defects (34). The wide range of NKX2.5 mutational car-
diac phenotypes suggests a primary involvement of this transcription factor
with other modifier genes at various stages of cardiogenesis. Ongoing efforts
to uncover the downstream targets and synergistic partners of NKX2.5 have
28 McDermott et al.

revealed a number of myocardial genes, including ANF, MLC-2v, N-Myc,

Msx2, eHAND, MEF2C (32), TBX5 (21), and GATA-4 (35).
1.3. Familial ASDs and VSDs: GATA4
A subset of familial, nonsyndromic cardiac septal defects has recently been
linked to mutations in GATA-4 (23), a member of the conserved GATA zinc-
finger transcription factor family. Before this, Pehlivan demonstrated that
individuals with a chromosomal deletion of 8p23.1, where GATA-4 localizes,
characteristically had a variety of cardiac septal defects (36). Taken together,
these data suggest that GATA-4 and, potentially, other 8p genes, regulate
septogenesis during cardiac development.
Initially, linkage of these CHMs to a single locus on chromosome 8p22–23
in a large, multigenerational family with an autosomal-dominant inheritance of
ASDs revealed the presence of GATA-4 within this region. Through sequence
analysis of GATA-4 in two large kindreds, Garg et al. (23) were able to associ-
ate two GATA-4 mutations with these congenital heart defects. Besides the
characteristic ASDs found in all affected members, individuals also presented
with a variety of other congenital heart defects, including VSDs, AV septal
defects (AVSDs), and pulmonic valvular stenosis. The association with AVSD
and conotruncal anomalies distinguishes this syndrome from HOS. Neverthe-
less, missense mutation of GATA-4 diminished DNA-binding activity and tran-
scriptional activity of the transcription factor, and it abrogated a physical
interaction between GATA-4 and TBX5.
GATA-4 mutations were not demonstrated in some ASD and VSD kindreds
that were analyzed (23). This observation, in addition to the finding that
GATA-4 is not consistently deleted in all individuals with CHMs who have 8p
mutations (36), suggests a role for other genes in close proximity to GATA-4 as
causative for the familial clusters. It is also conceivable that such genes may
mediate the effects of GATA-4 on cardiogenesis.
During mouse cardiogenesis, Gata-4 is expressed in the atrial and ventricu-
lar myocardium, endocardium, endocardial cushions, and outflow tract (37).
Disruption of Gata-4 in the mouse has revealed a phenotype that is consistent
with its expression pattern. Deletion of Gata-4 in mice causes arrested devel-
opment between embryonic days 7.0 and 9.5, caused by defects in cardiac
morphogenesis, specifically cardia bifida (38). However, Pu et al. (39) showed
that a conditional deletion of mouse Gata-4 leads to DORV, common AV canal,
and marked hypoplasia of both the trabecular and compact myocardium. In
vitro experiments using embryonic stem cells showed that GATA-4 is essential
for survival of cardioblasts and for terminal cardiomyocyte differentiation
(40,41). Several genes, such as α- and β-MHC, ANF, and cardiac TnC, are
transcriptionally regulated by Gata-4 (42) when studied by in vitro assays.
Genetics of Cardiac Septation Defects 29

Data also show that Gata-4 acts synergistically with Nkx2.5 to activate ANF
(43) as well as cardiac α-actin via the serum response factors (44), and is influ-
enced by interactions with FOG-2 to modulate GATA-dependent transcrip-
tional activation, thus, acting as either an activator or repressor (45,46). A
potentially cooperative relationship between TBX5 and GATA-4 (23) is
appealing, given the overlap in cardiac phenotypes associated with the muta-
tions in these genes.
1.4. Ellis–van Creveld Syndrome: EVC and
EVC2
Unlike other Mendelian forms of CHMs, Ellis van–Creveld syndrome (EvC)
is inherited in an autosomal-recessive manner (47). The hallmark features of
EvC are congenital heart defects, which occur in at least 50% of affected indi-
viduals, as well as chondroectodermal dysplasia and bilateral postaxial poly-
dactyly (48,49). Such findings have not been reported in syndromes with
septation defects caused by mutations in TBX5, NKX2.5, or GATA-4. Cardinal
cardiac features include ostium secundum or ostium primum ASDs, as well as
a common atrium. Complex CHMs have also been observed (48–52). Occa-
sional findings include polydactyly of the feet, and genitourinary anomalies
(49,51). EvC has been reported in a number of ethnic groups, but is particu-
larly common in the Lancaster County, PA Amish population, where more
than 12% of individuals are carriers for the disease, and approx 1 in 5000 people
are affected (50).
By studying affected families of Amish, Mexican, Ecuadorian, and Brazilian
descent, Polymeropoulos et al. (52) initially mapped the genetic locus for EvC
to chromosome 4p16.1. Subsequent positional cloning studies of affected
Amish individuals enabled investigators to identify the novel EVC gene at this
locus as a disease gene. The EVC protein is predicted to contain a leucine
zipper, as well as putative nuclear localization signals and a transmembrane
domain (53), but its function remains unknown. Galdzicka et al. (54) also iden-
tified the EVC2 gene. This gene is mutated in individuals affected by EvC, and
also localizes to chromosome 4p16. Ruiz-Perez et al. (55) reported mutations
in EVC2 in a number of other affected individuals of varying ethnicities, but
not in Amish families. EVC and EVC2 are arranged in the genome in a “head-
to-head” configuration, with transcription start sites separated by 2624 bp in
humans. Expression of EVC and EVC2 could be coordinated by the same pro-
moter or by shared elements of overlapping promoters (55). The EVC2 protein
is predicted to encode a transmembrane domain, three coil-coiled regions, and
a RhoGEF domain, and shares sequence homology to class IX nonmuscle myo-
sin tail domains, but is not homologous to EVC. Northern blot analysis of EVC2
revealed expression in the heart, placenta, lung, liver, skeletal muscle, kidney,
and pancreas (54). In situ hybridization of human embryonic tissue for EVC
30 McDermott et al.

revealed low levels of mRNA in the developing bone, heart, kidney, and lung.
Specifically, EVC expression was observed in the atrial and ventricular myo-
cardium, as well as the atrial and interventricular septa (53).
The availability of genetic testing, particularly in the setting of ultrasound
diagnosis (56), is an important advance in the management of at-risk pregnan-
cies and newborns with EvC. By identifying new mutations in the EVC and
EVC2 genes, more information can be gained to understand how these two
genes participate in cardiac and skeletal development. Further studies to eluci-
date the downstream targets may explain not only the mechanism by which
mutations in EVC and EVC2 lead to the manifestations of disease observed in
affected individuals, but also may explain the mechanism by which these mu-
tations produce either a skeletal or cardiac phenotype, or both.
1.5. VSD: 22q11.2 Genes and Other Candidates
VSDs are the most common form of CHM observed. They may occur as
isolated defects, or in conjunction with other CHMs, such as those discussed in
Subheading 1.3. VSDs are a common occurrence in individuals with 22q11-
deletion syndrome, also referred to as DiGeorge syndrome and velocardiofacial
syndrome (57,58). Individuals with 22q11 chromosomal deletions often have
characteristic facial features, palatal anomalies, mental/learning deficiencies,
and endocrine and immunological findings, in addition to the cardiovascular
defects. These characteristics aid in the diagnosis. McElhinney et al. (59)
sought to determine the contribution of 22q11 deletion to VSDs in a group of
125 prospectively enrolled individuals with conoventricular, posterior
malalignment, or conoseptal hypoplasia VSD. Although the authors identified
22q11 deletion in 10% of those individuals enrolled, the strongest predictors
for chromosomal deletion were anomalies of aortic arch branching or
sidedness, anomalies of the cervical aortic arch, or discontinuous pulmonary
arteries in conjunction with VSD. In general, the contribution of 22q11 dele-
tion to certain isolated VSDs is predicted to be minimal.
Recent evidence suggests that many features associated with DiGeorge syn-
drome are caused by haploinsufficiency of the TBX1 gene, a member of the T-
box gene family (60–62). Mice with a hemizygous deletion of the 1.5-Mb region
corresponding to human chromosome 22q11 exhibited conotruncal and par-
athyroid defects. After insertion of a human bacterial artificial chromosome
containing the TBX1 gene, however, only the conotruncal defects could be par-
tially rescued (62). Individuals who have the phenotypical features of 22q11.2-
deletion syndrome, but have intact 22q11.2 chromosomes, have been shown to
have mutations in TBX1, which localizes to this chromosomal region. Thus,
TBX1 may be a major determinant of the 22q11.2-deletion syndrome (63).
Genetics of Cardiac Septation Defects 31

Membranous VSD, with variable muscular septal involvement, has been

observed in association with biventricular cardiomyopathy in transgenic mice
lacking Hey-2/CHF1 (64). Based on its expression pattern, Hey-2/CHF1 has
been implicated in the development of the ventricle, vasculature, somites, and
retina (65,66). The Drosophila gene, gridlock, a member of the hairy/enhancer
of split-related family of genes, is expressed in a pattern similar to the mouse
Hey genes, and functions downstream of Notch (67). Although these genes
have yet to be implicated in human CHMs, other Notch ligands have been
implicated. Mutations in the JAG1 gene, a Notch-receptor ligand, result in the
autosomal dominantly inherited Alagille syndrome (68,69), a multisystemic
disorder with frequent cardiac involvement. Primarily, peripheral pulmonic
stenosis occurs, although ASD, VSD, and TOF can also occur.
1.6. AV Septal Defects
AVSDs, also referred to as endocardial cushion defects or AV canal defects,
result from developmental anomalies of the AV canal. The resulting AVSDs
can range in severity and complexity, and may be partial (atrial or ventricular
form) or complete (involve atrial and ventricular septa), which could reflect a
polygenic basis for the various clinical presentations.
Epidemiological data on AVSDs from the Baltimore–Washington infant
study have supported the idea of genetic heterogeneity and have provided other
useful information regarding the various subtypes of AVSD (70). Family his-
tory of CHMs is more commonly observed in individuals with the complete
form of AVSD and with the partial atrial form. Also of note, complete AVSD
and the partial ventricular form are more likely to occur in association with
extracardiac anomalies, whereas nearly 55% of the partial atrial form occur as
an isolated finding (70). Preconceptual maternal diabetes is a risk factor for the
complete form of AVSD, as well as other cardiac and noncardiac complica-
tions in newborns, thus, highlighting the importance of eliciting a detailed preg-
nancy history in the evaluation of such cases (71).
In humans, AVSDs are most commonly associated with Down syndrome
(trisomy 21). Down syndrome cell adhesion molecule has been proposed as a
candidate gene for CHMs associated with Down syndrome (70). AVSDs are
also commonly associated with other chromosomal anomalies, including 3p25
deletion, 8p2 deletion, trisomy 13, and trisomy 18, often presenting as ven-
tricular AVSDs (70,72). Such chromosomal etiologies are generally character-
ized by additional clinical manifestations, including mental and growth
retardation, as well other multiple congenital anomalies. AVSD is occasion-
ally detected in Turner syndrome (chromosomal complement 45,X) and
22q11.2-deletion syndrome (72). Autosomal-dominant AVSD, exhibiting
32 McDermott et al.

incomplete penetrance and variable expressivity, has also been reported, with
linkage to chromosomes 1p31–p21 and 3p25 (73,74).
The CRELD1, or cirrin, gene was proposed as an AVSD candidate gene on
3p25. CRELD1 is a cell adhesion molecule that is expressed during heart
development (75). Robinson and colleagues (76) analyzed the CRELD1 gene
in individuals with both the complete and partial forms of AVSD. They
reported distinct missense mutations in three patients, two patients with iso-
lated partial AVSD (ostium primum ASD) and one patient with AVSD and
heterotaxy. There were no mutations identified in 13 individuals with com-
plete AVSD, suggesting genetic heterogeneity among the various subtypes.
Each of the detected mutations occurred at highly conserved amino acid resi-
dues. Paternal inheritance was confirmed in one of the individuals with iso-
lated partial AVSD, and the mutation was also detected in two of the subject’s
siblings. Neither the father nor the siblings had any identifiable CHM on
echocardiogram, suggesting incomplete penetrance. These findings prompted
Robinson et al. (76) to conclude that CRELD1 is an AVSD susceptibility gene
and that mutations in CRELD1 are associated with an increased risk of devel-
oping partial AVSDs.
In some cases, Noonan syndrome, an autosomal-dominant, genetically het-
erogeneous syndrome that occurs in approximately every 1 in 1000 to 2500
live births, has been shown to result from mutations in the PTPN11, or SHP-2,
gene on chromosome 12q24.1 (77). This gene has been demonstrated to have a
role in cardiac semilunar valvulogenesis, among other developmental activi-
ties. The CHMs typically associated with Noonan syndrome are pulmonic
stenosis and hypertrophic cardiomyopathy, although AVSD has been reported
in approx 15% of cases (78). Individuals with Noonan syndrome also com-
monly have other diagnostic features, including webbed neck, dysmorphic
facial features, proportionate short stature, chest deformity, cryptorchidism,
mental retardation, and bleeding diatheses. Mutations in PTPN11 have also
been identified in individuals with multiple lentigines, electrocardiographic-
conduction abnormalities, ocular hypertelorism, pulmonary stenosis, abnormal
genitalia, retardation of growth, and sensorineural deafness syndrome (79).
AVSD has been reported, although very rarely, in individuals suggested to
have other Mendelian syndromes (e.g., EvC and HOS), but genetic analyses of
genes associated with these syndromes have not been reported to confirm these
clinical diagnoses. Similar to EvC, many autosomal-recessive syndromes in
which AVSD and other CHMs have been observed involve skeletal abnormali-
ties. McKusick–Kaufman syndrome, similar to EvC, is common in the Amish
population and is caused by mutations in the MKKS gene on chromosome
20p12 (80). This gene encodes a protein similar to the chaperonin proteins.
Genetics of Cardiac Septation Defects 33

Clinical features include hydrometrocolpos in females, postaxial polydactyly,

and CHMs. The autosomal-recessive oral–facial–digital syndromes, including
short-rib polydactyly, have also been reported to have a risk for AVSD.
In addition to the syndromes discussed in Subheading 1.6., AVSD is also
commonly seen in association with developmental defects involving left–right
axis formation. One example is Ivemark syndrome, characterized by asplenia,
CHMs (mostly ASDs, AVSDs, and conotruncal malformations) (81), malposi-
tion and maldevelopment of the abdominal organs, and abnormal lobation of
the lungs. Ivemark syndrome is a recessive condition, but is most often spo-
radic.
Individuals with Smith–Lemli–Opitz syndrome, a recessive condition
caused by mutations in the sterol δ-7-reductase on chromosome 11q12–q13
(82), are also afflicted with AVSDs. In one report, approx 21% affected indi-
viduals had a diagnosis of AVSD (83). Other common features of Smith–
Lemli–Opitz include failure to thrive, low birth weight, dysmorphic facies,
renal anomalies, genital anomalies in males, postaxial polydactyly, mental
retardation, and low cholesterol levels.
1.7. Pre-Implantation Genetic Diagnosis for Congenital Heart Defects
The ability to offer genetic testing for CHM has been limited until recent
years. Now that several causative gene defects, as discussed in Subheadings
1.1.–1.7., have been identified for some cases of familial CHMs, increasing
numbers of options are available. Before identification of these genes, couples
interested in prenatal diagnosis for CHMs were limited to genetic counseling
and general recurrence risk assessments, and to imaging modalities (such as
ultrasound) or testing for chromosomal causes of CHMs in conjunction with
amniocentesis or chorionic villus sampling. With the identification of single
genes responsible for Mendelian forms of CHMs, the ability to offer pre-
implantation genetic diagnosis (PGD) in combination with in vitro fertilization
(IVF) is now a potential option for some couples who prefer earlier diagnosis
than afforded by amniocentesis or chorionic villus sampling.
Successful PGD for CHM has been achieved for a pregnancy at 50% risk for
HOS (84) in a couple pursuing IVF for premature ovarian failure. The proband
had a previously reported mutation in exon 3 of TBX5, predicting a truncated
protein(Glu69ter) (14). The proband and his spouse wished to achieve a preg-
nancy unaffected by HOS, if possible.

2. Materials
1. TBX5 oligonucleotide primers.
2. Polymerase chain reaction (PCR) reagents and equipment.
34 McDermott et al.

3. DNA-sequencing equipment.
4. DNA from single blastomeres and genomic DNA from parents and controls.
5. DNA restriction enzymes.
6. Lymphocyte separation gradient.
7. Single-cell separation methods.

3. Methods
3.1. IVF and Blastomere Biopsy
IVF procedures, intracytoplasmic sperm injection (ICSI), and blastomere
biopsies were performed by the Cornell Center for Reproductive Medicine and
Infertility using standard techniques (85,86). This particular case required syn-
chronization of an oocyte donor and the proband’s spouse. Sperm from the
proband, who has a personal history of HOS, was used for ICSI. Informed
consent was obtained for all clinical procedures, blastomere biopsies, and
genetic testing, in accordance with Weill Medical College of Cornell Univer-
sity Committee on Human Rights in Research.
3.2. Sequence Analysis for TBX5 Glu69ter Mutation
DNA was isolated from single blastomere biopsies. Biopsies were performed
at 3 d after fertilization on five blastocysts obtained from fertilization (by ICSI)
of five donor oocytes, using methods previously described (85). DNA was iso-
lated from peripheral blood samples from the proband (positive control het-
erozygous for Glu69ter), as well as the oocyte donor (negative control), who
was previously determined not to carry a TBX5 mutation by bidirectional
sequence analysis of protein-coding exons 2 to 9.
Exon 3 of TBX5, as well as its flanking introns, was amplified from the
blastomeres using a nested PCR approach. This approach was used because of
the limited template DNA able to be isolated from these single cells. The valid-
ity of this method was confirmed by analyses of single lymphocytes isolated
from whole-blood samples from the proband, the oocyte donor, and controls,
in anticipation of testing the blastomeres.
Lymphocytes were separated from whole-blood samples by Ficoll–Paque den-
sity gradient, using previously described techniques (14). Single lymphocytes
were selected by direct micropipetting. Single lymphocytes and blastomeres were
prepared using techniques described by Xu et al. (86). Single cells and blas-
tomeres were placed into 500-μL microcentrifuge tubes, stored at –30°C with 25
μL of lysis buffer. These samples were heated at 65°C for 10 min and placed
immediately on ice, and 5 μL of neutralization buffer was added.
PCR was performed using standard techniques previously described for
amplification of exon 2 and exons 4 to 9 of TBX5. A nested PCR approach was
used to amplify exon 3. First-round PCR for exon 3 and its flanking introns
Genetics of Cardiac Septation Defects 35

was performed using primers 3GRN2 (5'-GGAAGGAGGAGCAGTCTC

TGTGTT-3') and 3GFN (5'-GTGTCTTTTCTCCTCGTCCCTCTCTCTAC
ACA-3') (84). Standard PCR reagents and AmpliTaqGold polymerase (Applied
Biosystems [ABI], Foster City, CA) were used with PCR conditions of 40
cycles of (95°C for 20 s; 67°C for 30 s; and 72°C for 45 s). The resultant PCR
product was 242 bp.
Second-round PCR (final volume, 50 μL) was performed using 6 μL of first-
round PCR product (1:100 dilution) as a template. Nested primers for the sec-
ond-round PCR amplification of exon 3 were: 3GRN (5'-AGTTTGGGG
AAGGAATGCCCACTAC-3') and 3GF1 (5'-GTGTCTTCTACACAACAA
ACCATCTCACCTT-3') (84). PCR was again performed with standard
reagents and AmpliTaq Gold polymerase with PCR conditions of 35 cycles of
(95°C for 20 s; 65°C for 30 s; and 72°C for 45 s). The product of the second-
round amplification was 182 bp. Negative controls were included in both
rounds of PCR. Two second-round PCR reactions were performed in parallel.
One reaction used a NED fluorescent dye (ABI)-labeled 3GRN (84) primer to
allow for visualization of restriction fragment length polymorphism (RFLP)
products. After PCR amplification, sequence and RFLP analysis of the PCR
products were performed.
Bidirectional sequence analysis was performed on an ABI 377 automated
sequencer, using BigDye Terminator sequencing (ABI) reagents, according to
the manufacturer’s recommended techniques.
3.3. RFLP Analysis
Twenty-five microliters of amplified PCR product were digested with DdeI
[4U] (Promega, Madison, WI) for 90 min at 37°C and analyzed by gel electro-
phoresis, as previously described (14). The presence of the Glu69ter mutation
resulted in a 123-bp product that could be visualized because of the use of the
fluorescent 3GRN primer (see Notes 1 and 2).
Four of the five blastocysts were determined to be homozygous normal for
TBX5. One blastocyst was determined to carry the Glu69ter mutation. The four
normal blastocysts continued to grow well in culture after the blastomere biop-
sies. Two of the four blastocysts were transferred to the recipient. The two
remaining blastocysts that were TBX5 homozygous normal were cryopreserved
through the clinical IVF program at Cornell for future transfer (see Note 3).
3.4. Clinical Follow-Up
Confirmation of pregnancy was confirmed by serum β-human chorionic
gonadotropin. High-resolution ultrasound and amniocentesis were performed
in the second trimester. There were no ultrasound anomalies suggestive of
HOS. Sequence and RFLP analysis of DNA extracted from waste amniocytes
36 McDermott et al.

confirmed the homozygous normal TBX5 genotype. Clinical karyotype was

normal. At delivery, cord blood was obtained for TBX5 genotyping, which
again was normal.
3.5. Conclusion
We have discussed several human genetic disorders that have primary
malformations of the atrial and/or ventricular septa. Although great strides have
been made in our understanding of the molecular basis of cardiac develop-
ment, specifically septation of the heart, many modulatory genes and signaling
pathways remain unknown or poorly characterized. Gene mutations may cause
a spectrum of cardiac defects. Not yet available on a routine clinical basis,
molecular genetic testing is performed via scientific research protocols. Muta-
tional screening of genomic DNA derived from patient blood samples is rou-
tinely performed using DNA confirmation-sensitive techniques and automated
sequencing. Although these standard genetic testing methods have allowed
basic scientists to rapidly screen numerous kilobases of genomic DNA, they
remain costly and are often not reimbursable by the patient’s health insurance
coverage. In the future, molecular genetic testing will become more readily
available as a standard clinical diagnostic test, allowing clarification of risks
for an individual’s family members, for reproductive options, and for possible
progression of their own cardiac disease. Choosing which specific genes to be
analyzed based on specific clinical presentation of probands will remain a criti-
cal challenge.

4. Notes
1. RFLP analysis has been successfully used for identification of gene mutations in
individuals (14). The presence of an RFLP is detected in DNA products obtained
from PCR amplification. Although RFLP analysis could be performed on pri-
mary PCR products, the yield of DNA obtained after PCR amplification from
single-cell biopsies is rather low in many cases. Therefore, it may be necessary to
perform a nested PCR reaction by using the product from the primary PCR as a
template and to perform the RFLP analysis on the DNA generated from this sec-
ondary PCR reaction (84,86).
2. The presence of a mutation should be confirmed by both sequence and RFLP
analyses of two distinct nested PCR reactions. It is necessary to examine two
distinct nested PCR reactions to exclude the likelihood that PCR-induced errors
have been introduced in the DNA (84,86).
3. After we successfully performed PGD for HOS using the assay design presented
in Subheading 3.2., the usefulness of coamplifying flanking single tandem
repeats to address preferential allelic amplification has been suggested, and such
a strategy should be taken into consideration when designing PGD assays (87).
Genetics of Cardiac Septation Defects 37

Acknowledgments
The authors are grateful to the patients and their physicians. Dr. Basson is an
Established Investigator of the American Heart Association and an Irma T. Hirschl
Scholar. Dr. Hatcher is supported by National Institutes of Health grant
K01HL080948. This work was also supported by the Smart Cardiovascular Fund.

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DiGeorge/Velocardiofacial Syndrome 43

3
Molecular and Genetic Aspects
of DiGeorge/Velocardiofacial Syndrome

Deborah A. Driscoll

Summary
Cytogenetic, molecular, and clinical genetic studies have contributed to our understanding
of the etiology, pathogenesis, and natural history of DiGeorge syndrome (DGS) and
velocardiofacial syndrome (VCFS). Submicroscopic deletions of chromosome 22q11.2 are the
leading cause of both of these disorders. The 22q11.2 deletion syndrome is recognized as one
of the most common microdeletion syndromes. The clinical features are highly variable and
include a variety of congenital anomalies, medical problems, and cognitive and neuropsycho-
logical difficulties.
Infrequently, other chromosomal rearrangements are found in patients with DGS/VCFS,
and, rarely, point mutations in the gene TBX1, a transcription factor, that maps to the deleted
region. The most sensitive and widely used diagnostic test for detecting the 22q11.2 deletion is
fluorescence in situ hybridization using probes from the commonly deleted region. Alterna-
tively, polymerase chain reaction can be performed to confirm failure to inherit a parental
allele in the region or to determine copy number. Prenatal diagnosis is also available, particu-
larly when a conotruncal cardiac defect is identified during a pregnancy or when a parent car-
ries a deletion. Genetic counseling is recommended before testing to review the natural history
of the disorder, testing options, and test sensitivity and limitations.
Key Words: 22q11.2 deletion; DiGeorge syndrome; velocardiofacial syndrome; fluores-
cence in situ hybridization.

1. Introduction
DiGeorge syndrome (DGS) was initially recognized in 1965, in a group of
children with congenital absence of the thymus and parathyroid glands (1).
Later, congenital heart defects and facial dysmorphia were also considered clas-
sic features (2). Until the mid-1990s, DGS was considered a relatively rare
sporadic developmental defect of the third and fourth pharyngeal arches (3).
During the past decade, numerous cytogenetic, molecular, and clinical genetic
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

43
44 Driscoll

studies of patients with DGS have contributed to our current understanding of

this disorder. Not long after the discovery that deletions of chromosome
22q11.2 are the leading cause of DGS, studies identified deletions in individu-
als with velocardiofacial syndrome (VCFS) and conotruncal anomaly face syn-
drome (CTAFS) (4–7). Shortly thereafter, it became apparent that deletions of
22q11.2 were a frequent cause of conotruncal cardiac malformations (8).
Today, diagnostic testing for the 22q11.2 deletion is widely available and DGS/
VCFS is recognized as one of the most common microdeletion syndromes, and
a frequent cause of congenital heart disease.
1.1. Clinical Features
The classic features of DGS/VCFS include congenital heart defects, immune
deficiencies secondary to aplasia or hypoplasia of the thymus, hypocalcemia
caused by small or absent parathyroid glands, palatal anomalies, and speech
and learning difficulties. In addition to case reports and smaller series, there
are several recent large, prospective studies that have contributed to our knowl-
edge of the types and frequency of congenital anomalies, medical problems,
and cognitive and neuropsychological difficulties that these patients are likely
to develop (9–11). Cardiovascular malformations found in 70 to 80% of DGS/
VCFS patients, typically involve the conotruncus and outflow tract including
interrupted aortic arch type B, truncus arteriosus (TA), tetralogy of Fallot
(TOF), and aortic arch anomalies. Although some patients can have a profound
immunodeficiency, requiring thymic transplantation, many maintain reason-
able lymphocyte counts. Characteristic facial features have been described,
which include a long face, a prominent nose with a bulbous nasal tip and nar-
row alar base, almond-shaped or narrow palpebral fissures, malar flattening,
recessed chin, hooded eyelids, and low-set prominent ears. Palatal abnormali-
ties, including cleft palate, submucous cleft palate, and velopharyngeal insuffi-
ciency, occur in approx 70% of DGS/VCFS patients. Other features include
feeding difficulties, renal anomalies, inguinal and umbilical hernias, skeletal
abnormalities, short stature, juvenile rheumatoid arthritis, hematological
abnormalities, neural tube defects, craniosynostosis, diaphragmatic hernia, and
hypospadias.
Neuropsychological evaluations indicate that these children are at risk for
cognitive impairment and neurological and psychiatric problems (9–13). Sei-
zures, asymmetric crying facies, ataxia, polymicrogyria, and cerebellar hypo-
plasia have been reported. A wide range of developmental outcomes has been
documented in children with the 22q11.2 deletion. Approximately 80% of these
children demonstrate significant motor delay. Expressive and receptive lan-
guage is delayed in more than three-fourths of these children. Cognitive devel-
opment ranges from normal intelligence to moderate retardation. Studies have
DiGeorge/Velocardiofacial Syndrome 45

found that verbal IQ scores are significantly higher than performance IQ scores
and suggest that these children are at risk for nonverbal learning disabilities.
Attention deficit disorder, with or without hyperactivity, emotional difficul-
ties, anxiety, and shyness, has been observed. There also seems to be a higher
than expected rate of psychiatric disorders, including depression, schizophre-
nia, and bipolar disorder, in adolescents and adults with the 22q11.2 deletion.
A wide range of phenotypic variability is associated with the 22q11.2 dele-
tion. Although some individuals present with classic findings of DGS/VCFS,
others have relatively subtle features, such as minor dysmorphic facial features
and mild cognitive impairment. Other disorders associated with the 22q11.2
deletion include CTAFS, Opitz/GBBB syndrome, and Cayler cardiofacial syn-
drome (asymmetric crying facies) (14–16).
1.2. Etiology
Deletions of chromosomal region 22q11.2 are the leading cause of DGS/
VCFS. Interstitial and submicroscopic deletions have been detected in approx
90% of patients with the diagnosis of DGS (17). The frequency of 22q11.2
deletions reported in VCFS patients is 76 to 81% (17,18). Chromosome
22q11.2 deletions were found in 84% of patients diagnosed with CTAFS (14).
Deletions of 22q11.2 are estimated to occur in as many as 1 in 4000 live births.
The estimated annual incidence in the Flemish region of Belgium in 1992–
1996 was 1 in 6395 newborns (19). A similar incidence of 1 in 5950 births
(95% confidence interval, 1 in 4417 to 1 in 8224) was reported in a large popu-
lation-based study in the United States. It has been estimated that 700 children
are born with the 22q11.2 deletion each year in the United States alone (20).
Less frequently, haploinsufficiency for this region of 22q11 occurs because
of an unbalanced translocation with monosomy 22pter→q11.2 (21). In rare
instances, DGS has been associated with other chromosomal abnormalities, in
particular, deletions of the short arm of chromosome 10 (del[10][p13]). Other
chromosomal rearrangements reported in association with DGS include mono-
somy and trisomy 18q, monosomy 18p, monosomy 12p with trisomy 1q, mono-
somy 5p, partial trisomy 1q, and duplication 9q (22). DGS may also occur
because of in utero retinoic acid and alcohol exposure, and poorly controlled
maternal insulin-dependent diabetes (3).
The 22q11.2 deletion is a common cause of conotruncal cardiac malforma-
tions. The reported frequency of the 22q11.2 deletion among individuals with
conotruncal cardiac defects is highly variable because of differences in ascer-
tainment and inclusion criteria. A large, prospective study of infants and chil-
dren with conotruncal cardiac defects, ascertained by cardiologists, reported
an overall deletion rate of 18% (23). However, the probands in this study were
not evaluated for the presence of extracardiac malformations, phenotypic fea-
46 Driscoll

tures of DGS/VCFS, or dysmorphia. Studies report lower detection rates when

only individuals with isolated, nonsyndromic cardiac defects are included.
Fokstuen et al. identified a 22q11.2 deletion in 8% of 110 cardiac patients, but
all of the patients with the deletion had additional anomalies or dysmorphisms,
whereas none of the isolated cases had the deletion (24). Voight et al. identi-
fied 22q11.2 deletions in only 2 of 81 patients with isolated TOF (25). The
majority of cardiac patients with the 22q11.2 deletion will have multiple minor
anomalies and dysmorphic features (20,24). In some cases, the dysmorphic
features can be very subtle, and features such as speech delay and learning
difficulties cannot be evaluated in a newborn or infant child (10).
The deletion frequency varies with the primary cardiac diagnosis and is
higher in patients with associated aortic arch abnormalities. Deletions of
22q11.2 occur in 50 to 82% of patients with an interrupted aortic arch, in par-
ticular, type B (23,26,27). Deletions of 22q11.2 have been identified in 30 to
40% of patients with TA (28,29). Patients with TA were more likely to have a
22q11.2 deletion in the presence of a right aortic arch and/or abnormal aortic
arch branching patterns (29). This also held true for ventricular septal defects
(VSD). In a prospective study of 125 patients with a conoventricular, posterior
malalignment, or conoseptal hypoplasia VSD, 10% had a 22q11.2 deletion. Of
these patients, 45% had an abnormal aortic arch laterality, abnormal aortic arch
branching patterns, or discontinuous pulmonary arteries had a deletion;
whereas only 3% of VSD patients with a normal aortic arch and normal branch
pulmonary arteries had a deletion (30). Approximately 16% of patients with
TOF have a 22q11.2 deletion (23,31). Deletions of 22q11.2 are rarely seen in
patients with transposition of the great arteries and double-outlet right ven-
tricle, but, when they occur, they are usually associated with anomalies of the
pulmonary artery, aortic arch, or ductus arteriosus (23,32).
1.3. Diagnostic Testing for DGS/VCFS
As part of the evaluation of an infant or child with suspected DGS/VCFS, a
karyotype and testing for the 22q11.2 deletion is recommended. When a chro-
mosomal abnormality is identified (translocation or deletion), then parental
testing is indicated. The value of testing patients with conotruncal defects has
been debated (33,34). There is no doubt that the 22q11.2 deletion is a signifi-
cant cause of some types of outflow tract defects; the presence of this deletion
should prompt a more thorough evaluation of the patient to look for
extracardiac manifestations. However, some of these features are subtle or may
not be apparent until childhood. Early identification of the deletion can lead to
increased awareness of possible medical problems and speech and learning
difficulties, and, thus, to earlier intervention (34,35). Further, early identifica-
DiGeorge/Velocardiofacial Syndrome 47

tion will assure that familial cases are identified and that families receive accu-
rate counseling of their risk and reproductive options in subsequent pregnan-
cies. Therefore, diagnostic testing for the 22q11.2 deletion is recommended in
patients with features of DGS/VCFS or a conotruncal cardiac defect, particu-
larly in the presence of aortic arch and pulmonary artery anomalies.
Indications for prenatal testing include the following:
1. Previous child with DGS/VCFS or the 22q11.2 deletion.
2. Parent with 22q11.2 deletion or mosaicism for the deletion.
3. Conotruncal cardiac defect is identified in utero (36,37).
Pre-implantation genetic diagnosis has been reported in a mildly affected
parent with a 22q11.2 deletion (38). The risk of an affected child in this case is
50%. Unaffected parents, without a deletion, who have had a previous child
with DGS/VCFS may consider prenatal testing because of the small possibility
of germline mosaicism (39,40).
Although there are several types of tests available, fluorescence in situ
hybridization (FISH) has become the standard method of choice for clinical
diagnosis and prenatal testing for the 22q11.2 deletion (17,36,41). In some
circumstances, polymerase chain reaction (PCR)-based studies may be help-
ful. Mutation analysis has been performed in a research setting but has not
been particularly useful clinically.
1.3.1. Cytogenetic Analysis
High-resolution cytogenetic analysis detects up to 25% of interstitial dele-
tions in the chromosome 22q11.2 region (6,42). The majority of deletions are
submicroscopic and are only detected by FISH. However, a karyotype is still
valuable for identifying other chromosomal rearrangements that have been
reported in patients with DGS, including translocations. Correct identification
of a cytogenetic abnormality in these patients has important implications for
their recurrence risk.
1.3.2. Fluorescence In Situ Hybridization
FISH is a sensitive and efficient test to detect submicroscopic deletions (see
Subheadings 2. and 3.). It is routinely used in commercial and hospital-based
cytogenetic laboratories as an adjunct to a routine karyotype. FISH can be per-
formed on metaphase spreads or interphase nuclei from peripheral blood lym-
phocytes, cultured amniocytes, or chorionic villi. FISH has also been used on
blastomeres obtained from a 6- to 10-cell embryo (38). In addition to testing
for the 22q11.2 deletion, FISH has also been used to simultaneously detect
chromosome 10p13p14 deletions in patients with features of DGS/VCFS (43).
48 Driscoll

2. Materials
1. Slides with chromosome preparations.
2. LSI DiGeorge/VCFS region/ARSA dual-color DNA probe (Vysis, Downers
Grove, IL).
3. 70, 80, and 100% ethanol.
4. LSI hybridization buffer (Vysis).
5. 50 and 70% formamide.
6. 2X standard sodium citrate (SSC).
7. 0.1% NP-40.
8. DAPI solution.
9. Cover slips.
10. Rubber cement.
11. Coplin jars.
12. Water baths.
13. Incubator.
14. Humidified box.
15. Slide warmer.
16. Fluorescence microscope equipped with a triple-band filter.

3. Methods
A detailed protocol and reagents, including labeled probes, are available from
Vysis (Downers Grove, IL). The test probes from the DiGeorge minimal criti-
cal region are cosmid clones for loci D22S75 (N25) and TUPLE1. The control
probe, arylsulfatase A (ARSA), maps to 22q13.3 and is used to ensure proper
hybridization (see Note 1). If commercial probes are not available, cosmids
from the commonly deleted region can be labeled with Spectrum–Orange–
dUTP (Vysis) by nick translation. An internal control probe for the distal long
arm of chromosome 22 is always recommended. FISH is performed on glass
slides with metaphase chromosomes or interphase nuclei. The slides are dena-
tured in 70% formamide/2X SSC, dehydrated in a series of ethanol washes (70,
85, and 100%), and air-dried. The probes are denatured in hybridization buffer
at 73 to 74°C. The probe is applied to the slides and allowed to hybridize in a
moist chamber overnight (12–16 h) at 37°C. A series of washes with formamide,
SSC, and NP-40 are performed at 46°C to remove the excess probe. Slides are
air dried and counterstained with DAPI to permit identification of the chromo-
somes. The slides are viewed with a fluorescence microscope. The test probe
from the DGS critical region appears orange; a single hybridization signal is
consistent with a deletion. The control probe that maps to the distal long arm,
22q13.3, appears green, and two signals should be present. Rarely, absence of a
signal from the control probe occurs and indicates a deletion of 22q13.3 (see
Note 1). At least 15 metaphases should be analyzed.
DiGeorge/Velocardiofacial Syndrome 49

3.1. Characteristics of the 22q11.2 Deletion

The vast majority of DGS/VCFS patients have a common 3-Mb deletion of
22q11.2. The majority of these deletions arise de novo. The deletion endpoints
are identical and have been shown to contain large (250–500 kb) blocks of
highly homologous chromosome low-copy repeats that predispose to aberrant
interchromosomal exchange events in proximal chromosome 22 during meio-
sis I (44,45). Crossover frequency is not related to proband gender, parental
age, or the presence of chromosome inversions (45). Further, no bias in paren-
tal origin of the deletion was found. The extent and size of the deletion can be
determined with FISH, using pairs of probes labeled with different colors.
However, because the size and location of the deletion within this region does
not seem to correlate with the phenotype, it is not recommended for clinical
use. Smaller deletions (1.5 Mb) within the commonly deleted region occur in
approx 15% of patients. The smaller deletions seem to be mediated by smaller
duplicated blocks of repeats (44).
3.2. Conclusion
In summary, genetic counseling is highly recommended when testing an af-
fected child or an at-risk pregnancy and should include a discussion of the clini-
cal features, the variability, the etiology, and the diagnostic tests, including the
test sensitivity and limitations. In general, FISH is a reliable and accurate test
for detecting the 22q11.2 deletion and is usually used as an adjunct to a routine
karyotype. Occasionally, the FISH assay can be difficult to interpret and re-
quire additional studies (see Notes 1–3). In some laboratories or situations,
PCR-based testing may be preferable to FISH. PCR is an efficient and cost-
effective method of screening patients for a deletion, and requires only a small
amount of DNA. It also eliminates the need to culture and harvest peripheral
blood lymphocytes, and to prepare metaphase chromosome spreads. Further, a
variety of sources of DNA can be used, including cheek swabs and postmortem
and paraffin-embedded tissue. Two types of PCR-based assays have been
developed as an alternative to FISH for the detection of the 22q11.2 deletion.
These alternatives to FISH are described in Notes 4 and 5.

4. Notes
1. Control probe absent. Infrequently, one of the control probes may fail to hybrid-
ize. This hybridization failure is highly suggestive of a distal deletion of chromo-
some 22q13.3 and should be confirmed using a chromosome 22-specific
subtelomeric probe. This may occur because of a terminal deletion or a
malsegregation of a subtle balanced translocation. In these cases, it is helpful to
analyze the parental chromosomes and to perform FISH with the chromosome
22-specific probes.
50 Driscoll

2. No evidence of 22q11.2 deletion in a patient with DGS/VCFS. Although the

22q11.2 deletion is the most common cause of DGS/VCFS, 10 to 15% of indi-
viduals with DGS/VCFS do not have a deletion in this region. A small number of
DGS/VCFS cases will result from another chromosomal abnormality, therefore,
a karyotype is recommended. Rarely, a point mutation may be implicated (see
Note 3). In some cases, a definitive etiology may not be identified. This is par-
ticularly true in a prenatal setting, in which most cases are suspected because of
an abnormal fetal echocardiogram. Because the detection rate for 22q11.2 dele-
tions varies with the type of cardiac defect, unless there are extracardiac anoma-
lies suggestive of DGS/VCFS, the detection rate will be much lower. Clinicians
are often perplexed when a patient with clinical features highly suggestive of
DGS or VCFS has a negative 22q11.2 deletion result (i.e., no evidence of a
22q11.2 deletion) and an apparently normal karyotype. The probes that are com-
mercially available (D22S75 [N25] and TUPLE1) are from the DGS/VCFS criti-
cal region and are deleted in the overwhelming majority of DGS/VCFS patients.
However, there have been a few reports of rare deletions outside of this region
(46,47). In research laboratories, it has been possible to characterize these dele-
tions using FISH with cosmid clones from region 22q11.2. Mutation studies of
patients with no evidence of a 22q11.2 deletion have also been performed (see
Note 3).
3. Mutation analysis. Approximately 25 genes reside within the commonly deleted
region of 22q11.2. Many of these genes have been considered as candidates for
DGS/VCFS, however, there is now compelling evidence that TBX1 is the caus-
ative gene (48–50). Heterozygous mice for a null mutation in Tbx1 develop the
outflow tract anomalies seen in DGS. Furthermore, the homozygous mutants have
other characteristic features, including abnormalities of the thymus, parathyroid
gland, facial structures, and cleft palate. Until recently, most studies had failed to
find mutations in several genes in the deleted region, including TBX1, in patients
without the 22q11.2 deletion who were diagnosed with DGS/VCFS,
nonsyndromic conotruncal malformations, or aortic arch anomalies (49,51,52).
Yagi et al. sequenced the TBX1 coding regions and identified three mutations in
two unrelated individuals and in three affected family members (53). These
patients all had features of either CTAFS or DGS, yet there was no evidence of
cognitive impairment that is common in the 22q11.2-deletion syndrome. These
studies suggest that TBX1 mutations are a rare cause of the physical manifesta-
tions in DGS/VCFS.
4. PCR-based analysis of microsatellite markers. Short tandem repeat polymor-
phisms or microsatellite markers within the commonly deleted region on chro-
mosome 22q11.2 can be used to detect a deletion by demonstrating failure to
inherit a parental allele (54,55). Using microsatellite markers from within the
commonly deleted region in infants with conotruncal cardiac malformations,
Bonnet et al. have confirmed or rejected a diagnosis of 22q11.2 deletion in 94%
of cases within 24 h (55). These markers are also useful for looking for loss of
heterozygosity in patients at risk for the deletion. The assay has a 100% sensitiv-
DiGeorge/Velocardiofacial Syndrome 51

ity and high specificity (85% or higher) when three or more markers in the region
proximal to locus D22S264 were used (54). Because the PCR-based assay is cost
efficient and rapid, it lends itself to population-based or newborn screening. The
assay requires a sample of DNA from blood, a cheek swab, dried blood spots, or
pathological specimens. A positive screen should be followed either by FISH to
confirm the presence of a 22q11.2 deletion or by parental studies to document
failure to inherit a parental allele. A negative screen in a patient suspected of
having DGS/VCFS does not exclude the possibility of a smaller deletion. Haplo-
type analysis using these markers has also been used to confirm or exclude
germline mosaicism in families with two or more affected relatives (39,40,56).
This has important implications for counseling families regarding the possibility
of a recurrence.
5. Quantitative PCR. Quantitiative PCR has also been developed for rapid detection
of the 22q11 deletion (57). Karyiazono et al. selected UFD1L as the test gene
from 22q11.2 and a control gene on chromosome 21, S100 b. The TaqMantm PCR
assay was capable of detecting a deletion of UFDIL with a 99.7% statistical con-
fidence. It can be performed rapidly on small quantities of DNA. However,
quantitiative PCR does require expensive equipment, including an ABI PRISM
7700 Sequence Detection System and software (PE Biosystems) for quantitative
analysis, and it cannot detect mosaicism or structural abnormalities, such as trans-
locations.

Acknowledgment
This work was supported in part by grants DC02027 and HL074731 from
the National Institutes of Health.

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Genetic Analysis for Cardiac Arrhythmias 57

4
Mutation Screening for the Genes Causing Cardiac
Arrhythmias

Jeffrey A. Towbin

Summary
In this chapter, the up-to-date understanding of the molecular basis of disorders causing
arrhythmias are outlined. Several arrhythmic disorders have been well described at the
molecular level, including the long QT syndromes (LQTS), Brugada syndrome, and polymor-
phic ventricular tachycardia. The genes identified have been determined using genetic linkage
analysis, cloning, and mutation analyses. In the past, cloning was common, but with comple-
tion of the Human Genome Project, cloning is now rarely needed. In this chapter, current
mutation screening methods, including denaturing high-performance liquid chromatography
(DHPLC) and DNA sequencing are described, and the current knowledge gained using these
studies is discussed.
Key Words: Mutation screening; DHPLC; DNA sequencing; long QT syndrome; Brugada
syndrome; idiopathic ventricular fibrillation; ion channels; polymorphic ventricular tachycar-
dia; pre-excitation; Wolff–Parkinson–White syndrome.

1. Introduction
Sudden cardiac death in the United States occurs with a reported incidence
of more than 300,000 persons per year (1). Although coronary heart disease is
a major cause of death, other etiologies contribute to this problem, including
arrhythmia disorders, myocardial disorders, and disorders in which both
arrhythmias and structural heart disease coexist. In cases in which no structural
heart disease can be identified, cardiac arrhythmias are usually suspected, in
particular, these disorders include the long QT syndromes (LQTS) (1,2), char-
acterized by electrocardiographic evidence of the measured interval between
the Q wave and T wave and T wave morphology abnormalities; ventricular
preexcitation (3); idiopathic ventricular fibrillation or Brugada syndrome (4),
characterized by electrocardiographic evidence of ST-segment elevation in the
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

57
58 Towbin

right precordial leads with or without right bundle branch block; and catechola-
minergic polymorphic ventricular tachycardia (5). In this chapter, the current
understandings of the clinical and molecular genetic aspects of inherited
arrhythmia diseases are discussed, and the methods used to identify the genes
causing these disorders are outlined. These methods include denaturing high-
performance liquid chromotography (DHPLC) and DNA sequencing.

2. Materials
2.1. Denaturing High-Performance Liquid Chromatography
1. Polymerase chain reaction (PCR)-quality deionized water.
2. GeneAMP 10X PCR buffer II (Applied Biosystems [ABI]) or equivalent (500
mM KCl; 100 mM Tris-HCl, pH 8.3).
3. 25 mM MgCl2.
4. 5 mM solutions of each dNTP (dCTP, dATP, dTTP, and dGTP).
5. 1 pmol/μL of each of the forward and reverse amplification primers (standard 20-
to 25-mers) designed to amplify single-copy loci (recommended size, ≤500 bp).
6. 5 U/μL AmpliTaq Gold polymerase (ABI) or standard Taq DNA polymerase in
conjunction with alternative “hot-start” schemes (6).
7. 25 to 50 ng/μL human genomic DNA: samples known to contain polymorphism
or mutation; and homozygous positive controls.
8. High-performance liquid chromatography (HPLC) buffers A and B (see Sub-
headings 2.2.1. and 2.2.2.).
9. HaeIII restriction digest of pUC18 DNA (Sigma-Aldrich, St. Louis, MO) or other
commercially available plasmid digest.
10. Thermal cycler (e.g., ABI Model 9600 or equivalent).
11. Appropriately configured HPLC instrumentation (WAVE DNA Fragment Analy-
sis System; Transgenomic; or similar systems from Varian or Hewlett-Packard).
12. Heat exchanger (HEX-440.010; Timberline Instruments).
13. DNASep column (Transgenomic) or Prototype dsDNA Column (Hewlett-Packard).
14. Precolumn filter with 0–5-μm frit (Upchurch Scientific).

2.2. DHPLC (see Notes 1–3)

1. Buffer A: 100 mM triethylamine acetate (TEAA), pH 7.0., 0.1 mM EDTA. Store
up to 1 wk at room temperature.
2. Buffer B: 100 mM TEAA, pH 7.0., 0.1 mM EDTA, 25% (v/v) acetonitrile. Store
up to 1 wk at room temperature.

2.3. Cycle Sequencing With a 5'-End-Labeled Primer

1. Blood or other DNA source from individual(s) to be tested.
2. 5 M sodium acetate, pH 4.8.
3. Isopropanol (pure).
4. 10 mM Tris-HCl, 1 mM EDTA (TE) buffer, pH 7.4.
Genetic Analysis for Cardiac Arrhythmias 59

5. Molecular weight markers: e.g., ϕX-174 plasmid digested with HaeIII (Hoefer
Pharmacia Biotech or Invitrogen).
6. 12.5 pmol oligonucleotide.
7. 10X T4 polynucleotide kinase reaction buffer.
8. 10 μCi/μL [γ-32P]ATP (3000 Ci/mmol), 10 μCi/μL [γ-33P]ATP (3000 Ci/mmol),
or 10 μCi/μL [γ-35S]ATP (1000 Ci/mmol).
9. 5 U/μL T4 polynucleotide kinase.
10. Dideoxynucleotides: 100 μM ddGTP (or 7-deaza-dGTP for GC-rich templates),
600 μM ddATP, 1000 μM ddTTP, and 600 μM ddCTP.
11. 5 U/μL Taq DNA polymerase.
12. 10X cycle-sequencing reaction buffer (see Subheading 2.4.1.).
13. Mineral oil (if needed, depending on thermal cycler).
14. Stop solution (see Subheading 2.4.2.).
15. Thermal cycler and thermal cycler tubes.

2.4. Reagents and Solutions for Cycle Sequencing

1. 10X cycle-sequencing reaction buffer (see Note 4): 100 mM Tris-HCl, pH 9.0.,
500 mM KCl, 40 mM MgCl2, 20 μM dATP, 20 μM dGTP or 7-deaza-dGTP, 20 μM
dCTP, 20 μM dTTP.
2. Stop solution (see Note 5): 90% (v/v) formamide, 0.1% (w/v) bromphenol blue,
0.1% (w/v) xylene cyanol.
3. 10X T4 polynucleotide kinase reaction buffer (see Note 6): 500 mM Tris-HCl,
pH 7.5., 80 mM MgCl2, 20 mM dithiothreitol.

3. Methods
Genetic mutations may be identified using a number of approaches. In 2005,
the most common approaches include DHPLC and/or DNA sequencing.
3.1. Denaturing High-Performance Liquid Chromatography
Single base substitutions, small insertions, or deletions can be detected in
100- to 1500-bp DNA fragments by fractionation of heteroduplexes on reverse-
phase columns by DHPLC (7). All single-copy regions of genomic DNA that
can be amplified by PCR can be rapidly evaluated using automated machines.
Heteroduplexes formed during PCR amplification of DNA from a heterozy-
gous individual will have different melting properties than exactly matched
homoduplexes amplified from the DNA of homozygous individuals (8). DNA
mutation detection by DHPLC analysis exploits the differential retention of
double-stranded homoduplex and heteroduplex species under conditions of par-
tial thermal denaturation, and involves a two-step process. DNA fragments are:
1. Amplified by PCR from genomic template DNA of hetero- or homozygous indi-
viduals.
2. Subsequently fractionated under partially denaturing conditions by HPLC.
60 Towbin

Because the primary sequence is often known for candidate regions sub-
jected to mutational analysis, the optimal temperature for DHPLC analysis for
each fragment (e.g., exon) can be determined by computer software analysis
(http://hardy-weinberg.stanford.edu/dhplc/melt.html). When more than one
significant melting domain is present in a fragment, additional analysis tem-
peratures are automatically provided. In cases in which the primary sequence
between the primer sequence regions is unknown, the optimal temperature
required for successful resolution of heteroduplex molecules has to be deter-
mined empirically by injecting PCR products at increasing mobile-phase tem-
peratures until a significant decrease in retention time is observed, indicating
that the duplexes are almost completely denatured (9). Subsequent analysis at
a temperature 1ϒC lower than the temperature that was determined is generally
recommended. The analysis of each sample by DHPLC is very rapid, and nearly
100% of sequence alterations (polymorphisms or mutations) can be detected
(7–9) (Fig. 1).
3.1.1. Amplify Target Sequences (see Notes 7–10)
1. Prepare sufficient PCR mix for 100 reactions (i.e., 2.5 mL total), according to
Table 1.
2. Mix well and dispense 24 μL into each PCR tube.
3. Add 1 μL genomic DNA (25 to 50 ng/μL).
4. Set up tubes containing negative (1 μL of water or some DNA not represented in
the genome of interest) controls, and, if possible, positive controls, of known
homozygous and heterozygous samples that carry a polymorphism or mutation.
5. Amplify using an ABI 9600 thermal cycler or equivalent, according settings given
in Table 2.
6. Denature for a final 3 min at 95°C, then allow to gradually reanneal during 30
min from 95°C to 65°C. Store PCR products at 4°C until DHPLC analysis.
7. Analyze 5 μL of PCR product by electrophoresis on a 1- to 1.5%-agarose gel and
stain with ethidium bromide to confirm amplification of desired target sequence.

3.1.2. Analyze PCR Products by DHPLC (see Notes 11–14)

1. Condition newly packed columns with 50% buffer A and 50% buffer B, using a
flow rate of 0.5 mL/min for at least 60 min at 50°C.
2. Test column performance at 50°C by injecting approx 0.5 μg of commercially
available HaeIII restriction digest of pUC18. Use a flow rate of 0.9 mL/min and
the following gradient conditions:
a. From 43% buffer B to 56% buffer B in 3 min.
b. From 56% buffer B to 68% buffer B in 7 min.
c. From 68% buffer B to 95% buffer B in 0.1 min.
d. 95% buffer B for 0.5 min.
e. From 95% buffer B to 43% buffer B in 0.1 min.
Genetic Analysis for Cardiac Arrhythmias 61

Fig. 1. Analysis of a gene by DHPLC and direct sequencing. (A) DHPLC analysis
of an exon of this gene identifies an abnormal DHPLC pattern in the affected subject
(top arrow) compared with the normal pattern present in controls (bottom arrow). (B)
DNA sequence analysis of genomic DNA identifies a A-to-G base substitution lead-
ing to an amino acid change in the affected subject.

Successful separation of the restriction fragments is monitored at the column out-

let by on-line UV absorbance at 254 nm.
3. Equilibrate column to analysis temperature predicted by the computation algorithm
at http://hardy-weinberg.stanford.edu/dhplc/melt.html. Alternatively, determine
optimum temperature conditions empirically by increasing column temperature
with 2 to 3°C increments, until a shift of approx 1 min in retention is observed.
4. Equilibrate column to starting buffer conditions (usually 50% buffer B) at a flow
rate of 0.9 mL/min.
5. Adjust gradient startpoints and endpoints according to the size of the PCR prod-
ucts (2) based on the retention times of the DNA restriction fragments of the
digest used to test the column performance (Subheading 3.1.2., step 2).
62 Towbin

Table 1
PCR Mix

Volume per 25-mL

reaction (μL) Final concentration

Deionized water 16.4

10X PCR buffer 2.5 1X
25 mM MgCl2 2.0 2 mM
DNTPs (5 mM each) 0.5 each 0.1 mM each
Forward primer (10 μM) 0.5 0.2 μM
Reverse primer (10 μM) 0.5 0.2 μM
5 U/μL AmpliTaq Gold polymerase 0.1 0.5 U

Table 2
PCR Amplification Cycles

1 cycle 10 min 95°C (denaturation)

14 cycles 20 s 94°C (denaturation)
45 s 72°C (extension)
20 s 63°C decreased by 0.5°C increments (annealing)
16 cycles 20 s 94°C (denaturation)
45 s 72°C (extension)
20 s 56°C (annealing)

6. Set autosampler to inject between 5 and 10 μL of sample, and begin DHPLC

analysis.
7. When not in use, continue to perfuse column at a very low flow rate (0.05 mL/
min) with 50% buffer A and 50% buffer B.
3.1.3. Sequence Polymorphic PCR Products (see Note 15)
Determine the exact chemical nature and the position of the mutation(s) by
sequencing the PCR product.
3.2. Cycle Sequencing (see Notes 16–18)
Candidate genes are screened for mutations by a DNA sequencing proce-
dure known as cycle sequencing (10). First, using PCR, a segment of the can-
didate gene is amplified from the genomic DNA of an affected individual (11).
The PCR product is then subjected to multiple rounds of further amplification
in a thermal cycler using a heat-stable DNA polymerase in the presence of
different dideoxynucleotides and a radiolabeled primer. The resulting
32 P-labeled sequence reaction products are fractionated on a denaturing poly-
Genetic Analysis for Cardiac Arrhythmias 63

acrylamide gel and visualized by autoradiography. DNA segments on the order

of 200 bp from 10 to 30 individuals can be screened on each gel. Cycle se-
quencing eliminates the need to subclone genomic fragments or PCR products,
which makes it a much simpler method than conventional sequencing for identi-
fying mutations. Clearly, automated DNA sequencing is a highly used modality.
However, this will not be described because it is an automated process.
3.2.1. Prepare Template DNA
1. Isolate and purify human genomic DNA using standard methods, resuspending
the DNA in water or TE buffer (pH 7.4 at the end of the procedure).
2. Using PCR, amplify the segment of interest from genomic DNA.
3. Add 50 μL of 5 N sodium acetate, pH 4.8, and 100 μL pure isopropanol to the 50-
μL PCR reaction. Incubate for 10 min at room temperature.
4. Microcentrifuge for 10 min at maximum speed (~16,000g), at room temperature.
Discard supernatant, and air-dry.
5. Resuspend the pellet in 50 μL water or TE buffer (pH 7.4). Quantify the amount
of resuspended DNA by analyzing a 5-μL aliquot on an agarose gel and compar-
ing the resulting band to a known amount of a size marker (e.g., 1 μg of ϕX-174
plasmid digested with HaeIII).

3.2.2. 5'-End-Label the Sequencing Primer

1. Prepare a 25-μL reaction mixture containing:
a. 12.5 pmol oligonucleotide sequencing primer.
b. 2.5 μL 1X T4 polynucleotide kinase reaction buffer.
c. 1.0 μL 5 U/μL T4 polynucleotide kinase (5 U total).
d. 3.0 μL 10 μCi/μL [γ-32P]ATP or [γ-33P]ATP (3000 Ci/mmol; 30 μCi total) or
2.0 μL 10 μCi/μL [γ-35S]ATP (1000 Ci/mol; 20 μCi total).
e. H2O to total volume of 25 μL.
2. Incubate 30 min at 37°C.
3.2.3. Perform Cycle-Sequencing Reaction
1. For each DNA template, prepare four thermal cycler tubes and add 3 μL of one of
the following to each tube: 100 μM ddGTP, 600 μM ddATP, 1000 μM ddTTP, or
600 μM ddCTP. Store tubes on ice.
2. Prepare sequencing cocktail by placing in a fresh tube:
a. 10 to 20 fmol sequencing template (DNA solution from Subheading 3.2.1.,
step 5).
b. 1 μL 5′-end-labeled sequencing primer (from Subheading 3.2.2., step 1).
c. 4 μL 10X cycle-sequencing reaction buffer.
d. 1 μL 2 U/μL Taq DNA polymerase (2 U total).
e. H2O to total volume of 30 μL.
3. Place 7-μL aliquots of cocktail into each of the four cycle sequencing reaction
tubes.
64 Towbin

4. Add mineral oil (if necessary), close caps, and start thermal cycling. Cycling con-
ditions will vary for different templates, sequencing primers, thermal cycler de-
signs, and so on. It is advisable to begin with standard PCR conditions and
optimize the sequencing reaction by varying reaction temperatures, cycling times,
and/or number of cycling rounds.
5. After completion of thermal cycling, add 5 μL stop solution to each reaction, heat
denature for 5 min at 95°C, and cool rapidly to less than 4°C.
6. Analyze sequencing reaction products on a 6 or 8% denaturing polyacrylamide
sequencing gel by loading 5 μL of the denatured reaction and running the gel as
far as required. If screening the DNA of multiple individuals simultaneously, the
G reactions, A reactions, T reactions, and C reactions should each be loaded
together on the gel.
7. Store sequencing reaction at –20°C, and load repeatedly, if necessary.
8. Dry gel and autoradiograph overnight.

3.3. Anticipated Results

3.3.1. DHPLC
In any mutational analysis scheme, it is important to distinguish between
common polymorphisms and clinically relevant mutations. This is achieved by
assessing the background polymorphic variation associated with normal con-
trol individuals (unaffected individuals of similar ethnicity or population com-
position). Estimates of the frequency of common sequence variation associated
with the human genome are approx 1 per kilobase in noncoding sequences and
lower in coding sequences. Therefore, most samples can be expected to be
monomorphic and, thus, display homoduplex signatures. However, the fre-
quency of a mutation or polymorphism may be high relative to the normal
control sample. Although DHPLC typically generates heteroduplex profiles
clearly distinct from homoduplexes (often of similar height), certain fragments
may display only subtle differences in profile topography. If additional resolu-
tion is not achieved by using a different analysis temperature, then the size of
the homoduplex peak becomes more significant than usual. Any significant
decrease in height with concomitant appearance of an earlier-eluting peak or a
pronounced shoulder is suggestive of sequence variation. In cases in which
multiple mismatches exist, it is possible that, very rarely, the heteroduplex may
completely denature and coelute with primers, dNTPs, and so on. The only
indication of such a situation would be a significant decrease in the homoduplex
peak height. Whenever possible, positive controls of known heteroduplex com-
position should be run at least once during the analysis process.
3.3.2. Anticipated Results: Cycle Sequencing
Cycle sequencing is best used to screen relatively short sequences (e.g., those
≤300 bp) for mutations. If the samples are loaded with all of the G reactions
Genetic Analysis for Cardiac Arrhythmias 65

next to one another, all of the A reactions next to one another, and so on, muta-
tions can be rapidly identified from the autoradiogram. That is, a single nucle-
otide difference in a probands will be reflected by the presence of a unique
band (and absence of another band normally seen) in one lane of the sequenc-
ing gel. If the proband is heterozygous, there should also be a band at that
normal position, but its intensity should be diminished compared with the prod-
ucts derived from other individuals.
3.4. Clinical Diseases
3.4.1. The Long QT Syndromes
3.4.1.1. CLINICAL DESCRIPTION
The LQTS are inherited or acquired disorders of repolarization, identified
by the electrocardiographic (ECG) abnormalities of prolongation of the QT
interval corrected for heart rate (QTc) higher than 460 to 480 ms, relative brady-
cardia, T-wave abnormalities, and episodic ventricular tachyarrhythmias (1,2),
particularly torsade de pointes. The inherited form of LQTS is transmitted as
an autosomal-dominant or autosomal-recessive trait. Acquired LQTS may be
seen as a complication of various drug therapies or electrolyte abnormalities
(1,2). Whether the abnormality is genetic based or acquired, the clinical pre-
sentation is similar. In many cases, the initial presentation is syncope, whereas,
in others, an ECG leads to the diagnosis. Tragically, some individuals have
sudden death as their initial presenting feature, and this has been reported to
occur in families in some cases. Typically, autopsy evaluation identifies a nor-
mal structural heart with no apparent cardiac cause of death.
3.4.1.2. CLINICAL GENETICS
Two differently inherited forms of familial LQTS have been reported. The
Romano–Ward Syndrome is the most common of the inherited forms of LQTS
and seems to be transmitted as an autosomal-dominant trait (1,2). In this disor-
der, the disease gene is transmitted to 50% of the offspring of an affected indi-
vidual. However, low penetrance has been described and, therefore, gene
carriers may, in fact, have no clinical features of disease (12). Individuals with
Romano–Ward syndrome have the pure syndrome of prolonged QT interval on
ECG, with the associated symptom complex of syncope, sudden death, and, in
some patients, seizures (1).
The Jervell and Lange-Nielsen Syndrome (JLNS) is a relatively uncommon
inherited form of LQTS (1,2). Classically, this disease has been described as
having apparent autosomal-recessive transmission (1,2). These patients have
the identical clinical presentation as those with Romano–Ward syndrome but
also have associated sensorineural deafness. Clinically, patients with JLNS
66 Towbin

usually have longer QT intervals as compared with individuals with Romano–

Ward syndrome, and also have a more malignant course. Priori and colleagues
reported autosomal-recessive cases of Romano–Ward syndrome (13), thus,
changing one of the sina qua nons of JLNS.
To date, six genes for LQTS have been identified (1,2,14–20), and a seventh
gene, causing a more complex disorder known as Andersen syndrome (LQTS,
ventricular arrhythmias, and hypokalemic periodic paralysis associated with
dysmorphisms in some individuals) (21,22), has been discovered (22–24).
3.4.1.3. GENE IDENTIFICATION IN ROMANO–W ARD SYNDROME
3.4.1.3.1. KVLQT1 or KCNQ1: The LQT1 Gene. The first of the genes
mapped for LQTS, initially termed LQT1, required 5 yr from the time that
mapping to chromosome 11p15.5 was first reported (14) to gene cloning. This
gene, originally named KVLQT1, but more recently called KCNQ1, is a
potassium channel gene that consists of 16 exons, spans approx 400 kb, and is
widely expressed in human tissues, including heart, inner ear, kidney, lung,
placenta, and pancreas, but not in skeletal muscle, liver, or brain (25). This
gene is the most commonly mutated of the LQTS genes. Although most of the
mutations are private (i.e., only seen in one family), there is at least one
frequently mutated region (called a hot spot) (25).
Analysis of the predicted amino acid sequence of KCNQ1 suggested that it
encodes a potassium channel subunit (15) (Fig. 2). Biophysical characteriza-
tion of the KCNQ1 protein confirmed that this is a voltage-gated potassium
channel protein subunit that requires coassembly with a β-subunit (called minK
or KCNE1) to function properly (26,27). Expression of either KCNQ1 or minK
(KCNE1) alone results in either inefficient or no current development. When
KCNE1 and KCNQ1 are coexpressed in either mammalian cell lines or Xeno-
pus oocytes, however, the slowly activating potassium current (IKs) is devel-
oped in cardiac myocytes (26,27). Combination of normal and mutant KCNQ1
subunits forms abnormal IKs channels, and these mutations are believed to act
through a dominant-negative mechanism (the mutant form of KCNQ1 inter-
feres with the function of the normal wild-type form through a poison pill-type
mechanism) or a loss-of-function mechanism (only the mutant form loses
activity) (28).
Because KCNQ1 and KCNE1 form a unit, mutations in KCNE1 could also
be expected to cause LQTS, as was subsequently demonstrated (16).
3.4.1.3.2. HERG or KCNH2: The LQT2 Gene. After the initial localization
of LQT2 to chromosome 7q35–36 by Jiang et al. (17), candidate genes (i.e.,
genes encoding proteins that could cause repolarization abnormalities if
mutated, such as ion channels, modulators of ion channels, members of the
 Ge
net
ic

An

aly

sis
67

for
Car
dia
c

Arr
hyth
mia
s
Fig. 2. Topology of ion channels in the heart. (Top left) KvLQT1 and minK, which constitute the IKs potassium channel. (Top
right) HERG and MiRP1, which constitute the IKr potassium channel. (Bottom left) The cardiac INa sodium channel encoded by
SCN5A. In addition, the LQT7 gene (Bottom right) encoding for Andersen syndrome, known as KCNJ2, encodes for the IK1
potassium channel.
68 Towbin

sympathetic nervous system, and so on) in this region were analyzed. HERG
(human ether-a-go-go-related gene), now known as KCNH2, a cardiac
potassium-channel gene, was one of the candidates evaluated and found to be
mutated in patients with clinical evidence of LQTS (18). This gene is the second
most common gene mutated in LQTS (second to KCNQ1). As with KCNQ1,
private mutations, which are scattered throughout the entire gene without
clustering preferentially, are seen.
KCNH2 consists of 16 exons and spans 55 kb of genomic sequence (18), and
its predicted topology (Fig. 2) is similar to KCNQ1. Electrophysiological and
biophysical characterization of expressed KCNH2 in Xenopus oocytes estab-
lished that it encodes the rapidly activating, delayed-rectifier potassium cur-
rent (IKr) (29,30). Electrophysiological studies of LQTS-associated mutations
showed that they act through either a loss-of-function or a dominant-negative
mechanism (31). In addition, protein trafficking abnormalities have been shown
to occur (32,33). This channel has also been shown to coassemble with β-sub-
units for normal function, similar to that seen in IKs. McDonald et al. (34) ini-
tially suggested that the complexing of KCNH2 with KCNE1 is needed to
regulate the IKr potassium current. Bianchi et al. subsequently provided confir-
matory evidence that KCNE1 is involved in regulation of both IKs and IKr (35).
In addition, Abbott et al. (36) identified MiRP1 (or KCNE2) as a β-subunit for
KCNH2.
Mutations in the pore region of HERG have been shown to result in an
increased risk of syncope and sudden death (37). This, in addition to the newly
created fee-for-service mutation analysis laboratory, capable of providing
direct sequencing results within weeks (Genaissance Pharmaceuticals), poten-
tially enables the use of genotype to phenotype correlation to effectively pre-
vent episodes of sudden death.
3.4.1.3.3. SCN5A: The LQT3 Gene. The positional candidate gene approach
was also used to establish that the gene responsible for the chromosome 3p21–
25-linked LQTS (LQT3) is the cardiac sodium channel gene, SCN5A (19).
SCN5A is highly expressed in human myocardium and brain, but not in skeletal
muscle, liver, or uterus. It consists of 28 exons that span 80 kb and encodes a
protein of 2016 amino acids whose structure consists of four homologous
domains, each of which contains six membrane-spanning segments, similar to
the structure of the potassium channel α-subunits (Fig. 2) (38). Expression in
Xenopus oocytes demonstrated that SCN5A mutations act through a gain-of-
function mechanism (the mutant channel functions normally, but with altered
properties, such as delayed inactivation) and that the mechanism of chromosome
3-linked LQTS is persistent noninactivated sodium current in the plateau phase
of the action potential (38–40). Later, An et al. (41) showed that not all mutations
Genetic Analysis for Cardiac Arrhythmias 69

in SCN5A are associated with persistent current, and demonstrated that SCN5A
interacted with β-subunits.
Polymorphisms in SCN5A have been shown to elevate the risk of arrhyth-
mias. Splawski et al. (42) showed this to occur in individuals of African de-
scent, whereas Viswanathan and colleagues (43) demonstrated modulation of
conduction system disease by the H558R polymorphism in a child with a nearby
mutation (T512I). These findings have fueled speculation about the potential
importance of polymorphisms in clinical features of subjects with ion-channel
dysfunction.
3.4.1.3.4. ankyrin-B: The LQT4 Gene. This gene was first localized to
chromosome 4q25–27 in a large French kindred in which the clinical syndrome
was characterized by sinus node dysfunction, QTc prolongation, episodes of atrial
fibrillation, as well as odd T-wave morphology (44). The identity of this gene
was uncovered by Mohler et al. using a candidate gene approach (20). The gene,
ankyrin-B (also known as ANKB or ANK2), plays a fundamental role in the
recognition of important interacting proteins that ensure appropriate localization
in cell membranes (20,45). Several of these proteins are involved in ion transport,
including the pore-forming subunits of voltage-gated sodium channels, the
transmembrane Na+–K+ ATPase and Na+–Ca2+ exchanger, and studies of mouse
models have demonstrated calcium-handling abnormalities. It was also
speculated that ankyrin-B affects sodium channels, leading to this broad, complex
phenotype (20,45).
3.4.1.3.5. minK or KCNE1: The LQT5 Gene. minK (also known as lsK or
KCNE1), was initially localized to chromosome 21 (21q22.1) and found to
consist of three exons that span approx 40 kb (46). It encodes a short protein
consisting of 130 amino acids and has only one transmembrane-spanning
segment, with small extracellular and intercellular regions (46). When
expressed in Xenopus oocytes, it produces a potassium current that closely
resembles the slowly activating, delayed-rectifier potassium current, lKs, in
cardiac cells (46,47). KCNE1 interacts with KCNQ1 to form the cardiac slowly
activating, delayed-rectifier IKs current (26,27); KCNE1 alone cannot form a
functional channel, but induces the IKs current by interacting with the
endogenous KCNQ1 protein in Xenopus oocytes and mammalian cells. Bianchi
et al. also showed that mutant minK results in abnormalities of IKs, IKr, and
protein trafficking (35). McDonald et al. (34) showed that KCNE1 also
complexes with HERG to regulate the IKr potassium current. Splawski et al.
(16) demonstrated that KCNE1 mutations cause LQTS when they identified
mutations in two families with LQTS. In both cases, missense mutations (S74L,
D76N) were identified, which reduced IKs by shifting the voltage dependence
of activation and accelerating channel deactivation. The functional
70 Towbin

consequences of these mutations includes delayed cardiac repolarization and,

hence, an increased risk of arrhythmias.
3.4.1.3.6. MiRP1 or KCNE2: The LQT6 Gene. MiRP1, the minK-related
peptide 1, also known as KCNE2, is a potassium-channel gene similar to
KCNE1 (36). This small integral membrane subunit protein assembles with
HERG (LQT2), to alter its function and enables full development of the IKr
current. It encodes a 123-amino acid channel protein with a single predicted
transmembrane segment, and the gene is mapped to chromosome 21q22.1, near
KCNE1 (minK) (36).
Three missense mutations associated with LQTS and ventricular fibrillation
were initially identified in KCNE2 by Abbott et al. (36), and biophysical analy-
sis demonstrated that these mutants form channels that open slowly and close
rapidly, thus, diminishing potassium currents. In one case, the missense muta-
tion led to the development of torsade de pointes and ventricular fibrillation
after intravenous clarythromycin infusion (i.e., drug induced).
Therefore, similar to KCNE1, this channel protein acts as a β-subunit but,
by itself, leads to ventricular arrhythmia risk when mutated. These similar chan-
nel proteins (i.e., KCNE1 and KCNE2) suggest that a family of channels exist
that regulate ion channel α-subunits.
3.4.1.4. THERAPY FOR LQTS
The standard of care for LQTS for many years has been the use of β-blockers
(1,2). A large study published by the Long QT Registry Investigators demon-
strated significant reduction in syncope, but sudden death still resulted in some
patients (48). Gene-specific approaches were originally reported by Schwartz
et al. (49), who used the sodium-channel blocking agent, mexiletine, for pa-
tients with LQTS, and demonstrated shortening of the QTc. Compton et al.
(50,51) reported the use of potassium infusion (serum potassium > 4.8) in
LQT1 patients, with similar results. However, only the potassium therapy stud-
ies have been followed up to show improved outcome (51). Recently, the use
of an internal cardioverter defibrillator has become a mainstay of therapy (52).
The use of genotype to phenotype correlations to predict those at risk for sud-
den death may be useful in choosing the proper therapeutic strategy (53,54).
3.4.1.5. GENETICS AND PHYSIOLOGY OF AUTOSOMAL-RECESSIVE LQTS (JLNS)
Neyroud et al. (55) reported the first molecular abnormality in patients with
JLNS when they reported on two families in which three children were affected
by JLNS and in whom a novel homozygous deletion–insertion mutation of
KCNQ1 in three patients was found. At the same time, Splawski et al. (56)
identified a homozygous insertion of a single nucleotide, which caused a frame-
Genetic Analysis for Cardiac Arrhythmias 71

shift in the coding sequence after the second putative transmembrane domain
of KCNQ1. Together, these data strongly suggested that at least one form of
JLNS is caused by homozygous mutations in KCNQ1 (55–57).
Generally, heterozygous mutations in KCNQ1 cause Romano–Ward syn-
drome (LQTS only), whereas homozygous (or compound heterozygous) muta-
tions in KCNQ1 cause JLNS (LQTS and deafness). The hypothetical
explanation suggests that although heterozygous KCNQ1 mutations act by a
dominant-negative mechanism, some functional KCNQ1 potassium channels
still exist in the stria vascularis of the inner ear. Therefore, congenital deafness
is averted in patients with heterozygous mutations. For patients with homozy-
gous mutations, no functional KCNQ1 potassium channels can be formed. It
has been shown that KCNQ1 is expressed in the inner ear (55), suggesting that
homozygous mutations can cause the dysfunction of potassium secretion in the
inner ear and lead to deafness. However, it should be noted that incomplete
penetrance exists, and not all heterozygous or homozygous mutations follow
this rule (13).
As with Romano–Ward syndrome, if KCNQ1 mutations can cause the phe-
notype, it could be expected that KCNE1 mutations could also be causative of
the phenotype (JLNS). Schulze-Bahr et al. (58), in fact, showed that mutations
in KCNE1 also result in JLNS syndrome. Hence, abnormal IKs current, whether
it occurs because of homozygous or compound heterozygous mutations in
KCNQ1 or minK, result in LQTS and deafness.
3.4.1.6. ANDERSEN SYNDROME
This complex phenotype includes hypokalemic periodic paralysis,
dysmorphic features, QTc prolongation, and ventricular arrhythmias (21). In
some patients, polymorphic ventricular tachycardia has been identified. The
dysmorphic features include syndactyly, hypertelorism, low-set ears, broad
forehead, micrognathia, cleft palate, clinodactyly, and scoliosis (22). In some
patients, renal anomalies and congenital heart disease, including bicuspid aor-
tic valve, coarctation of the aorta, and valvular pulmonary stenosis, have been
identified as well.
Andersen syndrome is inherited as an autosomal-dominant trait. The ge-
netic basis of this complex phenotype was identified as mutations in the chro-
mosome 17q23 KCNJ2 gene encoding the inward-rectifying potassium current,
Kir2.1 (23). Mutations expressed in Xenopus oocytes demonstrated a strong
dominant-negative effect and loss of function (23).
In many cell types, particularly cardiomyocytes and neurons, Kir2 channels
play an important role in setting the membrane potential and modulating excit-
ability. When inward rectifier current is reduced, the propensity for arrhythmias
72 Towbin

increases. Hence, in Andersen syndrome, mutations result in reduced current

and the development of cardiac arrhythmias (24).
3.4.2. Brugada Syndrome
3.4.2.1. CLINICAL ASPECTS OF BRUGADA SYNDROME
The first identification of the ECG pattern of right bundle branch block
(RBBB) with ST-elevation in leads V1–V3 was reported by Osher and Wolff
(59). Shortly thereafter, Edeiken (60) identified persistent ST-elevation with-
out RBBB in 10 asymptomatic males and Levine et al. (61) described ST-
elevation in the right chest leads and conduction block in the right ventricle in
patients with severe hyperkalemia. The first association of this ECG pattern
with sudden death was described by Martini et al. (62) and later by Aihara et al.
(63). This association was further confirmed in 1991 by Pedro and Josep
Brugada (4), who described four patients with sudden and aborted sudden death
with ECGs demonstrating RBBB and persistent ST-elevation in leads V1–V3.
3.4.2.2. CLINICAL GENETICS OF BRUGADA SYNDROME
Most of the families thus far identified with Brugada syndrome have appar-
ent autosomal-dominant inheritance (64). In these families, approx 50% of off-
spring of affected patients develop the disease. Although the number of families
reported has been small, it is likely that this is because of underrecognition as
well as premature and unexpected death.
3.4.2.3. MOLECULAR GENETICS OF BRUGADA SYNDROME
In 1998, our laboratory reported the findings on six families and several
sporadic cases of Brugada syndrome (65). Candidate gene screening was per-
formed and mutations in SCN5A were identified (65).
Biophysical analysis of the mutants in Xenopus oocytes demonstrated a
reduction in the number of functional sodium channels (which should promote
development of reentrant arrhythmias) and, in some mutations, sodium chan-
nels that recover from inactivation more rapidly than normal (64,65). Subse-
quent experiments revealed that, at physiological temperatures (37ϒC),
reactivation of some channels was actually slower, whereas inactivation of the
channel was importantly accelerated (i.e., the mutant is temperature sensitive)
(66). Kambouris et al. identified a mutation in essentially the same region of
SCN5A as a Brugada syndrome-causing mutation (R1623Q), but the clinical
and biophysical features of this mutation were found to be consistent with
LQTS and not Brugada syndrome (67). Subsequently, mutations have been
identified in which some family members have Brugada syndrome, whereas
other members of the same family have LQTS. It has also been shown that
individual patients can demonstrate both entities over time.
Genetic Analysis for Cardiac Arrhythmias 73

3.4.3. Polymorphic Ventricular Tachycardia

Polymorphic ventricular tachycardia is characterized by the occurrence of
salvoes of bidirectional and polymorphic ventricular tachycardias, typically in
relation to adrenergic stimulation or physical exercise but without evidence of
structural myocardial disease (5). The clinical outcomes of these patients are
reportedly poor, with estimates of mortality in the range of 30 to 50% by the
age of 20 to 30 yr. The disorder is commonly inherited, with transmission in an
autosomal-dominant pattern (68,69).
The first gene identified for this disorder was mapped to chromosome 1q42–
q43 (68). The gene was shown to be the cardiac ryanodine receptor (RyR2), the
same gene identified to cause the arrhythmogenic right ventricular dysplasia-
type 2 phenotype (67–72). Ryanodine receptors are the largest ion channels
known to exist and RyR2 is abundantly expressed in myocardium, and, to a lesser
extent, in the brain and gestational myometrium. This calcium-release channel is
activated after stimulation of voltage-sensitive L-type calcium channels on the
outer myocardial cell membrane, which permits the cellular entrance of tiny
amounts of calcium ions but which activates RyR2. This activation enables large
amounts of calcium ions to pass from the lumen of the sarcoplasmic reticulum
into the cytoplasm, initiating myocardial contraction. Mutations in this gene lead
to uncoupling of excitation–contraction coupling and to increased sensitivity of
calcium-induced activation of the calcium-release channel complex.
A second gene causing this disorder was reported by Lahat et al. in autoso-
mal-recessive polymorphic VT (73). This gene, localized to chromosome
1p13–1p21, was identified as the gene encoding calsequestrin 2, which serves
as the major calcium reservoir within the sarcoplasmic reticulum and interacts
with RyR2 (73,74).
3.5. Conclusion
Genetic screening to identify genes causing arrhythmia disorders has pro-
gressed from nearly impossible to passé in the past 15 yr because of the devel-
opment of rapid, high-technology, and high-throughput methods for mutation
screening. Fee-for-service laboratories are now offering genetic testing for
these disorders.

4. Notes
1. Use deionized distilled water in all solutions and protocol steps.
2. A 2 M stock solution of TEAA, pH 7.0, for DHPLC buffers (Subheadings 2.2.1.
and 2.2.2.) is commercially available from ABI and is recommended because the
pure base triethylamine, obtainable from vendors such as Fluka and J.T. Baker, is
a flammable chemical that has an irritant effect on skin, eyes, and respiratory
organs. If prepared in-house, make up a 1 M (rather than a 2 M) stock solution.
74 Towbin

Briefly, weigh 202.38 g of triethylamine into a 2-L volumetric flask. Add 500 mL
of water and stir with magnetic stirring bar at 300 rpm. Weigh 120.1 g of glacial
acetic acid into a beaker and add the acid slowly to the triethylamine solution,
which will heat up and form white fumes. Continue stirring and fill the flask with
water to approx 1900 mL. Once the solution has cooled to room temperature,
measure the pH value with the pH electrode. If the pH is less than 7.0, add drops of
triethylamine, if the pH is greater than 7.0, add acetic acid, until the pH is ad-
justed. Remove stirring bar and fill with water to the 2-L mark on the volumetric
flask. Add 100 mL of 1 M TEAA stock solution per liter of eluant. For eluant B,
add 25% (v/v) of a grade of acetonitrile with the lowest obtainable UV cutoff (i.e.,
the wavelength at which the absorbance becomes high; an appropriate grade is
available from J.T. Baker). EDTA is added (from 0.5 M stock) to prevent the
interaction of DNA with divalent and trivalent metal cations that strongly bind the
DNA to the stationary phase.
3. Provided that HPLC-grade reagents and an in-line vacuum degasser are used, it
is unnecessary to filter and degas the buffers before use.
4. Store cycle-sequencing reaction buffer (10X) in aliquots at –20°C.
5. Store cycle-sequencing stop solution in aliquots at room temperature.
6. Store T4 polynucleotide kinase reaction buffer (10X) in aliquots at –20°C.
7. The initial denaturation inactivates AmpliTaq Gold. The incremental decrease in
annealing temperature during the following 14 cycles improves the PCR speci-
ficity and minimizes the PCR optimization, provided that the melting tempera-
tures of the primers are similar (1).
8. This final denaturation and gradual reannealing regime ensures that equimolar
amounts of heteroduplex and homoduplex molecules are formed.
9. Amplicons can be stored at 4°C for several weeks.
10. Successful mismatch detection requires the comparison of at least two chromo-
somes. Therefore, in the case of haploid genomes, PCR products have to be mixed
with a reference. Determine yields for test and reference amplicons by agarose
gel electrophoresis in UV tracings at roughly equimolar ratios. Because hetero-
duplexes are overrepresented in UV tracings because of the encased UV absorp-
tion of the single-stranded components constituting the “bubble” formed around
the mismatch, heteroduplexes are successfully detected even when only one out
of eight chromosomes is mutated.
11. Baseline resolution of the 257-bp and 267-bp, and the 434-bp and 458-bp frag-
ments, respectively, should be obtained. If not, request replacement of the column.
12. Avoid direct contact between the stainless steel column and the hot metal sur-
faces of the column oven. The surfaces are warmer than the circulating air in the
oven; hence, direct contact will heat the mobile phase in the column to a higher
temperature than indicated on the column oven display. Such contact will also
result in discrepancies between the predicted and observed temperatures.
13. Equilibration time is dependent on the dead volume of the chromatograph (i.e.,
the volume of liquid pathway between solvent mixer and column outlet); dis-
place dead volume at least once, which typically takes 1 to 3 min.
Genetic Analysis for Cardiac Arrhythmias 75

14. For temperature optimization, start the gradient at 7% below the estimated per-
centage of buffer B at which the amplicion is expected to elute at 50ϒC (to
account for the shift in retention toward lower percentages of buffer B with in-
creasing column temperatures). Once the optimum temperature has been deter-
mined, a gradient window as small as 4.5% during 2.5 min can be set. For
amplicons up to 600 bp, increase the gradient by 1.8% of buffer B per minute.
For larger amplicons, use a shallower gradient, e.g., 1.2% of buffer B per minute.
15. Chromatographic profiles of single PCR products that show more than one peak
are indicative of the presence of mismatch.
16. Only 10 to 20 fmol of DNA template is needed per cycle-sequencing reaction. It is
convenient to calculate the equivalent amount of double-stranded DNA (i.e., how
much will constitute 10 fmol) as follows: nanograms of DNA template = 10 fmol ×
N × 6.6 × 10–3, where N is the number of basepairs of the sequencing template.
17. Human genomic DNA cannot be analyzed directly by cycle sequencing. To
screen genomic DNA for mutations, it is necessary to amplify the sequence of
interest beforehand by a standard PCR reaction.
18. The oligonucleotide sequencing primer is derived from sequence immediately 5′ to
the sequence being screened for mutations. Although either PCR primer can be used
as a sequencing primer, clearer results can be obtained by using a nested primer.

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FBN1 Mutation Analysis in Patients With MFS 81

5
Mutation Analysis of the FBN1 Gene in Patients
With Marfan Syndrome

Paul Coucke, Petra Van Acker, and Anne De Paepe

Summary
Marfan syndrome is an autosomal-dominant connective tissue disorder characterized by
pleiotropic manifestations involving the skeletal, ocular, and cardiovascular systems and re-
sulting from mutations in the gene for fibrillin, FBN1. The clinical diagnosis is based on a set of
well-defined clinical criteria (Ghent nosology). Nevertheless, the age-related nature of some clini-
cal manifestations and the variable phenotypic expression of the disorder may hamper the diag-
nosis. In those instances, molecular analysis of the FBN1 gene is helpful to identify at-risk
individuals. Mutations are spread over the entire FBN1 gene and there are no particular hot spots.
Different standard methodologies are available to identify these mutations, however, one of the
most sensitive techniques is denaturing high-performance liquid chromatography. This approach
allows the performance of the analysis in a semi-automated manner and has a mutation detection
rate of approx 95%.
Key Words: Marfan syndrome; fibrillin-1; molecular diagnosis; mutation analysis; DHPLC.

1. Introduction
Marfan syndrome (MFS) (OMIM 154700) is an inherited disorder of con-
nective tissue that affects mainly the skeleton, the eyes, and the cardiovascular
system. The prevalence of the disease is approx 1 in 10,000 and the disease
shows autosomal-dominant transmission (1). The diagnosis of MFS is based
primarily on clinical criteria and requires a combination of major and minor
clinical manifestations in different organ systems. Major manifestations are
highly specific for the condition and include ectopia lentis, dissection of the
ascending aorta, dural ectasia, and presence of at least four of eight manifesta-
tions in the skeletal system (2). Minor manifestations are numerous, but less
specific because they are commonly found in many other conditions as well as
in the general population. The presence of minor criteria only is insufficient to
establish the clinical diagnosis of MFS, but indicates that the particular body
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

81
82 Coucke et al.

system is involved. According to the current nosological criteria (Ghent Noso-

logy, 1996) the diagnosis of MFS in a sporadic patient requires the presence of
a major manifestation in at least two different organ systems and the involve-
ment of a third organ system (3). In familial instances, a positive family history
is considered a major diagnostic criterion. The diagnosis of MFS in a relative
requires the presence of one additional major manifestation in one organ sys-
tem and involvement of a second organ system. The clinical diagnosis can be
challenging because of the striking inter- and intrafamilial variability in phe-
notypic expression and the age-related nature of several clinical manifesta-
tions. Therefore, molecular testing of the FBN1 gene can be of value in the
diagnostic work-up for MFS in specific situations.
The FBN1 gene (OMIM 134797) involved in MFS was localized in 1990 on
chromosome 15q21.1 and, 1 yr later, the gene was isolated (4–6). The gene
spans approx 200 kb of genomic DNA containing 65 exons. The coding region
possesses 9663 nucleotides and, after translation, a protein of 350 kDa is
formed (7). FBN1, the protein product of FBN1, is a cysteine-rich monomeric
glycoprotein containing 47 epidermal growth factor-like motifs, which are
common in extracellular matrix proteins (8). Each motif contains six highly
conserved cysteine residues. Two other common motifs are the latent trans-
forming growth factor-β1-binding protein motif, containing eight cysteine resi-
dues and a Fib-motif, which is a fusion of portions of the epidermal growth
factor-like and latent transforming growth factor-β1-binding protein motifs (9).
Mutations causing changes in cysteine residues result in disturbances of in-
tramolecular or intermolecular disulfide bonds. FBN1 is a major structural
component of the extracellular microfibrils, providing numerous functions in
the body, including scaffolding for elastic fibers. To date, more than 500 dif-
ferent FBN1 mutations have been identified, including missense mutations
(65%), mainly resulting in cysteine substitutions; premature termination muta-
tions (20%); exon-skipping mutations (10%); and others, such as small inser-
tions, deletions, or splice site mutations (http://www.umd.necker.fr) (10). With
a few exceptions, all known FBN1 mutations identified to date are unique, and
approx 25 to 30% of cases represent new mutations (11). Because of the high
interfamilial and intrafamilial variability, genotype–phenotype correlations for
FBN1 mutations are hard to identify, with the exception of neonatal MFS, which
is caused by mutations clustered in exons 24 to 27 and exons 31 and 32 of the
FBN1 gene (12).
Various mutation detection methods have been designed for the identifica-
tion of sequence variations in the FBN1 gene (13,14). These techniques com-
prise single-strand conformation polymorphism analysis, heteroduplex analysis,
and direct sequencing (15,16). Denaturing high-performance liquid chroma-
tography (DHPLC), a new mutation detection technique that was recently in-
FBN1 Mutation Analysis in Patients With MFS 83

troduced, has allowed the automation of at least part of the laborious procedure
(17,18). DHPLC has several characteristics that makes it an attractive method-
ology to perform mutation analysis, especially for large genes with many ex-
ons. The advantages are the high sensitivity, rapid analysis time, on-line UV
absorbance detection, and lack of a post-polymerase chain reaction (PCR)
sample treatment requirement. The detection of mutations or polymorphisms,
independent of the location within the fragment, is based on differential reten-
tion of double-stranded homo- and heteroduplex fragments under conditions of
partial thermal denaturation (19). Separation of DNA fragments is dependent
on the elution strength of the organic solvent in the mobile phase and the num-
ber of ion pairs formed between the negatively charged DNA fragments and the
positively charged triethylammonium acetate (TEAA) ions adsorbed to the sta-
tionary phase. The technique allows the detection of single base substitutions,
small insertions, or deletions in 100- to 1000-bp DNA fragments by fraction-
ation of heteroduplexes under partially denaturing conditions. The analysis by
DHPLC is automated and very rapid, and nearly 95% of sequence alterations
can be detected.
To perform mutation analysis of the FBN1 gene, genomic DNA (gDNA)
and/or complementary DNA (cDNA) is isolated from peripheral blood leuko-
cytes or skin fibroblasts, respectively (see Note 1). Mutation screening of the
genomic sequences is performed by amplification of 65 fragments, each repre-
senting 1 exon with flanking intron sequences, whereas 24 overlapping frag-
ments are analyzed for the cDNA sequence. Mutation screening of the amplified
product is performed with DHPLC. PCR products resulting in aberrant patterns
are sequenced to determine the exact nature and position of the mutation.

2. Materials
1. Dulbecco’s Modified Eagle’s Medium (Invitrogen).
2. Fetal calf serum (FCS) (Invitrogen).
3. Penicillin G/streptomycin, kanamycine (Invitrogen).
4. Minimum Essential Medium (nonessential amino acids) (Invitrogen).
5. Easy DNA kit (Invitrogen).
6. Micro-To-Midi Total RNA Purification System (Invitrogen).
7. QIAmp DNA blood mini kit (Qiagen Inc, Valencia, CA).
8. PCR tubes.
9. PCR-quality water.
10. 10X PCR buffer (Invitrogen).
11. 25 mM MgCl2 (Invitrogen).
12. dNTP solution (dCTP, dATP, dTTP, and dGTP) (Amersham Bioscience).
13. 10 pmol/μL amplification primer for gDNA and cDNA FBN1 fragments (see Sub-
heading 3.3.).
14. 5 U/μL platinum Taq polymerase (Invitrogen) or standard Taq DNA polymerase.
84 Coucke et al.

15. 100 ng/μL human gDNA.

16. Thermal cycler (e.g., Perkin–Elmer 9600 or equivalent).
17. HPLC instrumentation (e.g., WAVE DNA Fragment Analysis System,
Transgenomic or similar systems from Varian or Hewlett–Packard).
a. 0.1 M TEAA buffer, pH 7.0.
b. Eluent A: 0.1 M TEAA.
c. Eluent B: 25% acetonitrile in 0.1 M TEAA.
18. Equipment and reagents for agarose gel electrophoresis and ethidium bromide
staining.
19. Additional equipment and reagents for sequencing analysis.
a. BigDye terminator cycle sequencing reaction kit (Applied Biosystems or
equivalent).
b. ABI3100 DNA analysis system (Applied Biosystems or equivalent).

3. Methods
The methods described below outline:
1. Sampling and tissue culture.
2. DNA isolation procedures.
3. Amplification of DNA fragments.
4. Mutation analysis by DHPLC.
5. Characterization of the mutation by DNA sequencing.

3.1. Sampling and Tissue Culture

Fibroblast cultures are established from a skin biopsy, usually from the in-
ner upper arm. The biopsy is mechanically diced and put into culture. The
medium used is Dulbecco’s Modified Eagle Medium supplemented with 10%
FCS, 100 U/mL penicillin plus 100 μg/mL streptomycin, 100 μg/mL kanamy-
cin, and 1X nonessential amino acids. The cells are grown at 37°C with 5%
CO2. Cells from the second passage are trypsinized and seeded in several dif-
ferent recipients for total RNA isolation (P60 cell culture disc) or for genomic
DNA isolation (if no blood is available) (T80 flask). Cells from passage 3 are
trypsinized, supplemented with 10% FCS and 10% dimethylsulfoxide, and
stored in liquid nitrogen. If more RNA of DNA is necessary, cells are grown
starting from the frozen stock.
3.2. Genomic DNA Isolation, Messenger RNA Isolation, and cDNA
Production
Genomic DNA is isolated from the fibroblasts or from leukocytes using kits
provided by Qiagen and Invitrogen. Before RNA extraction, cell cultures are
incubated with 100 μg/mL cycloheximide (Sigma-Aldrich, St. Louis, MO) for
16 hr. Consequently, total RNA is obtained from the skin fibroblasts cultures
FBN1 Mutation Analysis in Patients With MFS 85

using the Micro-to-Midi Total RNA Purification System (Invitrogen), as de-

scribed by the manufacturer. First-strand cDNA is synthesized from total RNA
(1 μg) using Moloney murine leukemia virus reverse transcriptase (Invitrogen),
using random hexanucleotide primers. For some experiments, RNA samples are
treated with RNase-free DNase (Invitrogen) before cDNA synthesis to avoid
genomic DNA contamination in the reverse transcriptase PCR experiments.
3.3. Amplification of DNA Fragments
The complete cDNA analysis comprises amplification of 24 overlapping
fragments with an average size of 450 bp. cDNA primers, together with their
respective annealing temperature, are represented in Table 1.
Mutation screening of the FBN1 genomic sequences is performed by ampli-
fication of 65 fragments, each representing 1 exon with flanking intron
sequences, with an average size of 260 bp (Table 2).
1. Prepare mix for 20 reactions (see Table 3 and Note 2).
2. Dispense 24 μL of mix into a PCR tube.
3. Add 1 μL of genomic DNA (100 ng/μL).
4. Set up negative control (1 μL water).

3.4. Amplification of DNA

Amplify using a touch-down PCR program on a thermal cycler, programmed
according to Table 4 (see Note 3).
PCR products are denatured at 96°C for 5 min and allowed to reanneal to form
homoduplexes and heteroduplexes by cooling slowly to room temperature.
Analyze 5 μL of PCR product by electrophoresis on a 2%-agarose gel, and
stain with ethidium bromide to confirm amplification of the desired fragment.
3.5. Mutation Analysis by DHPLC
DHPLC is performed on a WAVE system (Model 3500HT) using the Navi-
gator™ software purchased from Transgenomic (Santa Clara, CA).
1. Before the analysis, column performance should be tested by injecting commer-
cially available Mutation Control Standards (low and high range), according to
the guidelines of the manufacturer.
2. A blank should be run (0 μL injection volume), using the method of the samples
that will be analyzed, to equilibrate the column and preheat the oven.
3. Five microliters of crude PCR product is loaded into the system (see Note 4).
Running conditions: flow rate of 1.5 mL/min.
Both the column temperature and the acetonitrile gradient (Eluent A/Eluent B)
are determined with the Navigator software for each DNA fragment. To achieve
the best possible separation, the amplicon melting curves have to be located be-
tween 40 and 99% of the helical fraction. If more than one significant melting
86 Coucke et al.

Table1
FBN1 cDNA Primers and Annealing Temperatures
(Touch-Down PCR)

Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

1 F ATGCGTCGAGGGCGTCTGCT 60>48
R GCTACCTCCATTCATACAGCGA
2 F GATAGCTCCTTCCTGTGGCTCC 60>48
R CCGTGCGGATATTTGGAATG
3 F CCCCTGTGAGATGTGTCCTG 60>48
R TTGGTTATGGACTGTGGCAGC
4 F ACAGCTCTGACAAACGGGCG 60>48
R TGCAGCGTCCATTTTGACAG
5 F GCCAGTTGGTCCGCTATCTC 60>48
R ACATGAAAGCCCGCATTACAC
6 F AATGGCCGGATCTGCAATAA 60>48
R CTGGCCTCTCTTGTATCCACCA
7 F CTGGCTGTGGGTCTGGATGG 60>48
R GCAGTTTTTCCCAGTTGAATCC
8 F ATCTGTGAAAACCTTCGTGGGA 60>48
R AGGTGGCTCCATTGATGTTGA
9 F GTCTGCAAGAACAGCCCAGG 60>48
R TGGGACACTGACACTTGAATGA
10 F TACTCAAGAATTAAAGGAACA 60>48
R CGGCATTCGTCAATGTCTGTGC
11 F CATTGGCAGCTTTAAGTGCAGG 60>48
R ACCACCATTCATTATGCTGCA
12 F CCATTCAACTCCCGATAGGCT 60>48
R TTTTCACAGGTCCCACTTAGGC
13 F CAGGTGCTTGTGTTATGATG 60>48
R GCACAGACAGCGGTAAGA
14 F GATTGGAGATGGCATTAAGTGC 60>48
R TGTTGACACAGTTCCCACTGA
15 F CTACGAACTGGACAGAAGCGG 60>48
R ATACAGGTGTAGTTGCCAACGG
16 F ACTACCTGAATGAAGATACACG 60>48
R GACCTGTGGAGGTGAAGCGGTAG
17 F TCAACATGGTTGGCAGCTTCC 60>48
R AAAGATTCCCATTTCCACTTGC
18 F ACAATTGGTTCCTTCAACTG 60>48
R GCACAAATTTCTGGCTCTT

(continued)
FBN1 Mutation Analysis in Patients With MFS 87

Table1 (continued)

Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

19 F CTTGGATGGGTCCTACAGATGC 60>48
R CACATTCTTGCAGGTTCCATT
20 F GGTTATACTCTAGCGGGAATG 60>48
R TCCCACGGGTGTTGAGGCAGCG
21 F AGCGGAGACCTGATGGAGAGG 60>48
R CAGTTGTGTTGCTTGGTTGCA
22 F CAAGAGGATGGAAGGAGCTGC 60>48
R GAACTGTTCATACTGGAAGCCG
23 F CTACCTCCAGCACTACCAGTGG 60>48
R GTAGCCATTGATCTTACACTCG
24 F CACCTGGTTACTTCCGCATAGG 60>48
R ATGATTCTGATTGGGGGAAAA

F, forward; R, reverse.

domain is present in a fragment, additional analysis temperatures are selected,

with a maximum of four temperatures. The Navigator software automatically
calculates the corresponding gradient for each amplicon (see Note 5).
4. After eluting from the cartridge, the separated DNA fragments travel to the
detector, where they are detected by UV absorption. The data collected from the
detector are displayed in real-time on the computer monitor. Consequently,
selected injections are aligned using mutation calling (Navigator Software). This
allows the separation of the wild types from the mutations or polymorphisms (Fig.
1).

3.6. Characterization of Mutations by DNA Sequencing

Amplified fragments demonstrating alterations in DHPLC elution profile
are confirmed in a repeat analysis. Sequence variation is identified by auto-
mated bidirectional sequencing using an ABI3100 sequencer (Applied
Biosystems) with Big Dye terminator chemistry (Applied Biosystems), accord-
ing to the guidelines of the company.

4. Notes
1. If fibroblasts are available, mutation screening is usually started at the cDNA
level. Using this approach, only 24 cDNA amplicons have to be analyzed on the
WAVE, which is significantly faster than the mutation analysis on genomic DNA,
in which 65 exons need to be analyzed. Surprisingly, sequencing of cDNA frag-
ments showing an aberrant WAVE pattern often fails to reveal the causal base
change after sequencing. We assume that this is because of the uneven expres-
sion of the wild-type and mutant alleles, which is detectable by DHPLC but which
88 Coucke et al.

Table 2
FBN1 gDNA Primers and Annealing Temperatures
(Touch-Down PCR)

Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

1 F CAGACCGAGCCCCGG 62>50
R CATCCTGCCCGTTGTTCT + 6%DMSO

2 F TCTGCCAGGATTCATCTTGC 62>50

R CAACACAACAAAAGAAGGAC

3 F AAATCCATGTGCTAACAGAC 54>42

R GGTATAACCACATAAAATAA

4 F AAAGCGTCTCAGCTCTCTCC 60>58

R AAAATCCATCAGCACTTATCTC

5 F AAAGCGTCTCAGCTCTCTCC 62>50

R AGGTACCAGCATGTCTTTAC

6 F TCTGCATGATGGTTCCTGC 56>44

R CCATAGCAAATAAGATTAATCC

7 F TCACATTTTATTCTGCAATGAA 60>48

R TTTCTAATGTTGAGTTTTGCCT

8 F CCAGGGACATGATTTGACTAG 62>50

R TATGTGCTCCTTAACAAGCTTG

9 F GTTACAAGTATTATCTCAGCG 62>50

R GCTGGGATGGGATATTCTG

10 F AAATAAGGATGACTTCTGTGG 58>46

R AACTTATTTAATGACTAAAGTAGC

11 F ACTGATGAAAGATACCATAGTT 58>46

R AGGAACAGAATTACAACAGAC

12 F AGAATTATGAGGTATTGCTATG 60>48

R CAGTTAGCATATATGTCCCAC

13 F TCCCCTAAATAAAGCTATTTC 62>50

R AGACCCCTGATATTGAAACTG

14 F TTGGTTTCCTTCGTAAGCTT 56>44

R GGCACGTGAAGAACATGAT

15 F TTTTCAAGGGTTAAAACATAATTG 56>44

R GAGCGTTTGTTACCATTG

16 F CTCATCTGTTTGAAGTGACAG 60>48

R GCCAGCCTTCTGCCACC

17 F ACTTTGGAGGAAATGATGTGTGC 62>50
R GCCAGCCTTCTGCCACC

18 F TCAGAATATCTTACAGTGAG 60>48

R GCCAGCCTTCTGCCACC

19 F AGCAAAGTAGATACAGGCAAA 62>50

R AGTCTTATGGTTTTCTAATGGC

(continued)
FBN1 Mutation Analysis in Patients With MFS 89

Table 2 (continued)

Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

20 F TTAGCCCAGCTTTACTGTGTGG 58>46
R TTGATAAACATAGAAAAATCATTCTC

21 F TATAATTCCAAGGTGTATGTTTG 54>42

R AGATAAATGAAATACTAGGCTTC

22 F CTACTTCATGTTCCAGGTC 60>48

R CTGTTCCGTTTTGTAGTTCTC

23 F TATGAACTTACCAGGTTCAAAAT 54>42

R TTGGGTGTGTGTCTGTACC

24 F ACAGCAAATTATTATGTGTGCAG 65>53

R ATCAAGTAGAGTGCTGAGATC

25 F CAAGAACTTCCAACCTTCATG 58>46

R GTCTCAGGACAGCCTTAATT

26 F AATTAAGGCTGTCCTGAGACT 62>50

R GCTTCATGGAATCCTTCTCTT

27 F AAGATGGACACCCAGCAATG 62>50

R CACCCAAACATAAGCTTCCAAC

28 F AGTTGTTTGAATGACATCATTG 54>42

R TAACATAACATAACATAAAATAAAG

29 F CAGACATCCAAACCATATCAG 62>50

R GAACCTACTGAGAGATTCAAC

30 F AATAGTCTTATGCTAGTAGGC 62>50

R ACAGTGCTTATGACTAACAAG

31 F GGAAAGTACTCAATGATATCAAATAG 60>48

R ATCTATAATTATGATACCAATCTC

32 F CCAAAAGACATTTGTGCTGAG 62>50

R GTGTAATCTATGCAGTCCTTG

33 F GTGAGTAGGAAAGTAACAGAGG 56>44

R CTGACCCAGTCTTCAAAAAAG

34 F CGAGGAAGAGTAACGTGT 54>42

R TCATCAAGCCCAGCAAGGCTC

35 F TTGCCTAATTATATTTGGCAGGTTTT 65>53

R CTTGTCTTCTGTGACGGCCC

36 F CTCTAGATTGGGCCCTGTTC 58>46

R TTGAGAATGGAATGTTTGGTGC

37 F GTAGAAAGATTCTGCCTGATG 62>50
R GAACTGGCTGGAGTTGAAAT

38 F GGTGTTAACTTACTTCAGACG 62>50

R CCTGGTAGCTCCTGGCACTC
39 F CCTTGGGTTTATTTACAATGC 54>42

R TCTGCAAGACCTTATCATCCT

(continued)
90 Coucke et al.

Table 2 (continued)

Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

40 F AAGTTTTCATATTCACATACCACTT 62>50
R GATGAGAACCAAACATGCATTA

41 F GCTTGTTGAGTATCCACTTAG 62>50

R GCTTCCTTCGCTAAGACTG

42 F CCAATTATTGTTCTTTGCTGAC 60>48

R ACCAGAAAGTTCTGACAATG

43 F ACACGCACGCACTTTCCAT 62>50

R TGTGAAATTCGCCAAGTGTG

44 F TGCTGTACACATCTATGTTGTC 56>44

R TATTCTTCAGCTTAACTAATCTG

45 F GAGCTAGGATTACTCCTGAG 62>50

R TGCTGCATATCTGTCTGTG

46 F AAGTTCTCAGCCTATGGATG 60>48

R TAATTACAAAGAACACATATAAAAC

47 F TGATTATTGCTGGGATTATGAC 62>50

R CTGCATGATTCCTTGAGTGG

48 F GATGGAAGTCATGCCAGTG 62>50

R GGACACCCGACACTCCTC

49 F TGTGTTTGGTACCTGATGATG 62>50

R ACAAAGAAACAGAGCTTTGCC

50 F CTATGGTGCAATACGGACTC 62>50
R AAGGCCTACAGTCTTACTTAC

51 F AGCTTGTAATGAATTGCTATTG 60>48

R AAGCAGATTGAGAATACTGAG

52 F TTGTCCCTTCATTTAGATAGC 56>44

R CCTGATGGTGACTCACTAG

53 F TCTGATAGAATAAAAGGTATTATC 56>44

R TAAGACTTGTAATCAACCAATTG

54 F TTGGTAGGTTCCCTTTTGTTG 62>50

R AATTCCCAGCCTTCTCCTAC

55 F AACATTTTATGTTTAAAAGTCAGG 56>44
R AGCCCAGGTTCCTTCTGTCCACTGTC

56 F GCTCCATCCTCTATAAAATGG 62>50

R AAGTCTGGGTTTCCAGCATC
57 F GACCAAATTTTTAATATTTTGTTTG 62>50

R CCATATTTTCATCTGTGTTTCAC

58 F CATATTAATGTTGTCAATTTTATGA 62>50

R CCATAATCTAAATTTCCACTTG

(continued)
FBN1 Mutation
Table 2Analysis in Patients With MFS
(continued) 91
Exon Annealing
no. Direction Primer sequence (5'→3' direction) temperature

59 F GCGTGTACACATCATTTTTAG 56>44
R CTGTGGAGTTCTTACAGGCC

60 F ATCCTGTTTTGTTGGCTTGAC 62>50

R GAATCGCTACAATCCATGTAC

61 F TGATACAAAGAGAGCTTTGGG 62>50

R GCCAATAGCCACACAGGCCAC

62 F AGATTCTTGAAGTTTTTGGTGGTA 62>50

R CAGAAAGCAAGCAGTGTTTTG

63 F CAAGTGGCCAGATCCAATG 65>53

R GGTTCTCCTCTGCTAGGAC

64 F AGAACTCTTGTACCACCTAC 62>50

R AGTTTCTCCCTGGGGAGC

65 F TTTAATATGAGAGCTAAGTGGC 60>48

R TTGTACCTATGATATGATGATTC

Table 3
Preparing PCR Mixes
Volume (μL) Final concentration
dNTPs (1 mM) 3 0.12 mM
10X PCR buffer 2.5 1X
25 mM MgCl2 0.75 1.5 mM
Forward primer (30 μM) 0.5 0.6 μM
Reverse primer (30 μM) 0.5 0.6 μM
5 U/μL Taq polymerase 0.1 0.02 U/μL
PCR water 16.65
Total 24

Table 4
DNA Amplification Using a Touch-Down PCR
Program on a Thermal Cycler

1 cycle 1 min 94°C (denaturation)

12 cycles 20 s 94°C (denaturation)
15 s 62°C (annealing)a
1 min 72°C (extension)
24 cycles 40 s 94°C (denaturation)
40 s 50°C (annealing)
30 s 72°C (extension)
1 cycle 10 min 72°C (extension)
a1°C decrease per PCR cycle (62°C → 50°C).
92 Coucke et al.

92
 FB
N1

Mu
tati
on

An

aly
93

sis

in
Pat
Fig. 1. Sample chromatograms. The three figures display aligned chromatograms from different patients. The aberrant
ien
pattern is indicated with an arrow and the corresponding base change in the FBN1 gene is indicated. ts

Wi
th

MF
S
94 Coucke et al.

is often more difficult to identify by direct sequencing. To identify the base change
responsible for the aberrant WAVE pattern, the corresponding exons located
within the cDNA fragment are then separately analyzed by DHPLC. Consequently,
the exon containing the aberrant WAVE pattern is sequenced.
2. During the set up of the PCR reaction, it is important to avoid additives often
present in commercially available polymerase mixtures and reaction buffers, such
as gelatin, bovine serum albumin, Triton, and so on. These components can dam-
age the separation cartridge severely or reduce the amount of runs.
3. A touch-down PCR is not mandatory, however, by using this approach, it is pos-
sible to reduce the amount of different PCR programs. This allows amplification
of several amplicons in a single PCR run, making the total procedure much faster.
4. It is recommended that high-yield PCR product be loaded on the WAVE system
if UV absorbance is used as detection method. This is necessary to obtain clear
peaks in the chromatograms produced by the WAVE analysis. Low-yield PCR
products result in aberrant WAVE patterns that do not contain base changes.
5. To avoid elution of the fragment outside of the separation window during DHPLC
analysis, time shifts are adjusted in the method designed for each exon at each
oven temperature. This is done when the oven temperature differs at least 3°C
(plus or minus) from the predicted melting temperature of the amplicon by the
Navigator software.

Acknowledgments
The authors thank Dr. D. Milewicz and Dr. E. Putman for providing the
FBN1 cDNA primer sequences. This work was supported by grant G.0290.02
from the Fund for Scientific Research-Flanders to ADP.

References
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Marfan syndrome in a Scottish population. J. Med. Genet. 31, 51–54.
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3. De Paepe, A., Devereux, R. B., Dietz, H. C., Hennekam, R. C., and Pyeritz, R. E.
(1996) Revised diagnostic criteria for the Marfan syndrome. Am. J. Med. Genet.
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4. Kainulainen, K., Pulkkinen, L., Savolainen, A., Kaitila, I., and Peltonen, L. (1990)
Location on chromosome 15 of the gene defect causing Marfan syndrome. N. Engl.
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5. Lee, B., Godfrey, M., Vitale, E., et al. (1991) Linkage of Marfan syndrome and a
phenotypically related disorder to two different fibrillin genes. Nature 352, 330–
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6. Dietz, H. C., Cutting, G. R., Pyeritz, R. E., et al. (1991) Marfan syndrome caused
by a recurrent de novo missense mutation in the fibrillin gene. Nature 352, 337–
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FBN1 Mutation Analysis in Patients With MFS 95

7. Sakai, L. Y., Keene, D. R., and Engvall, E. (1986) Fibrillin, a new 350-kD glyco-
protein, is a component of extracellular microfibrils. J. Cell Biol. 103, 2499–2509.
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PCR products and DNA fragments: evidence for solvent-induced bends in DNA
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Mutations in Noonan Syndrome 97

6
Mutation Analysis of PTPN11 in Noonan Syndrome
by WAVE

Navaratnam Elanko and Steve Jeffery

Summary
The chapter details the methodology for polymerase chain reaction amplification and WAVE
denaturing high-performance liquid chromatography (DHPLC) analysis for all coding exons
for the gene PTPN11, which is mutated in approx 50% of cases of Noonan Syndrome. Although
DNA sequencing is initially required to determine the mutation(s) detected by WAVE
(sequencing methods are not described in this chapter), each mutation has its own DHPLC
signature, and experienced operatives can determine known mutations on this basis. The new
Navigator software has made this process more reliable.
Key Words: Noonan syndrome; WAVE; DHPLC; mutation analysis.

1. Introduction
Noonan Syndrome (NS) is a genetic disorder with an autosomal-dominant
manner of inheritance, although approx 50% of cases are sporadic new muta-
tions (1). The primary clinical features include a typical facial appearance with
widely spaced eyes and low-set ears, sparse curly hair, pectus deformities, and
often a cardiac lesion (most commonly pulmonary valve stenosis but some-
times hypertrophic cardiomyopathy). A gene locus for NS was identified at
12q24 in 1994 (2), but it was clear that the condition was heterogeneous. A
collaborative approach between three laboratories eventually found the gene
that was located at 12q24 to be PTPN11 (3). This gene encodes the protein,
src-homology region 2-domain phosphatase-2 (SHP-2), which is a nonreceptor
tyrosine phosphatase involved in a variety of cellular pathways (3), including
semilunar valvulogenesis (4). An interesting genotype–phenotype correlation,
with pulmonary valve stenosis more common in cases with a PTPN11 muta-
tion and hypertrophic cardiomyopathy more common in those without the
PTPN11 mutation, has been suggested by some groups (5–7). One publication
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

97
98 Elanko and Jeffery

found no difference in the distribution of cardiac defects between those with

and without PTPN11 mutations (8). Table 1 presents a list of the distribution
of mutations found to date in PTPN11 for a diagnosis of NS.
There is a variety of methods for screening for mutations in PTN11; the
method chosen depends partly on available funding and equipment. Although
direct sequencing is clearly the most likely to give the closest to 100% accu-
racy, it is possible to miss heterozygous changes even with this technology, and
it is comparatively expensive. Single-stranded conformational polymorphism
(SSCP) analysis, even if run on an automated sequencer, is only approx 95%
accurate (9) and requires fluorescently tagged primers, but WAVE analysis is
inexpensive, rapid, with 95 to 100% sensitivity reported (10,11). The initial
outlay expense for the equipment is clearly a problem for smaller laboratories,
in which SSCP slab gel analysis (sensitivity, 69–85%) is likely to be the favored
option, followed by direct sequencing of abnormal conformers. For SSCP, the
single-stranded DNA fragments produce the variously sized bands on a gel,
whereas, in denaturing high-performance liquid chromatography (DHPLC), the
heterozygous duplex of the normal and mutant DNA polymerase chain reaction
(PCR) fragments is detected on a column. DHPLC has the added advantage
over SSCP that larger fragments can be used (the largest fragment that has been
successfully analyzed in our lab was 743 bp). Because DHPLC is far superior
to SSCP in our hands, we detail the DHPLC methodology for the first step in
mutation detection. Any conformer that differs from the normal DHPLC pat-
tern is suggestive of a sequence variation, and direct sequencing should be per-
formed using an automated DNA sequencer, if available, or manually, if an
automated DNA sequencer is not available. Sequencing reactions are not de-
tailed in this chapter.

2. Materials
1. PCR machine (various suppliers, such as Techne, Hybaid, MJ Research, and
Applied Biosystems).
2. WAVE Nucleic Acid Fragment Analysis System (or WAVE System) 3500HT
(Transgenomics, Cheshire, UK or Omaha, NE).
3. DNA extraction kits (there are several on the market).
4. For PCR reactions: Taq polymerase plus buffer. There are a huge number on the
market and the WAVE user must be cautious in choosing because there are sub-
stances that are incompatible with the technology (see Note 1). Amplitaq Gold
with PCR Buffer 11 or Amplitaq Gold buffer and MgCl2 (Applied Biosystems,
cat. no. 8080241) are very robust, as is FastStart Taq (Roche).
5. dATP, dCTP, dGTP, and dTTP.
6. 20 pmol of each primer (see Table 2).
7. 50 ng DNA.
Mutations in Noonan Syndrome 99

Table 1
PTPN11 Mutations in NSa
Nucleotide Amino acid
Exon No. of cases substitution substitution Domain

1 1 C5T Thr2Ile N-SH2

2 3 A124G Thr42Ala N-SH2
3 1 C174G Asn58Lys N-SH2
3 2 G179C Gly60Ala N-SH2
3 2 G181A Asp61Asn N-SH2
3 4 A182G Asp61Gly N-SH2
3 5 T184G Tyr62Asp N-SH2
3 11 A188G Tyr63Cys N-SH2
3 1 G205C Glu69Gln N-SH2
3 1 T211C Phe71Leu N-SH2
3 2 G214T Ala72Ser N-SH2
3 2 C215G Ala72Gly N-SH2
3 21 C218T Thr73Ile N-SH2
3 2 G228C Glu76Asp N-SH2
3 3 G228T Glu76Asp N-SH2
3 6 A236G Gln79Arg N-SH2
3 2 A236C Gln79Pro N-SH2
3 4 A317C Asp106Ala N-SH2/C-SH2 linker
4 1 G417C Glu139Asp C-SH2
4 1 G417T Glu139Asp C-SH2
4 1 G417A Glu139Asp C-SH2
7 1 A767G Gln256Arg PTP
7 1 A836G Tyr279Cys PTP
7 2 A844G Ile282Val PTP
7 1 T853C Phe285Leu PTP
8 1 T854C Phe285Ser PTP
8 28 A922G Asn308Asp PTP
8 4 A923G Asn308Ser PTP
8 1 A925G Ile309Val PTP
13 1 G1502A Arg501Lys PTP
13 2 G1505C Ser502Thr PTP
13 1 G1508C Gly503Arg PTP
13 4 A1510G Met504Val PTP
14 1 C1678T Leu560Phe PTP
aFrom refs. 5–8. Index cases only.
 100 Elanko and Jeffery

Table 2
Primer Pairs and Tann to Amplify the PTPN11 Coding Sequence,
and Sizes of PCR Productsa

Product
Exon Primer sequence Tann Length

1b Forward 5'-gctgacgggaagcaggaagtgg-3' 60°C 589 bp

Reverse 5'-CTGGCACCCGTGGTTCCCTC-3'
2 Forward 5'-ACTGAATCCCAGGTCTCTACCAAG-3' 60°C 405 bp
Reverse 5'-cagcaagctatccaagcatggt-3'
3 Forward 5'-cgacgtggaagatgagatctga-3' 60°C 384 bp
Reverse 5'-CAGTCACAAGCCTTTGGAGTCAG-3'
4 Forward 5'-aggagagctgactgtatacagtag-3' 58°C 447 bp
Reverse 5'-catctgtaggtgatagagcaaga-3'
5 Forward 5'-ctgcagtgaacatgagagtgcttg-3' 60°C 329 bp
Reverse 5'-GTTGAAGCTGCAATGGGTACATG-3'
6 Forward 5'-tgcattaacaccgttttctgt-3' 54°C 282 bp
Reverse 5'-GTCAGTTTCAAGTCTCTCAGGTC-3'
7 Forward 5'-GAACATTTCCTAGGATGAATTCC-3' 56°C 271 bp
Reverse 5'-GGTACAGAGGTGCTAGGAATCA-3'
8 Forward 5'-GACATCAGGCAGTGTTCACGTTAC-3' 57°C 350 bp
Reverse 5'-CCTTAAAGTTACTTTCAGGACATG-3'
9 Forward 5'-GTAAGCTTTGCTTTTCACAGTG-3' 56°C 357 bp
Reverse 5'-CTAAACATGGCCAATCTGACATGTC-3'
10 Forward 5'-GCAAGACTTGAACATTTGTTTGTTGC-3' 60°C 284 bp
Reverse 5'-GACCCTGAATTCCTACACACCATC-3'
11 Forward 5'-CAAAAGGAGACGAGTTCTGGGAAC-3' 60°C 453 bp
Reverse 5'-GCAGTTGCTCTATGCCTCAAACAG-3'
12 Forward 5'-GCTCCAAAGAGTAGACATTGTTTC-3' 56°C 250 bp
Reverse 5'-GACTGTTTTCGTGAGCACTTTC-3'
13 Forward 5'-CAACACTGTAGCCATTGCAACA-3' 60°C 356 bp
Reverse 5'-CGTATCCAAGAGGCCTAGCAAG-3'
14c Forward 5'-ACCATTGTCCCTCACATGTGC-3' 60°C 259 bp
Reverse 5'-CAGTGAAAGGCATGTGCTACAAAC-3'
15 Forward 5'-CAGGTCCTAGGCACAGGAACTG-3' 60°C 321 bp
Reverse 5'-ACATTCCCAAATTGCTTGCCT-3'
aReproduced from ref. 5.
bBecauseof the high GC content of the exon 1 sequence, a PCR buffer designed for GC-rich
sequences is needed. There are several on the market. One effective buffer is the GC-rich PCR
System from Roche.
cGC-clamps were added at the 5' for DHPLC analysis: forward primer, 5'-

CCCGCCGCCCCCGCCG-3'; reverse primer, 5'-CCGCGCCCCCGCCCG-3' (product length, 290 bp).

Tann, annealing temperature.
Mutations in Noonan Syndrome 101

8. 96-well PCR plates that fit the PCR machine. We use PCR Plate, Thermo-Fast 96
(ABgene, cat. no. AB-0600). The plates used are important because they deter-
mine the Z-value (depth of the well) of the rack parameter setting of the
autosampler.
9. Adhesive PCR film (ABgene, cat. no. AB-0558).
10. WAVE-optimized DHPLC buffers and DNASep column from Transgenomic:
a. Buffer A: 0.1 M triethylammonium acetate (TEAA) in water, pH 7.0.
b. Buffer B: 0.1 M TEAA, 25% acetonitrile (ACN), pH 7.0.
11. Syringe wash solution: 8% ACN, in water.
12. Solution D: 75% ACN, 25% water.
13. DHPLC column: DNASep HT cartridge.
The solutions in steps 11 and 12 can easily made in-house with HPLC-grade
ACN and 18.2 ΜΩ-cm quality water.

3. Methods
Because there are areas of the gene in which mutations are more frequent,
there has to be a strategy for exon analysis. Exons 3, 8, and 13 should be ana-
lyzed first. Any samples in which there is a change detected by WAVE should
then be investigated by direct sequencing to determine whether the change is a
polymorphism or a mutation. Those samples with no base changes should then
have exons 7, 4, and 2 analyzed. Those samples still negative for any base change
would then be investigated for the remainder of the coding region of PTPN11.
3.1. Polymerase Chain Reaction
For exons 2 to 15, each 25-μL reaction contains approx 50 ng DNA, 1 U of
AmpliTaq Gold DNA polymerase, and 20 pmol of each primer (see Table 2).
WAVE analysis is extremely sensitive and can detect a base change even if
adjacent to the primer. Therefore, primers should be designed to avoid any
unwanted intronic polymorphisms, if possible. For each reaction, use 75 μM
each dNTP and the standard PCR buffer for the polymerase used, with a final
concentration of MgCl2 of 1.5 mM. Primer sequences, product lengths, and
annealing temperatures are shown in Table 2.
1. A master mix containing all components except for DNA should be prepared just
before starting the PCR reaction. There should be sufficient volume for all of the
samples, plus three extra (in case of error), and a negative control with no DNA,
to ensure that there is no contamination of the mix.
2. DNA should be diluted to give approx 50 ng/μL.
3. The master mix (24 μL) is added to as many wells as required in the PCR plate,
plus one well for the negative control, and one well for the positive control (a
known mutation), if a positive control is available. The plate is placed on the
PCR machine and an adhesive PCR film placed over the plate.
102 Elanko and Jeffery

4. All PCRs are performed using the same time parameters but varying annealing
temperatures. For the first cycle, an 8-min denaturing step at 94°C is used, fol-
lowed by 33 cycles of 94°C for 45 s; 54°C to 60°C for 30 s (see Table 2 for
relevant temperature for each exon); and 72°C for 45 s; with a final extension
step of 10 min at 72°C. The primers are designed to include intron–exon bound-
aries plus consensus sequences (see Note 2).
5. After PCR amplification, the plate is removed from the PCR machine and trans-
ferred to the WAVE analyzer.

3.2. WAVE (DHPLC) Analysis

The transgenomic WAVE machine operates using the principle of HPLC, a
chromatographic separation technique that was far more familiar to protein
biochemists than molecular biologists until recently. It uses a DHPLC column
packed with a nonporous hydrophobic separation matrix (polystyrene–
divinylbenzene copolymer beads) that detects the presence of heteroduplexes
that are formed by the hybridization between the wild-type and the variant
strands.
Proper maintenance of the WAVE system is crucial for reliable and repro-
ducible results.
Running a mutation standard (and a sizing standard) before analyzing a batch
of test samples is highly recommended (see Note 3). Any heterozygous
sequence variation in the target DNA produces a mixture of wild-type and mu-
tant PCR products when amplified. To enhance the formation of heterodu-
plexes, the PCR products (in the sealed PCR plate) are heated at 94°C for 5 min
and cooled slowly to 20°C at a rate of 1.2°C/min. A method can be set up in a
PCR machine to achieve this. Crude PCR product is used in the DHPLC analy-
sis and no post-PCR handling, other than this heteroduplexing process, is
involved (see Note 4).
The autosampler of the WAVE 3500HT system can accommodate two 96-
well plates on a temperature-controlled rack (see Note 5). Heteroduplexed
samples are automatically injected through the DNASep column that is sited in
a temperature-controlled oven. Oven temperature for analysis, which causes
partial denaturation of the DNA fragments, is predicted by the Navigator soft-
ware (Transgenomic), and the user is also able to choose alternate tempera-
tures depending on the melting profile of the DNA fragment (see Note 6).
Partially denatured homoduplexes and heteroduplexes have differential affini-
ties (mediated by the ion-pairing reagent, TEAA) toward the column and are
subsequently eluted by a linear ACN gradient formed by the automated mixing
of buffers A and B. The Navigator software also predicts the necessary gradi-
ent for this temperature-mediated heteroduplex analysis. More than one tem-
Mutations in Noonan Syndrome 103

perature is required in most of the cases to push the sensitivity toward 100%.
The number of temperatures needed for a thorough analysis varies, depending
on the melting properties predicted by the Navigator software and on the size
of the DNA fragment. Choosing the right temperature is important for success-
ful screening (see Note 6).
The flow rate during analysis is 1.5 mL/min and the gradient duration is 2.0
min. Each sample can be analyzed in approx 3.5 min (turn-around time).
The UV detector identifies the eluted products at 260 nm, and the progress
of analysis is displayed by the Navigator software as a real-time chromato-
gram, in which the peak height is measured in mV. Any peak that falls below 1
mV is considered invalid because this may lead to a false-positive assessment.
In these cases, a larger volume is reinjected or the PCR is repeated.
The peaks that differ in shape or width from the normal sample are scored as
possible sequence variants and are confirmed by direct sequencing. As opposed
to the previous software (WAVEMAKER), the Navigator software has the
capability to normalize the peaks of different heights and, hence, any peak
broadening can be readily identified.
DHPLC analysis is fast and inexpensive and the cost per injection can be
brought close to 45 cents when the resources are used sensibly.
3.2.1. Practical Procedure
The Buffer B percentages and temperature(s) used for all 15 exons of
PTPN11 are shown in Table 3 (when using the latest Navigator software, per-
centage of Buffer B is automatically calculated for the predicted temperature;
here, the buffer B gradient is 10% over 2 min, i.e., a 5% slope). We will use
exon 8 as an example for the WAVE analysis process, using a WAVE DNA
Fragment Analysis System 3500HT equipped with an accelerator module.
The DNA sequence (252 bp) that includes PTPN11 exon 8 is:
TtggactaggctggggagtaactgatttgaactgttttttcctgaagcagtccaggacttatgtgacCgtgg
tctctttttcttctagTTGATCATACCAGGGTTGTCCTACACGATGGTGATCCCAAT
GAGCCTGTTTCAGATTACATCAATGCAAATATCATCATGgtaagctttgctttt
cacagtgttttctgaccatacatttctagcctatttttgtattttaaatccttcctcatgtcctgaaag.
The primer sequences are in boldface type. Three known coding mutations
(922A>G, 923A>G, and 925A>G), and one intronic polymorphism (–21C>T),
are also shown in bold in the sequence, with the intronic polymorphism in
upper case bold italic type.
Launch the Navigator Software by double clicking the shortcut from the
desktop. In the Navigator Connection window, there are five tabs to access
primary pages. Three tabs, “DNA,” “Injection,” and “Analysis,” are necessary
to run samples.
104 Elanko and Jeffery

Table 3
Percentage of Buffer B and Temperatures Used
in DHPLC Analysis for PTPN11 Mutation Detectiona

Buffer B
Exon Loading (%) Initial (%) Final (%) Temperatureb

1 56 61 67 67°C
2 55 60 66 56°C, 57°C
3 54 59 65 57°C, 58°C
4 53 58 64 56°C, 57°C
5 51 56 62 56°C, 58°C
6 50 55 61 56°C, 57°C
7 50 55 61 56°C, 57°C
8 51 56 62 57°C, 58°C
9 52 57 63 56°C, 57°C
10 50 55 61 57°C, 58°C
11 54 59 65 59°C
49 54 60 64°C
12 48 53 59 58°C, 59°C
13 51 56 62 59°C
50 55 61 60°C
14 52 57 63 57°C
49 54 60 60°C
15 51 56 62 56°C, 57°C
Reproduced from ref. 5.
aPercentage of buffer A = 100% – % of Buffer B.
bWhere two temperatures are given, both are used.

3.2.2. DNA Page

1. Select the “DNA” tab to open the DNA page.
2. Under “Amplicons,” select the “+” button to create a new amplicon. Enter or
paste the sequence, and enter a name for the sequence (e.g., PTPN11 exon 8).
Right click at the entered sequence and select “Format Sequence.” The melting
profiles for the predicted analysis temperature and four additional temperatures
(which are changeable) are displayed. Usually, we keep the predicted tempera-
ture and choose at least one additional (higher than predicted) temperature for
analysis, based on the melting profile (see Note 6 for guidance on temperature
selection). Select only the predicted temperature at this point.
3. Click the “Method” tab, then click the green “+” button to create a new method.
In the “Method Setup” dialog box, enter a name for the method (e.g., PTPN11
exon 8). Select “Rapid DNA” as the “Application Type” from the drop-down
menu, and select “Generate” to create the new method, with the temperature as
suffix (e.g., PTPN11 exon 8~56.8). If more than one temperature is selected, that
Mutations in Noonan Syndrome 105

number of methods will be created. From the list of methods displayed, double click
the newly generated method to open the “Edit Method” window. (However, the
method generated by Navigator for predicted temperature hardly requires editing).
4. Select “Rapid Method” from the drop-down menu within “Application Type.”
This is applicable to the WAVE models with an accelerator module (e.g., 3500HT).
Enter 2.0 min for “Gradient Duration,” 5% for “Slope,” 3 for “Drop for Loading;”
Navigator calculates the buffer gradient automatically. Save the method. If another
temperature analysis is needed, tick the “Manual Mode” in the “Edit Method” win-
dow and enter the required “Time Shift” with a + or – sign to elute the peak to the
right or left, respectively. Save as a different method (see Note 6).

3.2.3. Injection Page

Select the “Injection” tab to open the Injection Page.
1. To create a “New Project,” select “File,” then “New Project” to open the “New
Project” dialog box and enter a new project name (e.g., March05) and save. Open
“Project Defaults” within the “Setup” dialog box and tick “Fast Clean” and “Dis-
able Tray Change Request.” Projects can be opened via the “File” menu.
2. Click the “+” button in the “Tray Type” area and enter a new tray name (e.g.,
Noonan 24Mar05) and specify the tray type using the drop-down menu (e.g.,
“96-well tray column-back” means that a 96-well plate is used in the back or
inside tray and the injections are performed column by column).
3. On the speed plate, select (click and drag down and across) the vials to be in-
jected. A right click on the highlighted area opens the “Speed Plate Injections”
window. Choose the relevant “Method Name” from the drop down menu. Enter
the injection volume (if different from the default volume of 5 μL) and click
“Generate” to create injections in the injection table. Here:
a. Vial number and volume to be injected can be altered.
b. The name of the sample can be entered or a list of names can be pasted, e.g.,
from Microsoft Excel®.
c. Another method could be chosen from the list to run injections.
d. Analysis (oven) temperature can be changed, with other injection or analysis
parameters, such as percentage of buffer B remaining the same. This facility
enables testing of other temperatures chosen in Subheading 3.2.2., item 2.
e. It is recommended that two blank runs (by entering zero as the volume) are
performed before the mutation standard or samples are injected.
4. Check the performance of the system by running a “Low temperature mutation
standard” before a batch of sample injections (see Note 3).
5. Place the samples in the autosampler and highlight the injections to be run (e.g.,
two blanks and two PTPN11 exon 8 normal samples) in the injection table, and
send them to the “Queue Transactions” table by clicking the green arrowhead
(“Run Injection”) button at the top. The computer takes control of the WAVE
system and injection starts after a brief equilibration period. As soon as each
sample run is completed, the injection row is grayed out; highlight these data and
send them to the “Analysis” page.
106 Elanko and Jeffery

Generate a second set of four injections; this time, enter the second tempera-
ture to be tested in the injection table. As in Subheading 3.2.3., step 5, queue
the injections. If the peak is not eluted between 1.5 and 2 min, note the neces-
sary time shift with a + or – sign (e.g., +0.6 min) to shift the peak to the right or
left, respectively. A new method has to be created including the second tem-
perature and the time shift in the “Edit Method” dialog box (see Subheading
3.2.2.), if necessary (also see Note 6).
3.2.4. Analysis Page
Select the “Analysis” tab.
1. The traces can be displayed either individually or in groups, with an adjustable
offset, and compared with a normal trace (see Fig. 1A). Ticking the “Show”
squares will display the traces, and selecting “Show All” displays all of the ticked
traces. A test trace is compared with a known normal trace. Any noticeable dis-
crepancy should be followed up by direct sequencing, unless the signature of the
Waveform suggests a particular base change that can be detected using a restric-
tion enzyme.
2. The Navigator software has a sophisticated “Normalizing” capability that makes
the analysis accurate and rapid (see Fig 1B). This facility was not available with
the previous WAVE software, WAVEMAKER, and is extremely useful in allow-
ing peak broadening to be distinguished. However, we did not find “Mutation
Calling” very useful (see Note 7).
3. To print traces (pdf files), highlight the rows, then select “File,” “Reports,”
“Analysis,” and “Build Report” (text can be added here).

4. Notes
1. Compatibility. Bovine serum albumin, autoclaved water, mineral oil, formamide,
proteinase K, undisclosed PCR ingredients (enhancers, stabilizers, or other addi-
tives), and gelatin are some of the substances that are not compatible with the
column in any magnitude. At levels higher than 1% in the PCR reaction mixture,
polyethylene glycol, Triton X-100, Nonidet P-40, Tween-20, sodium dodecyl
sulphate, and sodium lauryl sulphate are found to cause cartridge degradation.
The following PCR additives are allowed up to the limits shown in parentheses;
selecting the active clean option at the end of each injection and performing a hot
wash after 96 injections are recommended: dimethylsulfoxide (10%), glycerol
(2%), and betaine (2.5 M).
2. The PCR temperatures shown in Table 2 (from ref. 5) were transferred without
problem to our laboratory. However, it does sometimes happen that different
PCR machines in different laboratories do not produce the expected results. If the
amplimers produced are not clean enough or strong enough, it may be necessary
to carry out a temperature or Mg2+ optimization to improve the procedure.
3. WAVE Mutation Standard (8 μL) analyzed at 56°C shows peaks corresponding
to homoduplexes and heteroduplexes. Four distinct peaks should be observed
each time (see Fig. 2), and the retention time difference between the two hetero-
Mutations in Noonan Syndrome 107

Fig. 1. (A) PTPN11 exon 8 at 57.8°C. The presence of more than one sequence
variation, for example a mutation and a polymorphism, as shown here (as analyzed by
the WAVEMAKER software), results in an elution profile significantly different from
those produced individually. This characteristic feature allows the signature-based
identification of polymorphisms, which can be confirmed by an appropriate restriction
enzyme analysis, or by sequencing if no restriction site is produced or destroyed. The
Navigator software makes this kind of recognition even easier, as shown in (B). Chro-
matograms analyzed using the normalizing function of the Navigator software. In this
mode (which was not included in the previous software versions, namely, HSM and
WAVEMAKER), the peaks are brought to the same height; hence, the analysis
becomes simple. It also allows the user to predict the change (using previous knowl-
edge), based on the specific signatures (see Note 6).
108 Elanko and Jeffery

Fig. 2. Peaks that would be expected from the low-temperature mutation standard
at 56°C for hetero- and homoduplexes.

duplexes should be approximately equal to that of the homoduplexes. Any sub-

stantial deviation from the WAVE form should be corrected by performing a hot
wash, using fresh buffers and/or washing the column with a Transgenomic
DNASep wash solution (the in-line filter can also be changed). If this fails to fix
the problem, oven calibration should be performed (further advice available from
the Transgenomic Help Desk).
Hot wash: Reverse the column in the oven compartment, set the oven temperature
to 80°C, pump 100% wash solution D through the column for 20 to 30 min (flow
rate, 0.9 mL/min), and equilibrate the column by passing 50% buffer A and 50%
buffer B through the column for 20 to 30 min (at a rate of 0.9 mL/min). It is not
necessary to turn the column back. After the hot wash, retest the mutation standard.
4. Soon after heteroduplexing, the PCR plate can be frozen until the analysis. The
plate seal should not be removed while the plate is still cold; this will lead to
residual adhesive material left on the plate and may cause the PCR plate to be
dislodged from the autosampler tray! Use the hot lid (of the PCR machine) to heat
the plate seal and peel the seal off while it is hot.
5. Autosampler. The tray in the autosampler is usually set to 10°C. If condensation
is noticed, the temperature could be raised just enough to stop the condensation.
Samples can be injected by columns or by rows. The correct option should be
selected when a new tray is set up.
6. WAVE analysis temperature selection. The analysis temperature recommended
by the Navigator software is 56.8°C. DHPLC analysis is carried out at partial
Mutations in Noonan Syndrome 109

Fig. 3. PTPN11 exon 8 (252 bp) melting profile.

Fig. 4. PCR products (5 μL) analyzed by WAVE at two different temperatures;

both temperatures detected the –21C>T sequence variations in the region, which was
100% helical at these temperatures. WAVE forms, which are reproducible, correspond
to each variation.

melting temperatures at which the helical fraction falls between 40 and 99%. In
theory, any sequence variation in the region, which is 100% helix (shaded region
at 56.8°C), is likely to be missed. Hence, a second temperature, such as 58.8°C,
may be necessary (Fig. 3). However, it is common that a sequence variation is
detected even if the region is 100% helical (Fig. 4).
Using a second or even third temperature is common in the case of larger DNA
fragments. When using temperatures 2 or 3°C higher or lower than the predicted
temperature, addition of a positive or negative time shift to the method may be
necessary to increase or decrease the retention time of the peak. Testing is rec-
ommended for all of the available samples with mutations or polymorphisms at
different temperatures. Temperatures of less than 1°C difference are normally not
helpful. Higher temperatures tend to generate broad peaks, which could create
110 Elanko and Jeffery

difficulties when analyzing the data. Using the highest possible temperature with-
out jeopardizing the quality of the peak is very useful.
7. The “Mutation Calling” software should align the waveforms into groups of simi-
larity, but we did not find that it worked reproducibly, or that it separated the
groups properly. Hence, we instead use the “Normalizing” capability for this
purpose, and identify the variants by eye.

Acknowledgments
We thank Prof. Michael Patton, Dr. Andrew Crosby, Dr. Kamini Kalidas,
John Short, Dr. Adam Shaw, and Gayathri Sivapalan for their part in the NS
research at St George’s Hospital Medical School. We also thank Dr. Bruce
Gelb and Dr. Marco Tartaglia, who performed the initial WAVE analysis on
PTPN11 and shared their methodology with us.

References
1. Sharland, M., Morgan, M., Smith, G., Burch, M., and Patton, M. A. (1993) Ge-
netic counseling in Noonan syndrome. Am. J. Med. Genet. 45, 437–440.
2. Jamieson, R., van der Burgt, I., Brady, A., et al. (1994) Mapping a gene for Noonan
Syndrome to the long arm of chromosome 12. Nat. Genet. 8, 357–360.
3. Tartaglia, M., Mehler, E. L., Goldberg, R., et al. (2001) Mutations in PTPN11,
encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat.
Genet. 29, 465–468.
4. Chen, B., Bronson, R. T., Klaman, L. D., et al. (2000) Mice mutants for Egfr and
Shp2 have defective cardiac semilunar valvulogenesis. Nat. Genet. 24, 296–299.
5. Tartaglia, M., Kalidas, K., Shaw, A., et al. (2002) PTPN11 Mutations in Noonan
Syndrome: Molecular Spectrum, Genotype-Phenotype Correlation, and Pheno-
typic Heterogeneity. Am. J. Hum. Genet. 70, 1555–1563.
6. Musante, L., Kehl, H. G., Majewski, F., et al. (2003) Spectrum of mutations in
PTPN11 and genotype–phenotype correlation in 96 patients with Noonan syn-
drome and five patients with cardio–facio–cutaneous syndrome. Eur. J. Hum.
Genet. 11, 201–206.
7. Maheshwari, M., Belmont, J., Fernbach, S., et al. (2002) PTPN11 mutations in
Noonan syndrome type I: detection of recurrent mutations in exons 3 and 13.
Hum. Mutat. 20, 298–304.
8. Sarkozy, A., Conti, E., Seripa, D., et al. (2203) Correlation between PTPN11 gene
mutations and congenital heart defects in Noonan and LEOPARD syndromes. J.
Med. Genet. 40, 704–708.
9. Mogensen, J., Bahl, A., Kubo, T., Elanko, N., Taylor, R., and McKenna, W. J.
(2003). Comparison of fluorescent SSCP and denaturing HPLC analysis with di-
rect sequencing for mutation screening in hypertrophic cardiomyopathy. J. Med.
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10. Jones, A. C., Austin, J., Hansen, N., et al. (1999) Optimal temperature selection
for mutation detection by denaturing HPLC and comparison to single-stranded
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conformation polymorphism and heteroduplex analysis. Clin. Chem. 45, 1133–

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11. Choy, Y. S., Dabora, S. L., Hall, F., et al. (1999) Superiority of denaturing high
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formation-sensitive gel electrophoresis for mutation detection in TSC2. Ann. Hum.
Genet. 63, 383–391.
Williams–Beuren Syndrome 113

7
Williams–Beuren Syndrome Diagnosis Using
Fluorescence In Situ Hybridization

Lucy R. Osborne, Ann M. Joseph-George, and Stephen W. Scherer

Summary
Williams–Beuren syndrome (WBS) is most commonly caused by a 1.5-Mb hemizygous
deletion of chromosome 7q11.23. Other genomic rearrangements of this region have also been
described, some as polymorphisms and others as rare variants, the latter often being directly
associated with clinical symptoms. Fluorescence in situ hybridization of either metaphase or
interphase nuclei can be used to detect all of these chromosomal rearrangements, providing the
ability to test this segment of chromosome 7 in families with a suspected diagnosis of WBS.
Key Words: Chromosome 7; fluorescence in situ hybridization (FISH); deletion; inversion;
interphase; metaphase.

1. Introduction
Williams–Beuren syndrome (WBS) is a complex disorder, caused by dele-
tion of approx 1.5 Mb of DNA, spanning at least 25 genes, on one copy of
chromosome 7 (1,2). The incidence of WBS is estimated at between 1 in 7500
people and 1 in 20,000 people (3,4), and it is usually sporadic, although cases
of autosomal-dominant transmission have been described (5). WBS is almost
always associated with a recognizable facies and characteristic cardiovascular
lesions, most frequently, stenosis of the ascending aorta is found (in ~80% of
individuals); other symptoms occur less frequently (6). A unique cognitive and
behavioral profile is also associated with this disorder, involving mild mental
retardation, friendliness, anxiety, and developmental motor disabilities (7).
Although the vast majority (>95%) of individuals presenting with classic
features of WBS have a common 1.5-Mb deletion at band q11.23 on one copy
of chromosome 7, some individuals have a translocation, partial deletion, or an
inversion of the same genomic region that may result in a less severe pheno-
type (8–11). The use of a now well-defined DNA sequence assembly of the
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

113
114 Osborne et al.

human genome along with fluorescence in situ hybridization (FISH) mapping

technology makes it possible to clearly define rearrangements of the WBS
region in families with a suspected WBS proband. The flow chart shown in
Fig. 1 outlines a general step-wise order in which specific tests can be per-
formed on an individual with a suspected diagnosis of WBS. The initial screen
would examine for the common deletion using commercially available (qual-
ity assured) probes. Karyotyping (performed in parallel to or after the standard
diagnostic FISH test) and targeted FISH analyses could then be used to detect
macroscopic changes, such as translocations or smaller deletions/inversions,
respectively. Each type of analysis varies in the number of probes used and in
the cell stage analyzed after hybridization.
Alternative methods for the detection of deletions are available and are
described in Chapter 8. For example, genotyping of DNA from the proband
and parents with polymorphic markers can be used to search for loss of het-
erozygosity, indicating the absence of a parental allele. Commonly used poly-
morphic markers spanning the deletion region are listed in Fig. 2. Quantitative
polymerase chain reaction is also used to detect the reduction in probe copy
number associated with the deletion. This method requires more fine-tuning to
generate a panel of probes that amplify consistently, but is very useful when
DNA but no cells are available from the proband. Array comparative genomic
hybridization is another new powerful methodology that is being developed,
but is not discussed here because it is not yet in standard practice.

2. Materials
2.1. Preparation of Target DNA
1. Thermotron.
2. CO2 incubator.
3. Low-speed centrifuge.
4. Vacutainer blood collection tubes containing sodium heparin.
5. 8-mL flat-bottomed tubes.
6. T25 vented tissue culture flasks.
7. Cell culture medium 1: α-Minimum Essential Medium, 15% fetal calf serum
(FCS), 4 U/mL sodium heparin, 100 mg/mL streptomycin plus 100 U/mL peni-
cillin, and 2 mL/100 mL phytohemagglutinin (M-form [Invitrogen] reconstituted
in 10 mL water).
8. Cell culture medium 2: RPMI-1640 medium with pyruvate, 10% FCS, 100 mg/
mL streptomycin plus 100 U/mL penicillin, and 2 mM L-glutamine.
9. Cell culture medium 3: RPMI-1640 medium with pyruvate, 20% FCS, 100 mg/
mL streptomycin plus 100 U/mL penicillin, 2 mM L-glutamine, and 10 μg/mL
colcemid.
11. 0.075 M KCl, prewarmed to 37°C.
 Willi
ams–
Beur
en

Syn
dro
me
115

Fig. 1. Flow chart of the molecular analysis of individuals with a possible clinical diagnosis of WBS. ELN, elastin; Scr, screen;
Del, deletion; Dup, duplication.

11
116 Osborne et al.

116
Williams–Beuren Syndrome 117

12. Fixative (3:1, methanol:acetic acid; prepare same day and store at –20°C).
13. Glass microscope slides (precleaned, frosted).

2.2. Preparation of Probes for FISH Analysis

1. Luria Bertani broth.
2. Appropriate antibiotic (e.g., 20 μg/mL chloramphenicol; 20 μg/mL kanamycin;
or 100 μg/mL ampicillin).
3. Solutions for standard alkaline lysis DNA extraction.
4. DIG-Nick Translation Mix (Roche, cat. no. 1745816).
5. BioNick Labeling System (Invitrogen, cat. no. 18247-015).
6. Nick Translation Kit (Vysis, cat. no. 32-801300).
7. Spectrum Green dUTP (Vysis, cat. no. 30-803200).
8. 10 mg/mL salmon sperm DNA (Invitrogen, cat no. 15632-011).
9. 3 M sodium acetate.
10. TE buffer: 10 mM Tris-HCl, pH 7.5, 1 mM EDTA .
11. 100% ethanol.
12. Agarose gel electrophoresis equipment.

2.3. DNA Denaturation and Hybridization

1. Water baths at 37, 42, 62, and 75°C.
2. Hybridization buffer: 31% deionized formamide, 2.5% w/v dextran sulphate,
2.5X standard sodium citrate (SSC).
3. 1 mg/mL human Cot DNA (Invitrogen, cat. no. 15279-011).
4. Denaturing solution: 70% deionized formamide, 2X SSC, pH 5.5.
5. 70, 90, and 100% ethanol at –20°C.
6. 70, 90, and 100% ethanol at room temperature in Coplin jars.
7. 2X SSC, pH 7.0, 0.1% Tween-20.
8. 22 × 22-mm glass cover slips.

Fig. 2. (opposite page) WBS region at 7q11.23 and diagnostic reagents. Genomic
clones used for FISH analysis are shown above and below the annotated genes (orien-
tation of gene transcription indicated by direction of arrows). The clones given in the
darker font give strong single-copy signals under FISH examination. The exception is
CTA-208H19, which sometimes gives a second, fainter signal. Microsatellite DNA
markers are also shown. The WBS low-copy repeats (LCRs) are indicated by the ver-
tical shaded blocks and have been divided into segments of nearly identical sequence
(A–C) shown in their correct orientation in relation to the centromere and telomere.
The breakpoints of the common deletion and the two inversions (inv-1 and inv-2) are
shown at the bottom of the figure. The common deletion breakpoints cluster within the
hatched boxes, with 95% of the deletions residing in the B block and the remaining 5%
residing in the A block of the medial LCR. The inversion breakpoints have not yet
been fine-mapped at the nucleotide level, but have been localized within the regions
marked by hatched boxes.
118 Osborne et al.

9. Rubber cement.
10. Coplin jars.
11. Wash solution 1: 1:1, deionized formamide: 2X SSC at 42°C; must always be
freshly prepared.
12. Wash solution 2: 0.05% SSC at 62°C.

2.4. Immunodetection
1. Water baths at 37 and 40°C.
2. Blocking solution: 0.5% bovine serum albumin (BSA).
3. 2X SSC.
4. Wash solution 3: 4X SSC, 0.1% Tween-20 at 40°C.
5. Anti-digoxigenin–rhodamine antibody, for detection of digoxigenin-labeled
probe (anti-digoxigenin–rhodamine FAb fragments [Roche, cat. no. 1207750]
reconstituted in double-distilled water; working concentration, 1 µg conjugate/
mL; 0.5% BSA).
6. Avidin, Alexa Fluor 488 antibody, for detection of biotin labeled probe—green
signal (Molecular Probes, cat. no. A-21370; reconstituted in phosphate-buffered
saline; working concentration, 10 µg conjugate/mL; 0.5% BSA).
7. Avidin-Cy5 antibody, for detection of biotin labeled probe—yellow signal
(MetaSystems, B-tect, cat. no. 0901-060-NI; working solution, detection 1 + 3
solution and blocking reagent solution, 1 µL: 50 µL).

2.5. Chromosome Counterstaining and DAPI Staining

1. Coplin jars.
2. 22 × 40-mm glass cover slips.
3. DAPI solution (0.2 µg DAPI/mL; 2X SSC).
4. 2X SSC.
5. Antifade solution.

3. Methods
Outline of methods:
1. Preparation of target DNA.
2. Preparation of probes for FISH analysis.
3. Denaturation and hybridization of the target DNA and the probes.
4. Immunodetection.
5. Counterstaining.
6. Visualization and interpretation of the results.

3.1. Preparation of Target DNA

Metaphase chromosomes should be prepared for standard WBS deletion
testing or partial deletion testing, and interphase nuclei prepared for WBS
inversion testing. Both preparations can be made from either peripheral blood
or lymphoblastoid cell lines and they can be safely stored at –20°C until they
are required for making slides.
Williams–Beuren Syndrome 119

3.1.1. Peripheral Blood Lymphocyte Culture and Harvest

1. Collect venous blood into a Vacutainer tube containing sodium heparin. If blood
is collected in a Vacutainer tube containing anticoagulant citrate-dextrose, in-
crease the sodium heparin in the medium to 6 U/mL.
2. Dispense 6 mL of cell culture medium 1 into 8-mL flat-bottomed tubes and add 5
to 8 drops of blood to each tube.
3. Incubate horizontally in a 37°C CO2 incubator for 70–72 h.
4. 25 min before harvesting, add 83 ng/mL colcemid and reincubate at 37°C.
5. Pellet cells at low speed (120g) for 10 min, remove supernatant, resuspend, add 8
mL of prewarmed hypotonic solution, and incubate for 15 min at 37°C.
6. Pellet cells again, remove supernatant, resuspend, and add 1 mL of cold fixative,
drop-by-drop, using a Pasteur pipet, while agitating the tube.
7. Add 7 mL of cold fixative and incubate at –20°C for at least 1 h.
8. Pellet cells again, remove all but 1 mL of supernatant, resuspend pellet.
9. Make a test slide to ensure that metaphases are present.
10. Add 7 mL of cold fixative to the resuspended cells. Repeat Subheading 3.1.1.,
step 8 three times.

3.1.2. Lymphoblastoid Cell Line Culture and Harvest

When receiving lymphoblast cell lines cultures for cytogenetic preparations,
check for cell concentration using an inverted phase–contrast microscope. As
the cells grow, the color of the medium progressively changes from orange to
yellow, indicating they have reached confluence (2–3 d). Cells are then grown
upright in T25 vented tissue culture flasks, using cell culture medium 2, at
37°C in a CO2 incubator. The final volume of culture should not exceed 20 mL
in this size flask. To obtain a high mitotic index, it is important to feed and to
harvest the cells at the same time on each consecutive day (days 1, 2, and 3).
1. Allow cells to reach confluence, then split 1:1 with fresh cell culture medium 2.
2. Allow cells to reach confluence and perform the following procedures at the same
time each day:
Day 1: Inoculate 5 mL of prewarmed culture medium 2 with 5 mL of culture.
Day 2: Feed cultures 1:1 using prewarmed culture medium 3.
Day 3: Half an hour before harvesting, add 0.5 μg of colcemid and reincubate
for 15 min.
3. Transfer the contents of each flask to a 15-mL conical, screw-cap tube, pellet the
cells (120g) for 10 min, remove the supernatant, and resuspend by gentle agita-
tion.
4. Add 8 mL of prewarmed hypotonic KCl. Mix by inverting tubes and place at
37°C for 15 min.
5. Pellet the cells, remove the supernatant, resuspend by gentle agitation, and add
ice-cold fix, drop-by-drop, with shaking, to approx 1 mL. Bring volume up to 10 mL
with fixative.
120 Osborne et al.

6. Place at –20°C overnight.

7. The next day, repeat Subheading 3.1.2., step 5 and change fixative twice.
3.1.3. Slide Preparation
1. Turn on the Thermotron and allow to equilibrate at required conditions of tem-
perature and humidity (empirically determined).
2. Pellet cell preparation (120g) for 10 min, remove supernatant and resuspend in
enough fresh fixative so that the cell suspension appears faintly turbid.
3. Clean the slide surface using a few drops of fixative (3:1, methanol:acetic acid)
and wipe dry using a lint-free tissue. Place slide on the flat surface of the
Thermotron, add one drop of cell suspension onto the center of the slide and
leave to dry.
4. Check the slides under the phase contrast microscope to ensure good chromosome
quality and to assess the cell density. Metaphases should be 3 to 4 per field (at
10X magnification), well-spread, and have minimal or no visible cytoplasm
present.
5. If slides are being used for interphase FISH procedures, it is important to have a
much higher density of cells per field to facilitate more efficient data acquisition,
especially when a scanning microscope is being used. To accomplish this with-
out compromising the quality of the spread, cell concentration of the cell suspen-
sion is retained, but the number of drops per slide on the same spot is increased
until the desired density is reached. Nuclei should be close together, but without
their walls touching.
6. Slides can be stored at room temperature for up to 3 wk.

3.2. Preparation of Probes for FISH Analysis

3.2.1. Selection of FISH Probes
3.2.1.1. CLONE SELECTION
The locations of specific probes in relation to the WBS deletion are shown
in Fig. 2. These clones are all in the public domain and are available through a
number of sources, including our own genome resource center (available at:
www.tcag.ca).
3.2.1.2. DETECTION OF THE COMMON WBS DELETION
For standard WBS-deletion FISH testing, the commercially available Will-
iams Syndrome Region Probe from Vysis may be used. This probe is dual-
color and prelabeled, and consists of a probe (~180 kb in size) spanning the
elastin gene locus, the LIMK1 gene, and microsatellite marker D7S613 (see
Fig. 2 for locations). The probe also contains a control probe for the region
containing loci D7S486 and D7S522 (7q31). Alternatively, the P1 artificial
chromosome (PAC) clone RP11-122H9 is equivalent to the Vysis WBS probe; we
use RP1-13N03, which maps to 7p22.3, as a chromosome 7 short-arm control.
Williams–Beuren Syndrome 121

3.2.1.3. DETECTION OF SMALLER DELETIONS

Probes used for detecting smaller deletions may be chosen from the panel
shown in Fig. 2. We routinely use the cosmid clones 34b3 and 82c2 from the
LL07NC01 chromosome 7-specific cosmid library to check for partial dele-
tions of the elastin gene, and RP5-1186P10 and CTA-208H19 to check for
deletions that do not include elastin.
3.2.1.4. DETECTION OF LARGER DELETIONS
We routinely use RP11-815K3 to assay for deletions extending in a centro-
meric direction and CTB-139P11 to detect deletions extending in a telomeric
direction from the common deletion interval (Fig. 2).
3.2.1.5. DETECTION OF INVERSIONS
Three-color interphase FISH analysis is used for inversion detection.
Because of the proximity of the probes (<2 Mb apart), their order can only be
readily determined when visualized in interphase nuclei. The three probes are
labeled individually with red, green, and yellow labels, then mixed and hybrid-
ized to interphase nuclei preparations. The three probes consist of two within
the common deletion region and another outside just to the telomeric side. The
probes we use are CTA-208H19, RP5-1186P10, and CTB-139P11 because this
combination will detect both inversion-1 and inversion-2 (shown in Fig. 2)
(see Note 1).
3.2.2. Genomic Clone Propagation, Amplification,
and Isolation of DNA
1. Inoculate a single bacterial colony containing the cloned DNA of interest into 5
mL of Luria Bertani broth supplemented with the appropriate antibiotic in a 15-
mL snap-cap tube and incubate at 37°C overnight, with shaking.
2. Pellet cells (1700g for 10 min), discard supernatant, and extract the plasmid DNA
using a standard alkaline column-based lysis protocol (e.g., QIAprep kit from
Qiagen) as follows:
3. Resuspend the cell pellet in 300 μL of P1 solution using the vortex.
4. Lyse cells by adding 300 μL of P2 solution and mix gently. Incubate at room
temperature for 5 min. The appearance of the suspension should turn change
from turbid to translucent.
5. Neutralize by slowly adding 300 μL of P3 solution, shaking while adding. A
thick white precipitate will form. Place tubes on ice for at least 5 min.
6. Centrifuge tubes at 1700g for 10 min. Transfer the supernatant to a 1.5-mL
eppendorf tube and discard pellet.
7. Centrifuge the eppendorf tubes at 18,000g for 10 min.
8. Precipitate DNA: transfer 750 μL of supernatant to another eppendorf tube con-
taining 800 μL of isopropanol. Avoid transferring any of the white precipitate
122 Osborne et al.

material. Mix by inverting the tubes several times. Place the tubes at –20°C for at
least 30 min (tubes can be left at –20°C overnight at this stage).
9. Centrifuge the tubes for 15 min at 18,000g at 4°C. Discard supernatant.
10. Wash the DNA pellet by adding 800 μL of 70% ethanol. Invert tubes several
times to mix. Centrifuge at 14,000 rpm for 5 min at 4°C.
11. Carefully remove the supernatant by pipetting.
12. Allow pellets to dry at room temperature (10–20 min). Pellets will turn from
white to translucent when most of the ethanol has evaporated.
13. Resuspend the DNA in 30 μL of double-distilled, autoclaved water and allow to
sit at room temperature for 1 h to ensure complete resuspension.

3.2.3. Probe Labeling

3.2.3.1. DIGOXIGENIN (RED SIGNAL)
Use 300 to 400 ng bacterial artificial chromosome (BAC)/P1 artificial chro-
mosome (PAC) clone DNA in 16 μL of sterile ddH2O and label using the DIG-
Nick Translation Mix (Roche), according to the manufacturer’s instructions,
with the following modifications:
Add 4 μL DIG-Nick Translation Mix, mix and centrifuge briefly.
Incubate for 5–7 h at 15°C.
Place reaction on ice and proceed with steps in Subheading 3.2.4.
Stop the reaction with 2 μL of 0.5 M EDTA (pH 8.0) and add 6 μL of
salmon sperm DNA.
Separate the unincorporated nucleotides from the labeled DNA probe by
repeated ethanol precipitation. Add 0.1 volume of 3 M sodium acetate and 2.5
volumes of cold (–20°C) ethanol, mix and freeze at –20°C for 30 min. Pellet at
18,000g for 10 min. Remove supernatant and dry pellet. Resuspend the pellet in
20 μL autoclaved ddH2O.
3.2.3.2. BIOTIN (GREEN SIGNAL)
Mix the components in a microcentrifuge tube on ice and spin briefly.
5 μL 10X dNTP mix
600–750 ng BAC clone DNA
5 μL 10X enzyme mix
Distilled water to 45 μL
Incubate at 15°C for 3–5 h
Place the reaction on ice and proceed with steps in Subheading 3.2.4. to
check the size of fragments.
Add 5 μL stop buffer and 6 μL salmon sperm DNA. Separate the unincorpo-
rated nucleotides from the labeled DNA probe by repeated ethanol precipita-
tion. Add 0.1 volume of 3 M sodium acetate and 2.5 volumes of cold (–20°C)
Williams–Beuren Syndrome 123

ethanol, mix and freeze at –20°C for 30 min. Pellet at 20,000g for 10 min.
Remove supernatant and dry the pellet. Resuspend the pellet in 20 μL of auto-
claved ddH2O. Biotinylated probes are very stable and can be stored at –20°C
for at least 1 yr.
3.2.3.3. DIGOXIGENIN AND BIOTIN COMBINED (YELLOW SIGNAL)
Label two sets of DNA separately with digoxigenin and biotin, as described
in Subheadings 3.2.3.1. and 3.2.3.2. and mix in a ratio of 3 parts digoxigenin
to 2 parts biotin.
3.2.3.4. SPECTRUM GREEN (DIRECT LABEL)
Mix the components in a microcentrifuge tube on ice and spin briefly.
1 μg BAC clone DNA
2.5 μL of 0.2 mM Spectrum Green
5 μL of 0.1 mM dTTP
10 μL of dNTP mix
5 μL of 10X nick translation buffer
10 μL nick translation enzyme
Nuclease-free water to 50 μL
Incubate 8–16 h at 15°C
Stop the reaction by heating in a 70°C water bath for 10 min and chill on ice.
Add 6 μL of salmon sperm DNA. Separate the unincorporated nucleotides from
the labeled DNA probe by repeated ethanol precipitation. Add 0.1 volume of 3 M
sodium acetate and 2.5 volumes of cold (–20°C) ethanol, mix, and freeze at –
20°C for 30 min. Pellet at 18,000g for 10 min. Remove supernatant and dry the
pellet. Resuspend the pellet in 20 μL of autoclaved ddH2O and store at –20°C.
3.2.4. Determination of Labeled Fragment Length
The length of the labeled fragments should be checked after the labeling
reaction is complete, but before the probe is cleaned and precipitated ready for
use. At the appropriate step during the labeling process (see Subheading x.x.),
place the reaction on ice and take a 3 μL aliquot for testing. Add gel-loading
buffer, place sample on ice for 3 min, and run the sample on an agarose minigel,
along with a DNA molecular weight marker. The probe should range between
200 and 500 nucleotides in length. If necessary, reincubate the reaction at 15°C
and check the fragment size again.
3.3. DNA Denaturation and Hybridization
Ready the slides and appropriate probes that have been labeled with differ-
ent fluorochromes. At least 2 μL of labeled probe is required for each slide.
124 Osborne et al.

Place a Coplin jar containing denaturing solution in a water bath at 75°C.

Label eppendorf tubes, one for every probe being used (to avoid confusion, it
is best to use different colored tubes for different probes) and prepare the probe
mix, which consists of:
1 μL human Cot DNA (1 mg/mL)
7 μL hybridization buffer
2 μL required labeled probe
Vortex probe mixes briefly and then spin down (when hybridizing using
three probes, use the same volumes as Subheading 3.3. for each probe, and
use a 22 × 40-mm cover slip).
3.3.1. Probe Denaturation
Ensure that the temperature in the water bath is at 75°C, then immerse probes
for exactly 5 min. Remove samples and place samples into water bath at 37°C
for 20–30 min to reanneal.
3.3.2. Pretreatment and Denaturation of Target DNA
1. Before pretreatment, slides are aged for 2–3 h at 55°C.
2. Pretreat slides with 2X SSC plus 0.1% Tween-20 at 37°C for 30 min.
3. Removes slides, drain briefly, and dehydrate (for 2 min each) through an ethanol
series at room temperature.
4. Have a 70, 90, and 100% ethanol series ready at –20°C.
5. Place slides in denaturing solution (70% deionized formamide in 0.6X SSC) at
75°C.
6. Drain denaturing solution into waste beaker, using forceps to retain slides in jar.
7. Immediately add ice-cold 70% ethanol to jar and discard ethanol at once.
8. Add ice-cold 70% ethanol to jar and leave for 3 min.
9. Drain slides briefly on a paper towel, and submerge in ice-cold 90% ethanol for
3 min.
10. Drain slides briefly on a paper towel, and submerge in ice-cold 100% ethanol for
3 min; remove slides, drain, and air-dry slides on rack.
3.3.3. Hybridization
1. Label slides with the probe names to be used.
2. Combine the chosen probes, mix by flicking the tube, and spin down.
3. Place the probe solution on the cells and drop on a 22 × 22-mm cover slip. Seal
with rubber cement and mark the area covered by the cover slip on the back of
slide with a diamond pencil.
4. Place slides in a moist, dark chamber and leave at 37°C overnight.
Williams–Beuren Syndrome 125

3.3.4. Washing
It is extremely important to ensure that the slides do not dry out during the
washing process, because this will cause excessive background fluorescence.
1. Prewarm the Coplin jar containing 200 mL of Wash solution 1 at 42°C and 500 mL
of Wash solution 2 at 62°C.
2. Remove cover slips from the hybridized slides and clean any residual rubber
cement.
3. Place slides into Wash solution 1 at 42°C and shake for 5 min. Repeat two times.
4. Repeat twice with Wash solution 2; after removing the last wash, let the slides
cool for a few minutes before adding 2X SSC.

3.4. Immunodetection
The following steps 1, 2, and 3 are only necessary in interphase FISH test-
ing, when using a combination of FISH probes including one that is labeled
with biotin and being detected with Avidin-Cy5. For all other probes, begin at
step 4 (see Note 2). The following procedures must be performed in the dark
because the detection process is light sensitive.
1. Remove slides from 2X SSC and blot excess liquid from edges without allowing
slides to dry out. Apply 40 μL of blocking solution (0.5% BSA) to each slide and
cover with a plastic cover slip.
2. Incubate at 37°C for 30 min in a dark, humidified chamber.
3. Remove cover slips and rinse slides in Wash solution 3 at 40°C with shaking for
5 min. Transfer slides to a Coplin jar containing fresh 2X SSC at room tempera-
ture.
4. Each slide requires 20 μL each of anti-digoxingenin and avidin, and Alexa Fluor
488, premixed.
5. Take one slide at a time out of the SSC, drain by shaking, blot the back of slide,
but do not allow the slide to dry out.
6. Add detection solution to each slide, drop a plastic cover slip over the slide, and
remove any air bubbles.
7. Place slides in moist, dark chamber and incubate at 37°C for 30–60 min. Be very
careful not to let the slides dry out.
8. Remove the plastic cover slip and put slides in a Coplin jar with Wash solution 3
preheated to 40°C. Place the Coplin jar containing the slides on a shaker for 5
min. Repeat twice.

3.5. Chromosome Counterstaining and DAPI Banding

Successful FISH mapping of DNA probes requires identification of both the
specific chromosome as well as the banding localization. In our laboratory, we
126 Osborne et al.

use DAPI banding as a routine method of staining when analyzing the rela-
tional mapping of two or more probes.
1. After the last wash, drain the slides and place them in DAPI solution for 5 min.
2. Drain the slides and place them back into jar of 2X SSC to prevent drying.
3. One slide at a time, drain briefly, add 15 μL of Antifade solution to the area, and
place a cover slip on the slide.
Slides are now ready for viewing and can be stored in the dark at –20°C to
preserve the signal.
3.6. Image Capture and Analysis
3.6.1. Microscopy
The images of the DAPI-stained chromosomes and hybridized, fluorescently
labeled probes are captured on an epifluorescence microscope (e.g., Zeiss,
Leitz, Nikon, or Olympus). The microscope should be equipped with a high-
intensity mercury arc lamp source and objectives that include lenses of high
numerical aperture and low self-fluorescing, UV-transmitting light. For scan-
ning metaphases and interphase nuclei, dry objective magnifications of ×10
and ×20 are appropriate. The visualization and localization of fluorescent probe
signals requires oil objectives of ×63 and ×100 (see Note 3).
3.6.2. Image Capture
The filter sets chosen for viewing fluorescent signals and counterstained
chromosomes will depend on which fluorochromes are used and the type of
mapping being performed. A narrow bandpass filter can be used for viewing a
single fluorochrome, but the detection of multiple fluorochromes simulta-
neously requires a wide bandpass filter. The use of such filters (from Chroma
or Omega Optical) often results in a loss of signal intensity, necessitating the
use of a high-resolution cooled-charged couple device camera. These cameras
capture each fluorescent signal in grayscale and the individual fluorochrome
images are then transferred to an image analysis software program, such as
Adobe Photoshop, for the addition of color and merging of the signals.
Registration is critical when capturing images using two or more different
filters. Even slight changes in registration when switching between filters can
potentially result in error in signal localization. Automatic computer-controlled
filter wheels and software packages that enable the capture of real-time images
are now available and can minimize this problem.
Williams–Beuren Syndrome 127

3.6.3. Analysis
3.6.3.1. DELETION DETECTION
For the detection of deletions of the WBS region on metaphase chromo-
somes, it is advisable to score at least 20 nuclei in which the signals on both
chromosome 7 copies are clear.
3.6.3.2. INVERSION DETECTION
For three-color inversion testing, it is necessary to score a larger number of
interphase nuclei because of the three-dimensional nature of the molecules
being viewed in the cell. Only chromosomes in which the three probe signals
are clearly visible and are aligned in a linear orientation with respect to each
other should be scored. At least 50 to 60 chromosomes are needed to reliably
determine whether an inversion of the WBS region is present. It is also advis-
able to have the scoring performed independently by two people to remove any
bias regarding the interpretation of the probe order.
The large number of chromosomes scored is necessary because an altered
order of probes will be seen on some chromosomes, even if an inversion is not
present. This is because of the orientation of the chromosomal DNA on the
slide not corresponding to its actual orientation in the genome.
When scoring the interphase nuclei, we report the number of chromosomes
with the following probe order (see Fig. 2):
Expected: CTA-208H19 to RP5-1186P10 to CTB-139P11
Inversion-1: RP5-1186P10 to CTA-208H19 to CTB-139P11 (first described
in ref. 10)
Inversion-2: CTA-208H19 to CTB-139P11 to RP5-1186P10 (first described
in ref. 11)
When an inversion is truly present on one chromosome 7, approx 50% of
chromosome 7s will be scored as such, with 50% being scored as normal. The
occurrence of less than 20% of chromosomes scored as Inv-1 or Inv-2 is con-
sidered within normal experimental variation.

4. Notes
1. The three probes used for interphase inversion testing may be labeled individu-
ally in two ways:
Red signal: labeled with digoxigenin, detected with anti-digoxigenin–rhodamine
128 Osborne et al.

Green signal: labeled with biotin, detected with avidin, Alexa Fluor 488
Yellow signal: probe labeled with digoxigenin and biotin separately and
mixed
or,
Red signal: labeled with digoxigenin, detected with anti-digoxigenin–
rhodamine
Green signal: labeled with Spectrum Green
Yellow signal: labeled with biotin, detected with avidin–Cy5
2. When using a combination that includes a probe directly labeled with Spectrum
Green, the additional steps are needed to block nonspecific hybridization of Avi-
din–Cy5 and prevent generation of a high background signal.
3. The oil used for high-power objectives should be nonfluorescing.

References
1. Ewart, A. K., Morris, C. A., Atkinson, D., et al. (1993) Hemizygosity at the elas-
tin locus in a developmental disorder, Williams syndrome. Nat. Genet. 5, 11–16.
2. Peoples, R., Franke, Y., Wang, Y. K., et al. (2000) A physical map, including a
BAC/PAC clone contig, of the Williams-Beuren syndrome—deletion region at
7q11.23. Am. J. Hum. Genet. 66, 47–68.
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Genet. 37, 85–88.
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Williams syndrome. J. Child Neurol. 17, 269–271.
5. Morris, C. A., Thomas, I. T., and Greenberg, F. (1993) Williams syndrome: auto-
somal dominant inheritance. Am. J. Med. Genet. 47, 478–481.
6. Morris, C. A., Demsey, S. A., Leonard, C. O., Dilts, C., and Blackburn, B. L.
(1988) Natural history of Williams syndrome: physical characteristics. J. Pediatr.
113, 318–326.
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cal, cognitive, and behavioral features. Child Adolesc. Psych. Clinics N. Am. 5,
929–943.
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hemizygosity implicated in impaired visuospatial constructive cognition. Cell 86,
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9. Tassabehji, M., Metcalfe, K., Karmiloff-Smith, A., et al. (1999) Williams syn-
drome: use of chromosomal microdeletions as a tool to dissect cognitive and
physical phenotypes. Am. J. Hum. Genet. 64, 118–125.
10. Osborne, L. R., Li, M., Pober, B., et al. (2001) A 1.5 million-base pair inversion
polymorphism in families with Williams–Beuren syndrome. Nat. Genet. 29, 321–
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7: DNA sequence and biology. Science 300, 767–772.
Molecular Diagnostics of Supravalvular Aortic Stenosis 129

8
Congenital Heart Disease

Molecular Diagnostics of Supravalvular Aortic Stenosis

May Tassabehji and Zsolt Urban

Summary
Supravalvular aortic stenosis (SVAS) is a congenital heart disease that can occur as an iso-
lated autosomal-dominant condition or as part of the developmental disorder Williams–Beuren
syndrome (WBS) and is caused by heterozygous genetic lesions involving the elastin (ELN)
gene locus on chromosome 7q11.23. SVAS is one of many phenotypic features associated with
the contiguous gene microdeletion disorder, WBS, and is caused by deletion of the ELN locus
on one chromosome 7 homolog. Point mutations, chromosomal deletions, and translocation
involving ELN have also been described in individuals with nonsyndromic SVAS. In addition,
ELN is involved in the connective tissue disorder, autosomal-dominant cutis laxa, and has been
implicated as a susceptibility gene for hypertension and intracranial aneurysms. The molecular
analysis of ELN defects is, therefore, an area of significant interest. Genetic screening can be
achieved using a variety of techniques to detect both mutations and gross chromosome rear-
rangements involving the ELN locus, providing the ability to screen families and individuals
with SVAS and associated elastinopathies.
Key Words: Supravalvular aortic stenosis (SVAS); autosomal-dominant cutis laxa (ADCL);
elastin; chromosome 7; mutation; deletion.

1. Introduction
The characteristic elastic properties of many tissues are caused by the pres-
ence of the protein ELN. Tissues rich in ELN include major arteries (28–32%
dry weight), aorta (50%), lungs (3–7%), elastic ligaments (50%), tendons (4%),
and skin (2–3%). ELN itself is a major component (~90%) of elastic fibers,
which endow connective tissues with the critical properties of elasticity and
resilience, and complement collagen fibrils, which provide tensile strength (1).
Smooth muscle cells, endothelial cells, fibroblasts, and chondrocytes all syn-
thesize ELN. ELN (initially synthesized as a 72-kDa soluble monomer,
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

129
130 Tassabehji and Urban

tropoelastin [TE]) is a very hydrophobic protein and has a characteristic pri-

mary structure of alternating hydrophobic and crosslinking domains. The
hydrophobic domains are thought to be responsible for the resilience of the
protein. After secretion, individual TE molecules are covalently crosslinked by
the enzyme, lysyl oxidase, to form an insoluble network of elastic fibers. ELN
is synthesized mainly during development, and has an extremely slow turnover
(half-life approaching the age of the organism), so little remodeling of elastic
fibers occurs during adult life. The human ELN (NM_000501) maps to chro-
mosome 7q11.2. Comparative studies show that ELN has 34 exons compared
with the bovine eln, and that human exon 34 is homologous to bovine exon 36
(2,3). Functionally distinct hydrophobic and crosslinking domains of the pro-
tein are encoded in separate alternating exons in the gene (Fig. 1). The exon-
to-intron ratio is unusually large (20:1) and the introns contain large amounts
of repetitive sequences that seem to predispose this region to genetic instabil-
ity. Molecular defects in ELN have been described in two conditions:
supravalvular aortic stenosis (SVAS) and autosomal-dominant cutis laxa
(ADCL).
1.1. Elastinopathies
SVAS (MIM 185500) is a congenital narrowing of the ascending aorta that
is frequently progressive and can lead to heart failure and death if not treated
early, therefore patients often need corrective surgery in early infancy (4) (Fig.
2). SVAS can occur sporadically, as a familial condition with autosomal-domi-
nant inheritance (5) or as a component of Williams–Beuren syndrome (WBS)
(4). The expression of SVAS is highly variable, both in familial SVAS and
among patients with WBS. This chapter focuses on isolated or nonsyndromic
SVAS. SVAS is caused by point mutations (3,6–11) or gross chromosomal
abnormalities (large deletions or translocations) involving ELN (12–15) that
abolish the function of one copy of the gene. It seems that most, if not all,
SVAS mutations described result in functional haploinsufficiency for ELN (8–
11). Affected individuals, therefore, express only 50% of the normal amount
of TE during development, which results in reduced arterial ELN content and,
consequently, abnormally increased proliferation of vascular smooth muscle
cells (11). This manifests as the characteristic marked media thickening in great
arteries seen in SVAS patients.
ADCL (MIM 123700) is a connective tissue disorder characterized by lax
inelastic skin and other internal organ involvement (often hernias) (15). The
skin of ADCL patients tends to hang in loose folds, giving an appearance of
premature aging. ELN mutations associated with ADCL are generally single
nucleotide deletions near the end of the gene that result in in-frame frame-
shifts, predicted to replace the C-terminal amino acids with novel ones (16–
Molecular Diagnostics of Supravalvular Aortic Stenosis 131

Fig. 1. ELN structure and functional domains. MAGP, microfibril-associated gly-

coprotein.

Fig. 2. Angiogram of a patient with SVAS. Note the typical hourglass-shaped nar-
rowing of the ascending aorta.
132 Tassabehji and Urban

18). However, recently, a partial tandem duplication in ELN was also described
to cause ADCL (19). Unlike SVAS, in ADCL, mutant TE protein is produced
that is thought to alter the architecture of elastic fibers, resulting in a different
pathomechanism to SVAS (16,19).
In addition to its involvement in SVAS and ADCL, ELN has been suggested
to be a susceptibility gene for hypertension and intracranial aneurysms (20).
Thus, mutational molecular analysis of ELN defects has become an area of
significant interest.
1.2. Genetic Lesions Involving ELN
Previous studies have described the point mutations in ELN that cause
nonsyndromic (isolated) SVAS or ADCL. In most cases, unrelated families
have different molecular defects. More than 50 different ELN mutations have
been described in patients with SVAS, and 5 ELN mutations have been
described in patients with ADCL (16–19). Most mutations (>85%) are truncat-
ing, caused by nonsense or frameshift mutations (which result in premature
stop codons) or by splicing mutations, both at the consensus acceptor and donor
splice junctions as well as in introns, which lead to truncated protein because
of aberrant splicing. Missense mutations are not common (~10% of cases) and
their contribution to the SVAS pathology is yet to be comprehensively defined
(7,10). The defect in ELN generally seems to be quantitative, with insufficient
levels of ELN being produced. In fact truncating mutations in ELN, caused by
mutations that introduce premature termination codons, have been shown to
result in haploinsufficiency for ELN as a consequence of nonsense-mediated
decay (a cell surveillance mechanism in place to ensure that only error-free
messenger RNAs [mRNAs] are accurately translated) of the mutant mRNA
(9–11). This confirms that functional haploinsufficiency is the most likely
pathological mechanism underlying SVAS.
Recurrent mutations have been described in ELN, some of which include the
truncating Y150X (exon 9), Q442X (exon 21), and K176X (exon 10) muta-
tions and splice mutations at the acceptor splice junction of exon 16. However,
given that most families have unique ELN defects, screening for known muta-
tions or hot spots is unlikely to be an efficient approach for molecular diagno-
sis. When screening for mutations, it is important to be aware that common
intragenic polymorphisms exist in the ELN gene. Those described within or
near exons include:
1. 196+71G>A in intron 4 (allele frequencies: G, 0.96; A, 0.04).
2. 233–94G>A in intron 5 (G, 0.92; A, 0.08).
3. 326–59G>A in intron 6 (G, 0.93; A, 0.07).
4. 1264G>A in exon 20, giving the expressed polymorphism of G442S (G, 0.62; A,
0.38).
Molecular Diagnostics of Supravalvular Aortic Stenosis 133

5. 1315+17T>C in intron 20 (T, 0.80; C, 0.20).

6. 1501–24T>C in intron 23 (T, 0.64; C, 0.36).
7. 1828G>C in exon 26, giving the expressed polymorphism G610R (G, 0.93; C, 0.07).
8. 2273–34C>T in intron 32 (C, 0.73; T, 0.27).
9. *502_*503insA in the 3'-untranslated region (A–, 0.76; A+, 0.24).
10. *659G>C in the 3'-untranslated region (G, 0.61; C, 0.39).
This chapter proposes a flow chart for the molecular analysis of suspected
ELN-related pathologies (Fig. 1 in Chapter 7 on WBS) and discusses methods
for the discovery and analysis of point mutations and single nucleotide poly-
morphisms (SNPs) and for detecting large deletions and rearrangements in-
volving the ELN locus. Finally, methods for indirect analysis of inherited ELN
defects are discussed.

2. Materials
2.1. Polymerase Chain Reaction
1. Vortex mixer.
2. Bench-top centrifuge.
3. Thermal-cycling machine.
4. Agarose gel electrophoresis equipment (horizontal electrophoresis tank and
power pack, gel tray, and combs).
5. Short-wavelength UV transilluminator (254–300 nm).
6. 0.5-mL thin-walled eppendorf tubes or 96-well polymerase chain reaction (PCR)
plates.
7. Sterile deionized water (dH2O).
8. dNTPs (20 mM stock; the final concentration of each dNTP [dATP, dCTP, dGTP,
and dTTP] is 5 mM). Add 25 μL of each 100-mM stock dNTP to 400 μL of dH20
to make 20 mM stock. Store at –20°C.
9. Taq DNA polymerase and 10X PCR buffer (provided by manufacturer). For
increased specificity, use Amplitaq gold™ DNA polymerase (PerkinElmer LAS,
UK, cat. no. N808-0145) with the 10X PCR buffer supplied with the Taq poly-
merase (100 mM Tris-HCl, pH 8.3, 500 mM KCl, and 0.01% w/v gelatin) for
“hot-start” specificity.
10. Oligonucleotides resuspended with sterile water to 5 μM stocks.
11. 25 mM MgCl2.
12. Target DNA: 50–100 ng of total genomic DNA.
13. 10X TBE electrophoresis buffer: 108 g Tris-base, 55 g boric acid, and 20 mL of
0.5 M EDTA, distilled water to a final volume of 1 L).
14. Molecular weight marker (1-kb ladder).
15. High-quality mineral oil.
16. Ethidium bromide.
17. 5X gel-loading buffer: 1X TBE containing 20% glycerol and 0.1 g of bromophe-
nol blue tracking dye.
18. Molecular biology-grade agarose solid.
134 Tassabehji and Urban

2.2. Single-Strand Conformation Polymorphism/Heteroduplex Analysis

1. Vertical polyacrylamide gel electrophoresis (PAGE) and gel casting apparatus
(e.g., Gibco-BRL SA32 gel system with a metal cooling plate).
2. 1-mm gel spacers.
3. Heating block.
4. Acrylamide plus methylene bis-acrylamide at a 49:1 ratio (Sigma–Aldrich Com-
pany, Dorset, UK, cat. no. A-0924). A 40% stock solution mixture is made using
deionized water and stored at 4°C.
5. TEMED.
6. 10% (w/v) ammonium persulphate solution.
7. 1X TBE electrophoresis buffer (dilute 10X stock TBE 1:9 with distilled water).
8. Formamide loading buffer: 10 mL of molecular biology-grade formamide; 200 μL
of 0.5 M EDTA; 5–10 mg of xylene cyanol; and 5–10 mg of bromophenol blue.

2.3. Silver Staining of PAGE Gels

1. Gel shaker.
2. Hoefer SE 1200 Easy Breeze™ Air Gel Dryer (Amersham Biosciences).
3. Porous cellophane sheets.
4. Solution I: 10% (v/v) ethanol and 0.5% (v/v) acetic acid.
5. Solution II: 0.1% aqueous solution of silver nitrate (AgNO3).
6. Solution III: aqueous solution of 1.5% (w/v) sodium hydroxide and 0.1% (v/v)
formaldehyde (stock 37% [v/v]). This solution must be prepared immediately
before use. Add 1.6 mL of 37% (v/v) formaldehyde stock solution to 400 mL of
1.5% (w/v) sodium hydroxide.
7. Solution IV: 0.75% (w/v) aqueous solution of sodium carbonate (Na2CO3).
Warning: Formaldehyde has high toxicity, is a severe irritant, and is a car-
cinogen.
2.4. Denaturing High-Performance Liquid Chromatography
All solutions and water used must be at least high-performance liquid chro-
matography (HPLC) grade.
1. WAVE denaturing HPLC (DHPLC) system (Transgenomic, Omaha, NE).
2. DNASep 4.8 mm × 50-mm cartridge.
3. Buffer A: 0.1 M triethylammonium acetate solution, pH 7.0.
4. Buffer B: 0.1 M triethylammonium acetate, 25% (v/v) acetonitrile, pH 7.0.
5. Syringe wash solution: 8% (v/v) acetonitrile, aqueous solution.
6. Solution D: 75% (v/v) acetonitrile, aqueous solution.

2.5. Cycle Sequencing

1. Thermal-cycling machine with a heated lid (e.g., PE Applied Biosystems [ABI],
Warrington, UK; or GeneAmp PCR System 9700 thermal cycler).
Molecular Diagnostics of Supravalvular Aortic Stenosis 135

2. ABI PRISM® 3100 Genetic Analyzer or ABI PRISM 377 automated DNA
sequencer.
3. 0.2-mL thin-walled eppendorf tubes or 96-well plates.
4. Quickstep 2 kit (Edge BioSystems, Gaithersburg, MD, cat. no. 33617).
5. ABI PRISM BigDye Terminator Cycle Sequencing Kit v3.1.
6. Microspin G50 columns (Pharmacia Amersham, cat. no. 275330-01).
7. 3 M sodium acetate, pH 5.0.
8. Ethanol (100%).
9. Formamide sequencing loading buffer: five parts molecular biology-grade deion-
ized formamide to one part 25 mM EDTA, pH 8.0; with 50 mg/mL blue dextran
can be purchased from ABI (HiDi loading buffer, ABI, cat. no. 4311320).

2.6. Microsatellite Genotyping

1. Vertical PAGE gel electrophoresis apparatus.
2. Bench-top microcentrifuge.
3. Heating block (at 95°C).
4. Phenol plus chloroform (1:1).
5. Formamide loading buffer.
6. 40% (19:1) acrylamide:bis-acrylamide solution (Sigma-Aldrich, cat. no. A2917).
7. TEMED.
8. 10X TBE electrophoresis buffer.
9. Sucrose loading buffer: 4.0 g sucrose, 1.0 mL 10X TBE buffer, bring up to 10 mL
with dH2O. Heat to 68°C to dissolve the sucrose. Add 5 mg xylene cyanol and 5 mg
bromophenol blue.
10. 10% (w/v) ammonium persulphate solution.
11. ABI PRISM 377 automated DNA sequencer (or automatic sampling on an ABI
PRISM 3100 Genetic Analyzer).
12. Loading buffer: 12.0 μL formamide + 3.0 μL blue dextran (50 mg/mL in 25 mM
EDTA) + 0.3 μL Genescan®-350 TAMRA marker.
13. HiDi loading buffer (ABI, cat. no. 4311320).

2.7. RNA Preparation

1. Bench-top microcentrifuge.
2. Sterile, disposable plasticware is required throughout.
3. Confluent cultured human fibroblast cell lines in 25- or 75-cm2 flasks.
4. TRIzol® reagent (Invitrogen Life Technologies, Paisley, UK, cat. no. 15596-018).
5. 10 U/μL DNase I, RNase-free.
6. RNase-free water for resuspension of RNA pellets (e.g., Gibco Ultrapure,
Invitrogen, cat. no. 10977-015).
7. Diethylpyrocarbonate (DEPC)-treated double-distilled water. Add 0.1% DEPC
to double-distilled water. The mixture is strongly agitated and left to stand over-
night in a fume cabinet before autoclaving to inactivate the DEPC before use.
8. Chloroform, analytical quality.
136 Tassabehji and Urban

9. Phenol plus chloroform plus isoamyl alcohol, 25:24:1 (v/v), molecular biology
grade.
10. Chloroform plus isoamyl alcohol, 24:1 (v/v), molecular biology grade.
11. Isopropyl alcohol, molecular biology grade.
12. Absolute ethanol, analytical grade.
13. 75% ethanol prepared with DEPC-treated water.
14. RNase-free Tris-EDTA buffer. Prepared either with commercially available
RNase-free stock solutions of Tris-HCl and EDTA or with DEPC-treated stock
solutions. However, because Tris-HCl contains an amino group that interacts with
DEPC and makes it unavailable for RNase inactivation, it must be treated with
1% DEPC.
15. 200 mM Tris-HCl, pH 8.0 (1% DEPC-treated; see Subheading 2.7., item 14).
16. 25 mM MgCl2.
17. 3 N NaCl prepared with DEPC-treated water.
18. DNase I, amplification grade, with buffer.

2.8. First-Strand Complementary DNA Synthesis and Reverse

Transcriptase PCR
1. Thermal-cycling machine with a heated lid.
2. Oligo(dT)20.
3. Total RNA.
4. 25 mM MgCl2.
5. 0.1 mM dithiothreitol.
6. 10 mM dNTP.
7. 200 U/μL SuperScript III reverse transcriptase (RT) and 10X RT buffer
(Invitrogen).
8. 40 U/μL RNaseOUT Recombinant RNase Inhibitor (Invitrogen).
9. Escherichia coli RNase H (2 U/μL).
10. DEPC-treated water.
11. 10 μM control primers.
12. 200 mM Tris-HCl (pH 8.4), and 500 mM KCl.
13. Platinum® Taq DNA Polymerase (Invitrogen).

3. Methods
High-throughput low-cost technologies are often required to detect disease-
causing SNPs and mutations. The large size of ELN requires a reliable method
for the identification of disease-causing variants. Several different technolo-
gies can be used for ELN mutation screening and detection; in this chapter, we
describe three technologies that are currently in use and discuss their advan-
tages and limitations:
1. Single-strand conformation polymorphism (SSCP)/heteroduplex (HD) analysis.
2. DHPLC.
3. Direct sequencing.
Molecular Diagnostics of Supravalvular Aortic Stenosis 137

SSCP/HD is a comparatively inexpensive and accessible technique. It is,

however, time consuming, with limited throughput, and is less sensitive com-
pared with other techniques. Alternatively, DHPLC or direct-sequence analy-
sis are sensitive and high-throughput techniques for the detection of point
mutations and SNPs in genes. Although direct DNA sequencing is potentially
both a high-throughput and a sensitive method, limitations include the rela-
tively high cost of screening a large gene such as ELN, and the necessity of
reviewing sequence chromatograms to avoid missing putative sequence
changes. In addition, detection of mosaics (the presence of two populations of
cells with different genotypes in one patient, in which usually one of the two is
affected by a genetic disorder, resulting from a mutation during development
that is propagated to only a subset of the adult cells) is difficult. In contrast,
DHPLC provides a sensitive, rapid, and low-cost method for the analysis of
sequence variants. The presence of HDs can be readily recognized by quick
visual inspection of the chromatograms. Disadvantages of DHPLC are that the
presence of a common SNP in the same DNA fragment may obscure the detec-
tion of a gene defect and the expense of the equipment required.
Therefore, each technique has advantages and disadvantages, but by using com-
binations of these techniques more than 95% mutation detection can be achieved.
3.1. SSCP/HD Analysis
The combined SSCP/HD analysis technique is widely used for mutation
detection (schematic depicted in Fig. 3A). SSCP is based on the principle that
the electrophoretic mobility of nucleic acids in a nondenaturing gel depends on
both shape and size. The secondary structure conformation adopted by single-
stranded DNA is flexible, unlike double-stranded DNA, and is determined by
intramolecular interactions and base stacking, which depends on sequence
composition. The secondary structure of single-stranded DNA can, therefore,
be altered by a single nucleotide base change resulting in measurable differ-
ences in electrophoretic mobility under nondenaturing conditions. HDs are
formed when a mixture of wild-type and mutant double-stranded DNA mol-
ecules are denatured by heating followed by slow reannealing. HD DNA
exhibits distinct slower electrophoretic mobility compared with the correspond-
ing homoduplex, because a double-stranded configuration that is more open is
adopted surrounding the mismatched bases. The position and the type of nucle-
otide mismatch determine the conformation of HD. Although SSCP is largely
empirical (no theory is available for predicting the dependence of conforma-
tion on sequence, and of mobility on conformation), in combination with HD
mutation screening, SSCP provides a more efficient mutation-screening
method, with detection rates of up to 90% and detection sensitivity limits of
approx 1 mutant cell in the presence of 10 normal cells.
138 Tassabehji and Urban

Fig. 3. SSCP/HD ELN mutation screening technique. (A) Schematic of the SSCP/
HD technique. ss, single strand; ds, double strand.

For SSCP/HD, the protocol involves:

1. Amplifying the target sequence from genomic DNA by PCR.
2. Denaturing the amplicon to single-stranded DNA and performing electrophore-
sis on a nondenaturing polyacrylamide gel.
Bands of the single-stranded DNA migrating in the gel at positions different
from the wild type indicate the presence of a mutation (see Fig. 3B). The sen-
sitivity of PCR SSCP tends to decrease as the fragment length increases. For
fragments of approx 200 bp, more than 90% of single base changes can be
detected; whereas for fragments of 400 bp, the detection rate is lowered to
80%. Sequences larger than 350 bp can be divided into shorter segments by
generating overlapping fragments or digesting the amplicon (if suitable restric-
tion sites reside within it) before analysis. HDs will form during PCR if the
DNA has two different alleles that result in a mixed population of wild-type
and mutant DNA. After denaturation and reannealing (by heating and cooling),
four distinct species can form in nondenaturing polyacrylamide gels: wild-type
homoduplex, mutant homoduplex, and two HDs. The formation and stability
of the HDs depends on the type of mutation in the fragment; for example, dele-
tions and insertions create relatively stable heteroplexes, whereas single base
missense changes are less stable because of their sensitivity to temperature,
Molecular Diagnostics of Supravalvular Aortic Stenosis 139

Fig. 3. (continued) SSCP/HD ELN mutation screening technique. (B) Examples of

mutations which result in HD formation and abnormal ss conformers using SSCP/HD
screening (* indicates SVAS patients with ELN gene mutations). (C) Sequence trace
showing the sequence frameshift that occurs in an SVAS patient with a heterozygous
deletion of 1 bp in exon 5 (229delG).

solvents, and ionic strength of the buffer; therefore, electrophoresis conditions

must be optimized to detect all changes.
This combined SSCP/HD technique represents a simple but efficient method
for point mutation analysis and can detect missense, frameshift, nonsense, and
splice-site mutations (3,6,8–10,16).
3.1.1. PCR Amplification of ELN Gene Exons
Exons comprising ELN are amplified from human genomic DNA using PCR.
The primers used to amplify the ELN exons and the PCR amplification anneal-
ing conditions are summarized in Table 1.
140 Tassabehji and Urban

1. Prepare a 10X stock of the oligonucleotides at a concentration of 5 μM, using the

following equation to calculate oligonucleotide stock concentrations:
OD260nm × 100
μM (pmoles/μL) =
N
OD260nm = optical density at 260 nm of the undiluted primer stock; N = number of
bases in the oligonucleotide.
2. For each 10 μL PCR reaction add:
a. 1 μL 10X PCR buffer: 166 mM ammonium sulphate; 670 mM Tris-HCl (pH
8.0 at 25°C); 37 mM magnesium chloride; 67 μM EDTA; and 0.85 mg/mL
bovine serum albumin (PCR buffers are provided with the Taq polymerase
supplied by manufacturers and have different formulae).
b. 1.5 μL of 20-mM dNTP stock (5 mM of each dATP, dCTP, dTTP, and dGTP).
c. 1 μL of 5-μM forward primer.
d. 1 μL of 5-μM reverse primer.
e. 5.4 μL distilled sterile water.
f. 0.1 μL of 5-U/μL Taq polymerase.
g. 1 μL of 50-ng/μL genomic DNA (50–100 ng genomic template).
3. If using a thermal-cycling machine without a heated lid, add a drop of mineral oil
to avoid evaporation. The melting temperature (Tm) of a specific oligonucleotide
primer can be calculated using the formula: Tm = 2(A + T) + 4(G + C), where A,
C, G, and T are the nucleotides in the primer (formula developed for hybridiza-
tion assays with oligonucleotides at a salt concentration of 1 M) (21). Usually,
the chosen annealing temperature is calculated as Tm –5°C. The parameters for
thermal cycling, including annealing temperatures, have been determined em-
pirically for each pair of ELN oligonucleotide primers (summarized in Tables 1
and 2).
Cycling parameters: initial denaturation: 94°C for 3 min; followed by 30 cycles
of:
a. Denaturation: 94°C for 1 min.
b. Annealing: annealing temperature for 1 min.
c. Extension: 72°C for 1 min.
d. Final extension: 72°C for 5 min.
4. Monitor 2 μL of the amplified PCR products by electrophoresis on ethidium bro-
mide-stained agarose gels (1% w/v containing 0.5 μg/mL of ethidium bromide)
in 1X TBE buffer. Alternatively, the gel can be stained after electrophoresis by
soaking for 30 min in a dilute solution of ethidium bromide (0.5 μg/mL in 1X
TBE) and visualized on a short-wavelength UV transilluminator.

3.1.2. SSCP/HD Electrophoresis

Samples for combined SSCP/HD analysis can be unprocessed PCR products
ranging from 100 to 400 bp in size. It is important that the PCR product is clear
of nonspecific artifacts before mutation screening to avoid interference with
the assay. SSCP/HD analysis is performed by upright PAGE in a cold room
Molecular Diagnostics of Supravalvular Aortic Stenosis 141

Table 1
Primer Sequences for the ELN Gene for Mutation Screening
and Microsatellite Markers for Genotyping a

PCR Anneal
ELN amplicon temperature
exons Forward PCR primer 5' to 3' Reverse PCR primer 5' to 3' size (bp) (°C)

1 CAGCCGACGAGGCAACAATTAGGC TGAGCGTCTAGTCACCTGGCCCA 228 60

2 TCCATGTAATTGTGGGTTTTGCC CAATGTTCCTACCTTCTGTAGTG 261 60

3 CTTGCCCAAGGTCACGTAGTTAG ATGAGGGAGTCCTTGATGCTCGG 259 60

4 GGTTGGATAAGTAGTAGATGGAT AGGCTAATCGGTGTCCACACCTC 249 60

5 TCCAGGAGACATTTCCCACTCTG GGCAGTTGGTATCAGCATCAGTC 255 60

6 AGGCAGGGCCAGAGCGTAGGAGT AAGCCTGAGTTGAGGGAAGGTTC 254 60

7–8 TACGCAATGCCTCACCTGTCCTG TGCCCTCTGTCCTCCAGCCCCAG 255 60

9 CTGCCTGGGTGGGAAGGGCTG GGCCTTACTATGATGCCCAGGCT 273 65

10 GTTCCCAGCAGGGCCTGCAAGGC GGCCCTGAGCCAGTCCAGGATCC 231 65

11 CGCAGCATGCGATGACTGGTCTG GGAGAAATTGGGCAGGCTTGGAT 258 60

12 GAGATTCAGGGAGTCCCTCGAAG CACCCGGCCGAGTGGTGCATCTT 255 60

13 TGGTGGGAGCCCAGCAAGGCATG AGATTCCCACTCCAAGACCCCAA 235 60

14 AGTGTGATGTCTGCACAGATGAC ACCAGGGTCTGGATGCAGGGTG 227 65

15 CTGAAGCTCCCATGTATACCCAC GTCAATAGTAATGGGAATGGAG 245 60

16–17 CGTCTAAGTGGCCATCCTGCCTG TTGCGGCTAGGGTCTCCGAGGTC 378 65

18 ATACTCTACTAACCACCCTTCTA TGGCAATAGTCTCAATATTTCTC 300 60

19 GCATGAAAGGAGATGGCCCAAC TTTAGTTCTGGCAAGTAAAGGC 223 60

20 CTCTTTCCCAATCCATCAGCATC CCCATCCCTTCTCAACCCATGTC 297 60

21 GAGGTCGTATCCATGCCTTACAG TCCAGGCCATTTCAGTCCTGGAG 253 60

22 AAAGTGAGTACTGGGAGGGGCAA CGACCTTGGTCAACTCCAGGGAC 208 65

23 GTCCCTGGAGTTGACCAAGGTCG CCCAGAATGTGACAGCTTAAGTG 300 60

24 AGCTTCTGTCCTCTTTGATCAGG GGGCCCCTCAGGCTCATTGACTC 254 60

25 TGGCTCCCGGCATTGGCCCTGGTG CCTGGCTGTTGCCCCTAACCAGC 239 60

26 GGCATGCTCCCTGCCTGCTGTCG CCCAGATGCTTAGGAGAACCTAA 313 60

27 CAGCTTCAGGGCTTTGAGGAAGC GTGACCACCCCAGTCCTGTGCTG 242 65

28–29 AACACTCATTTTCCCTCCTCTCC GCCTGGGGGCCTGGCGGCAGCTC 290 60

30 CCATCGAAGGCCAGGGGAGACC CCATCTCTGTCTCGCATACACAC 261 60

31 GGTGGCATTGGCATTCCTGAGCCG GTTAAGGAATGTCCCAGACAAGAT 220 65

32 TTCCTTAACCCAGAACCCAGCAG CCTTGTGTGGACATGGGCTCTGG 242 60

33 CCAGACAGAGGTCTTGGGTGAGC CCCTTCTGAGCAGGAGATGGCAC 233 60

34 CTTCTTGGAGCCTCCATTCGAG TTCTCCACCAAGCAGTAGCACC 244 55

Microsatellite markers

ELNi1 GCCCACATGGGCAGATTGCT CCCTCATCCACAGACAGGTC 254–286 60

ELN ATGAGACGTGGTCAAGGGTAT GGGATCCCAGGTGCTGCGGTT 161–175 60

Helg18/19

(continued)
142 Tassabehji and Urban

Table 1 (continued)

PCR Anneal
ELN amplicon temperature
exons Forward PCR primer 5' to 3' Reverse PCR primer 5' to 3' size (bp) (°C)

LIMK1GT TGGGGCAGGAGAATGATGTG AGTCTTCTTTGCGGGCTATGTTA 180 60

D7S613

G18333 CCTGAAGGTAGGTAGTTTAACC CTGGGTTCAACCGATTCTCC 147 60

D7S2472

Z53057 TCTAAAGTCTGCCAGGCTAC GCAGCGAGACTCCATC 83–103 55

D7S3195

G68161 TTGCAGGGCTGTGAGGATTAAC TCTGGTCATAAATTGGAACTCCATAGA 405 60

D7S3196

G68162 AGGCTGTCTCTAAATAAATTCCGTCAA TGTCCTCCCACAAGTCCGTAAA 225 60

D7S1870

Z51768 TTCACTCAGGAAGTGGC TGGTGATGTGCTTTACTACG 108–132 60

D7S2490

Z53428 TGTAAGCCACCGCACCT AGCACCCGGCATAGATGT 134–156 55

D7S2476

Z53107 GGGCAACATAGCACGATT CAGGAGTCAGTTAGATAAGGTCAC 128–160 60

D7S672

Z24075 ACATGAAGGTCTACCAGTAGCC CACTTTGGTTGGAGCAAGG 132–160 60

RT-PCR primers

ELN 5'–3' CATTCCTGGTGGAGTTCCTG TGGGAAAATGGGAGACAATC 2224 55–60

ELN

X18–21 GGGATCCCAGGTGCTGCGGTT ACCGTACTTGGCAGCCTT 287 55

β-ACTIN GCTCG TCGTCGACAACGGCTC CAAACATGATCTGGGTCATCTTCTC 353 60

aGenbank accession numbers for the sequences are included.

(~4°C) to control temperature and the DNA bands are visualized using silver
staining. Alternatively, temperature-controlled electrophoretic units run at 4°C
can be used. Because the conformation adopted by single-stranded DNA is sen-
sitive to a range of parameters (e.g., fragment length, gel matrix composition,
ionic strength, and temperature) achieving high detection rates by SSCP/HD
requires running gels under the conditions specified here for ELN.
1. An upright PAGE gel electrophoresis system that can accommodate glass plates
approx 33.8 cm long is required for SSCP/HD analysis with 1-mm-thick spacers
to aid gel handling for subsequent staining. The acrylamide used has a 49:1 ratio
of acrylamide to crosslinking reagent (methylene bis-acrylamide). The percent-
age of the gel depends on the molecular weight of the sample product, for ex-
 Molecular Diagnostics of Supravalvular Aortic Stenosis 143

Table 2
PCR and Chromatography Conditions for DHPLCa
Amplicon Primer 1 Primer 2 Size Temp Oven Buffer B

hELNe01 CTCTTTCCCTCACAGCCGAC GTCTAGTCACCTGCCAAAGGG 238 58 66.0°C 52%

hELNe02 TTCTTGTTTCCATGTAATTGTGG GGCGTGTCAATGTTCCTACC 268 56 60°C 53%

hELNe03 CAAGGTCACGTAGTTAGGCA GCCTCCTCCCACCGCCTGGA 286 60 62.4°C 54%

hELNe04 GTGATTCCACACTGCCCACA GTTGCCTTGTCCTGTTCCTA 241 54 61.1°C, 62.5°C 52%

hELNe05 GATCGACCCTGAGCATCACA GTCCCCGTCAGTGCCCAGGA 308 60 61.5°C, 63.0°C 54%

hELNe06 GTCTGGCAGAGAGCGGAAGA GGAGGGCCCCACGGAAGCCA 274 60 63.0°C, 64.0°C 53%

hELNe07 GCTAGCTGTGCCCAGTCTGA CTCCGGCTCCAGGCTGAGGA 298 60 63.5°C, 63.9°C 54%

hELNe08 GCAAGGCTTGGTGGAGCCAA CGCAGGCACCAGCCTGGCTA 249 60 63.5°C, 64.7°C 52%

hELNe09 CTGCCCCTGTCGGGCACAGA GCCTCAGTCTCCCAAAGCAA 262 60 62.5°C 53%

hELNe10 GAGGGGAGGGGTTCCCAGCA GGATCCCACCCCATTTCACA 224 58 63.7°C, 64.1°C 51%

hELNe11 CCTTGGTGCTGTCTGGCCCA GGGTGCCACTTTGTGCTACA 252 60 61.0°C, 61.8°C, 63.8°C 53%

hELNe12 GAAGCAGGATGGTTTCTGGA GAACCACCACACCCGGCCGA 245 63 62.4°C 52%

hELNe13 CTTTAGCACCTGTGGGGGTA CGAGGTGCTCTCCTGGCCCA 238 60 62.9°C 52%

hELNe14 GGTGATGTCTGCACAGATGA CTGGAGCCTGGAAGATCAGT 161 58 62.5°C, 63.5°C, 64.5°C 48%

hELNe15 GAAGCTCCCATGTATACCCA CTTTGGAGGCAGGCTGTCAA 258 58 62.5°C, 64.0°C 53%

hELNe16 CCCAGACAGGCCCATCTGGA GTGGCCATCTCAAGGACACA 280 58 62.6°C, 63.1°C 54%

hELNe17 GTGTCCTTGAGATGGCCACA CCCGAGCCGTGGACTTACCA 153 58 64.8°C, 65.2°C 47%

hELNe18 CTCTGAGGTTCCCATAGGTT CACACACACGCCCAGCTCA 215 60 59.2°C, 63.9°C 51%

hELNe19 CCAACACACAGATGGGTAGA GGCAAGTAAAGGCCAGGACA 197 63 60.7°C, 62.2°C 50%

hELNe20 CTTTCCCAATCCATCAGCAT CATCCCTTCTCAACCCATGT 293 60 direct sequencingb

hELNe21 CCTTACAGGCAGAAGAGCTT CAGTTTGCCCTGAGGTTGGA 205 58 63.3°C, 64.6°C 50%

hELNe22 CCATTCTCTTCTTCCTCCGA CTCCAGGGACCCTTCCATGA 242 58 62.0°C, 65.3°C 52%

hELNe23 GGAAGACTGAGCCTAGAGAT CACAGGAGAAAGCAGTTCTC 188 60 62.0°C, 64.0°C 50%

hELNe24 GCTTCTGTCCTCTTTGATCA AGAGAGGGGGATTAGAGATG 298 54 59.0°C, 63.5°C, 64.4°C 54%

hELNe25 CCCGCCTCCATCTCTAATC AACCAGCTCTGAGATCGTTG 139 58 62.9°C, 64.6°C 46%

hELNe26 TGCCTGCTGTCGCCACCACT GCTTAGGAGAACCTAACAAG 295 62 63.8°C 54%

hELNe27 CAATAGAGGCCAAGGAAGTC CAAGGGAGCCACAAGTGGTT 179 60 62.5°C 49%

hELNe28 GTCTGCTTGCCTTGTGTCC GAACACAGACCGAGTTCAGG 180 56 61.6°C, 64.9°C 49%

hELNe29 GGAGGGAATCTAACCAGTAC GCAGGGACTCTGAGTCTACA 212 56 63.5°C, 65.5°C, 66.8°C 51%

hELNe30 ACAGGCCGAGGCTTCAGTC TCCATCTCTGTCTCGCATAC 199 56 61.0°C, 62.5°C, 64.0°C 50%

hELNe31 CAGGTGGCATTGGCATTC GTCCCAGACAAGATCTTCAG 212 56 62.6°C, 64.0°C 51%

hELNe32 GAACCCAGCAGGGATATCA CCCACTGCTAGATGGACA 202 60 62.0°C, 63.6°C 50%

hELNe33 TGCAGGCAGAAAGTGATGAG GCCCTTCTGAGCAGGAGAT 208 60 62.3°C, 63.2°C 51%

hELNe36 GATTAGAGCCGAAACTGAG TGCCCTGTGGATCTGCAAG 257 54 62.6°C 53%

aTemp, annealing temperature; Oven, DHPLC oven temperature; Buffer B, Buffer B mixing ratio with
Buffer A at the start of the elution gradient.
bNot screened by DHPLC because analysis of chromatograms is complicated by varying allelic combi-

nations for common polymorphisms 1264G>A and 1315+17T>C.

144 Tassabehji and Urban

ample: 500 bp, 7% (w/v); 300 bp, 7.75% (w/v); and 200 bp, 8% (w/v).
2. Prepare an 8% (w/v) nondenaturing PAGE gel that has been allowed to polymer-
ize for at least 1 h:
a. 15 mL of 40% (49:1) acrylamide:bis-acrylamide solution.
b. 7.5 mL of 10X TBE.
c. 62.5 μL TEMED.
d. dH2O to a final volume of 52 mL.
e. Add 500 μL of freshly made 10% (w/v) ammonium persulphate solution.
3. Make up 1 L of electrophoresis buffer (1X TBE) and refrigerate at 4°C for at
least 1 h before use.
4. Rinse unpolymerized acrylamide out of the PAGE gel wells, add cold electro-
phoresis buffer (1X TBE) to the buffer chambers and allow the gel to refrigerate
in a cold room at 4°C for 2 h before loading.
5. Prepare the PCR samples (ELN amplicons) for loading by mixing with an equal
volume of formamide loading buffer, then denature by heating at 94°C for 3 min
and immediately snap-cool on ice. Load between 5 and 10 μL (depending on
amplification efficiency). Some PCRs do not form HDs readily in formamide. If
this is the case, preload the wells with 1–2 μL of the PCR sample before heat
denaturation.
6. Electrophorese at 300 V constant voltage overnight (~16–18 h); the xylene cyanol
dye front will have run a distance of approx 25 cm. Note that smaller PCR prod-
ucts may require a reduced electrophoresis voltage.
7. Remove the top glass plate from the PAGE gel and gently peel the gel off of the
plate into a tray for visualization by silver staining (modified from ref. 22).

3.1.3. Silver Staining of DNA in PAGE Gels

1. Carefully transfer the polyacrylamide gel into a plastic tray. Fix the gel in 400
mL of solution I for 6 min, then add solution II and incubate for 15 min.
2. Decant off the solution, rinse the gel with distilled water, and add 400 mL of
solution III and incubate for 20 min in a fume cabinet.
3. Pour off the solution and rinse the gel twice with distilled water, then fix with
400 mL of solution IV for 10 min.
4. The gel can be stored permanently by drying between two sheets of porous cello-
phane soaked in distilled water and locked into the drying frame (Easy Breeze
gel drying system) to air-dry.

3.2. Denaturing High-Performance Liquid Chromatography

DHPLC detects mutations on the basis of mismatches between amplified
DNA fragments that result in the formation of HDs. These are thermally less
stable than their corresponding homoduplexes, and are resolved by means of
ion-pair reversed-phase liquid chromatography at elevated column tempera-
tures, typically in the range of 50 to 70°C, depending on the GC-content of the
Molecular Diagnostics of Supravalvular Aortic Stenosis 145

sequences. Temperature is the most important parameter that affects the sensi-
tivity of DHPLC in detecting mutations.
1. PCR amplification of genomic amplimers is essentially conducted as described in
Subheading 3.1., using the oligonucleotide primers and annealing temperatures
described in Table 2. The final volume of the PCR reactions is generally 25 μL
(see Note 1). To facilitate the formation of HDs, the amplimers are denatured and
slowly ramped to room temperature in 30 min. For the GeneAmp 9700 PCR ma-
chine (ABI), the following incubation regimen is used: 95°C, 3 min; 3% ramp to
37°C; 37°C, 20 min; 25°C, 20 min.
2. For all amplicons, the following DHPLC conditions are used:
a. Percentage of buffer B for loading = indicated buffer B concentration
(Table 2) – 5%.
b. Loading volume = 8 μL; loading duration = 0.5 min.
c. Gradient slope = 2%/min (starting at the indicated Table 1 buffer B concen-
tration).
d. Gradient duration = 4.5 min.
e. Clean duration = 0.5 min (with 100% buffer D).
f. Percentage of buffer B for equilibration = indicated buffer B concentration
(Table 2) – 5% (same as for loading).
g. Equilibration duration = 0.9 min.
Several amplimers contain more than one melting domain. Thus, for complete
coverage of the amplimers, it is necessary to conduct DHPLC screening at mul-
tiple oven temperatures, as indicated in Table 2. An example of DHPLC condi-
tions is shown in Table 3.
3. At the conclusion of the DHPLC, chromatograms are reviewed using the Naviga-
tor (Transgenomic, v1.5.3) software or equivalent, and compared with normal
control chromatograms (Fig. 4A). Amplimers with altered chromatograms are
further analyzed by direct DNA sequencing (Fig. 4B, Subheading 3.3.). Chro-
matograms are often allele specific and can be directly used for genotyping of
known variants. This characteristic is particularly useful in investigating the
occurrence of patient-derived variants in collections of normal control DNA.

3.3. Mutation Detection by Direct Sequencing

Mutations can be identified in PCR-amplified DNA fragments by direct
sequencing using fluorescence-based cycle-sequencing technology (ABI
BigDye Terminator v3.1 kit). Essentially, all of the exons are amplified from
the patient’s genomic DNA and sequenced in both the forward and reverse
orientation, using the ELN PCR primers. A normal control individual is se-
quenced alongside the patient’s DNA, so that the sequence traces can be com-
pared for heterozygous mismatches. In addition, mutations detected by the
mutation-screening techniques identified in Subheadings 3.1. and 3.2. are
146 Tassabehji and Urban

Table 3
Example of DHPLC Running Conditions for Amplimer
hELN01

Time Buffer Buffer Buffer

(min) A (%) B (%) D (%)
Loading 0.0 53 47 0
Start gradient 0.5 48 52 0
Stop gradient 5.0 39 61 0
Start clean 5.1 0 0 100
Stop clean 5.6 0 0 100
Start equilibration 5.7 53 47 0
Stop equilibration 6.6 53 47 0

characterized by sequencing using this method. Generally, PCR reactions

should be strong and specific, because nonspecific products in the PCR reac-
tion (including primer–dimer) will be sequenced using this method and gener-
ate a high background interference.
1. Set up a 40-μL PCR reaction using primers specific to the region requiring
sequencing from the patient DNA sample and a normal control sample.
2. Monitor 3 μL of the PCR-amplified product on a 1% ethidium bromide agarose
gel to confirm successful amplification, then purify the PCR products before
sequencing to remove primers and unincorporated dNTPs, using the Quickstep 2
kit or any other commercially available PCR clean-up kit.
3. The Quickstep 2 kit protocol involves briefly vortexing the poly(4-
hydroxystyren) (SOPE) resin and adding one-fifth of the volume of the PCR re-
actions to be purified to the SOPE resin and vortexing to mix.
4. Centrifuge the Performa Gel Cartridges for 3 min at 750g, then add the PCR
product onto the center of the column and centrifuge for 3 min at 750g. To deter-
mine the concentration of DNA recovered, 2 to 3 μL of the eluate is monitored,
and can then be used directly in BigDye sequencing reactions.
5. Set up the BigDye terminator cycle sequencing reactions as follows:
a. x μL of purified PCR reaction (~300–600 ng of product).
b. 4 μL of BigDye terminator mix.
c. 0.32 μL of 10-μM sequencing primer.
d. Milli-Q water to give a final volume of 10 μL.
6. Use the following cycling sequence conditions with a PE ABI GeneAmp PCR
System 9700 thermal cycler. If you have a different thermal cycler, please con-
sult ABI (www.appliedbiosystems.com) for the cycling conditions.
a. 96°C, 1 min.
b. 96°C, 10 s.
c. 50°C, 20 s.
Molecular Diagnostics of Supravalvular Aortic Stenosis 147

Fig. 4. Mutation detection using DHPLC. (A) Chromatogram of DHPLC analysis

at 62.6°C of exon 16 amplicons obtained from a normal control and a SVAS patient.
Arrow indicates HD peaks in the SVAS sample. (B) Sequence analysis confirmed the
presence of a splice-site mutation (800–3C>G) in the same SVAS patient.
148 Tassabehji and Urban

d. 60°C, 4 min.
e. 25 cycles or step 6, b–d.
f. 4°C.
7. Unincorporated dye-labeled terminators must be removed by Sephadex G-50 col-
umn purification (Micro-spin G50 columns ) or by ethanol precipitation. Do not
use ethanol precipitation to clean up samples that will be run on a sequencing
apparatus that uses capillary electrophoresis columns (e.g., ABI PRISM 3100
Genetic Analyzer), because the high salt concentrations retained in the samples
affect the output quality significantly.
8. For G50 column purification: resuspend the Sephadex resin in the columns by
gentle vortexing, then snap off the bottom closure. Prespin the columns for 1 min
at 735g (4000 rpm for a MSE Micro Centaur microcentrifuge). Place the columns
in a clean 1.5-mL tube and apply the sample to the center of the compacted resin
bed. Spin the columns for 2 min at 735g (4000 rpm for a MSE Micro Centaur
microcentrifuge). The purified samples are collected in the bottom of the support
tube. Discard the columns and retain the flow-through samples.
9. For ethanol precipitation, add 0.1 volume of 3 M sodium acetate and 2.5 volumes
of cold (–20°C) ethanol to the sequence reaction. Leave at room temperature for
20 min and pellet by centrifugation at 13,000 rpm for 15 min. Remove the super-
natant and wash the pellet by adding 150 μL of 70% ethanol. Centrifuge at 13,000
rpm for 5 min, discard the supernatant, and allow the pellet to air-dry for 5 min at
room temperature.
10. Resuspend the pellet in 15 μL of formamide sequencing loading buffer (for the
ABI PRISM 3100 Genetic Analyzer) or 0.8 μL formamide loading buffer (for
ABI PRISM 377 automated DNA sequencer) by vortexing. Centrifuge samples
briefly, then denature for 2 min at 95°C and immediately store on ice until ready
to load (to avoid reannealing of the DNA). Load the samples (automatic sam-
pling on a 96-well plate format for the ABI PRISM 3100 Genetic Analyzer and
0.4 μL for the ABI PRISM 377 automated DNA sequencer) and sequence on the
appropriate sequencing platform using the conditions recommended by the manu-
facturer. Data is subsequently analyzed using the installed DNA Sequencing
Analysis Software (see Fig. 4B).

3.4. Analysis of Partial Deletions and Translocations at the ELN Locus

Some SVAS cases occur because of gross chromosome rearrangements,
such as translocations or deletions, which involve ELN and can be detected by
cytogenetic analysis through karyotyping (in the case of translocations) (11)
and by fluorescent in situ hybridization (FISH) analysis (for microdeletions at
the ELN locus) (6). The methodology for FISH analysis is described in Chapter
7, when applied to diagnose the microdeletion condition, WBS. For
nonsyndromic SVAS cases with partial deletions in the region including ELN,
the FISH probe cosmids 82c2 and 34b3 can be used to detect microdeletion
using the protocols described in Chapter 7.
Molecular Diagnostics of Supravalvular Aortic Stenosis 149

3.5. Indirect Methods of Molecular Diagnosis

3.5.1. Genotyping With Microsatellite Markers or SNPs
Microsatellites or dinucleotide repeat polymorphisms are short, tandemly
repeated, consensus sequences that, because of their high allelic diversity, are
popular and simple markers for molecular genotyping and linkage analysis. An
informative dinucleotide (dG-dT)n repeat polymorphism resides in intron 18
(11 bases downstream of ELN exon 18) of the human ELN gene and consists of
eight alleles with sizes ranging between 161 and 175 bp (Genbank accession
number L01989) (23). In addition, a highly polymorphic tetranucleotide repeat
marker is located in intron 1 of ELN (24). This microsatellite marker (along-
side others, such as LIMK1GT, D7S1870, and others shown in Fig. 2 of Chap-
ter 7) can be used for determining the parental origin of a WBS deletion, and
aids diagnosis when FISH analysis is not available. In addition, this
microsatellite marker can be used in linkage analysis to track the mutant allele
in autosomal-dominant SVAS families in which the mutations have not been
defined, or to establish the ELN deletion status in sporadic SVAS patients with
ELN deletions when FISH analysis is not possible because of lack of the
appropriate samples or resources. The technique involves PCR amplification
of DNA using oligonucleotide primers complementary to a region flanking the
microsatellite locus, size fractionation of the amplified product on a
nondenaturing polyacrylamide gel, and detection of DNA fragments either by
silver staining of the gel or using a fluorescent detection system (if a fluores-
cent PCR primer is used). Typical molecular genotypes from SVAS and WBS
families using the nonfluorescent technique are shown in Fig. 5.
3.5.2. Nonfluorescent ELN (GT)n Polymorphism Genotyping
1. All amplifications are carried out as described in Subheading 3.1.1., apart from a
reduction in the number of cycles to 27 cycles. Product sizes vary from 128 to 154 bp.
2. PCR products are purified by phenol extraction. An equal volume of buffer-satu-
rated phenol plus chloroform (1:1) is added to the DNA solution, mixed by
vortexing, then separating the phases by centrifugation at 12,000g for 5 min.
3. Carefully remove the aqueous (top) layer to a new tube, being careful to avoid
the interface. Mix 4 μL with an equal volume of sucrose loading buffer and load
onto an 8% polyacrylamide nondenaturing gel prepared using the following re-
agents (for a 16-cm gel):
a. 5 mL of 40% (19:1) acrylamide:bis-acrylamide solution.
b. 2.5 mL 10X TBE.
c. 30 μL TEMED.
d. Deionized H2O to a final volume of 25 mL.
e. Add 200 μL of freshly made 10% (w/v) ammonium persulphate solution.
f. Allow to polymerize for 1 h at room temperature.
150 Tassabehji and Urban

4. Electrophoresis is performed at 300 V constant voltage for 3 h (room temperature)

on a vertical PAGE apparatus setup. The DNA bands are visualized by silver stain-
ing (Subheading 3.1.3.).

3.5.3. Fluorescent Nonfluorescent ELN (GT)n Polymorphism Genotyping

Fluorescent microsatellite analysis can also be preformed using primers that
have been commercially fluorescently tagged at the 5'-end with 6-FAM, HEX,
NED, or TET phosphoramidites. These should be stored in the dark at –20°C.
1. Make up the following PCR cocktail:
a. Forward plus reverse primer mix (10 μM stocks) 2.0 μL
b. 10X PCR buffer*: 2.0 μL
c. 2 mM dNTP mix 2.0 μL
d. 25 mM MgCl2 1.6 μL
e. Taq polymerase (5 U/μL) 0.16 μL
f. dH2O 10.84 μL
g. DNA (20–50 ng/μL) 2.0 μL
h. Total 20.0 μL
*100 mM Tris-HCL, pH 8.3; 500 mM KCl; and 0.01% w/v gelatin (Perkin-Elmer
buffer). Amplitaq gold DNA polymerase. This enzyme confers a “hot-start” that
improves the efficiency and specificity of PCR reactions.
2. Conditions for PCR amplification are: 94°C (4 min), then 30 cycles at (94°C, 30 s;
60°C, 45 s; 72°C, 45 s), and a final extension at 72°C for 10 min.
3. PCR amplimers are diluted 1:10, and 1 to 2 μL are added to 15.3 μL of standard
or loading buffer (12.0 μL formamide + 3.0 μL blue dextran [50 mg/mL in 25 mM
EDTA] + 0.3 μL Genescan-350 TAMRA) or HiDi loading buffer.
4. Denature samples at 96°C for 2 min, and place on ice. Load 0.4 to 0.8 μL of each
sample mix on an ABI PRISM 377 automated DNA sequencer (or automatic
sampling on an ABI PRISM 3100 Genetic Analyzer) using the Genetic Analyzer
and Genescan software to analyze the alleles, according to the manufacturer’s
instructions.

3.5.4. Analysis of ELN Expression in Cultured Fibroblast Cells

RNA isolation and RT-PCR protocol:
1. To look for any mutations not detected using techniques given in Subheadings
3.1.–3.4. (e.g., intronic or whole exon deletions) that may affect the ELN mRNA
transcript.
2. To examine the consequences of any intronic mutations detected residing outside
of the consensus donor or acceptor splice junctions, or missense mutations that
may affect normal splicing but do not have obvious pathological features (10).
Established skin fibroblast cultures from the affected and a normal control indi-
vidual are required for RNA expression studies.
 Mo
lec
ular

Dia
gno
stic
s
151

of
Sup
rava
lvul
ar

Fig. 5. Linkage analysis using polymorphic microsatellite repeats at 7q11.23. (A) WBS family. The WBS child shows
monoallelic inheritance for all of the markers except for D7S672, which lies outside of the commonly deleted region in WBS. (B)
Ao
An individual with sporadic SVAS showing a hemizygous deletion of the ELN but not the D7S1870 marker. M, mother; F, father. rtic
Alleles are highlighted with a black dot.

Ste
nos
is
152 Tassabehji and Urban

3.5.5. Total RNA Preparation

A number of procedures are available for preparation of total RNA from
tissues or cultured cells. A reliable and simple method involves the use of a
modified 14 M solution of guanidine salts and urea (Chaosolv) that act as dena-
turing agents. The isolated RNA should be treated with DNase I to remove
genomic DNA contamination. This is a protocol for preparation of total RNA
from cultured human fibroblast cell lines grown in 25- or 75-cm2 flasks, which
has been adapted from the TRIzol Reagent protocol. During RNA isolation
and analysis, it is essential to maintain an RNase-free environment. All re-
agents, tubes, and pipets should be RNase free.
1. Aspirate culture medium from cells grown in monolayer that have reached 70 to
100% confluence, and wash cultures twice with sterile phosphate-buffered saline.
2. Add 1 mL TRIzol reagent per 10 cm2 of cells (i.e., 1 mL for 1 × 106 cells), and
lyse cells in TRIzol by pipetting up and down in a 21-gage needle and syringe
until solid matter disappears, then incubate at room temperature for 5 min.
3. Transfer lysate to 1.5-mL polypropylene microcentrifuge tubes (maximum vol-
ume of 1 mL into a 1.5-mL tube).
4. Add 0.2 mL of chloroform per 1 mL of RNA reagent, shake vigorously for 15 s,
then incubate at room temperature for 2 to 3 min.
5. Centrifuge the homogenate at 12,000g for 15 min at 4°C. The homogenate will
form two phases: DNA and protein reside in the lower organic phase and in the
interface, with RNA in the upper aqueous phase.
6. Transfer the colorless aqueous phase, which contains the RNA, to a fresh
microcentrifuge tube. Only recover approx 95% to avoid carrying over contami-
nants from the organic/aqueous interface.
7. Precipitate the RNA by adding an equal volume of isopropanol. Leave for 10 min
at 4°C, then centrifuge at 12,000g (4°C) for 10 min.
8. Discard the supernatant and wash the RNA pellet twice with 75% ethanol (1 mL
of 75% ethanol per 1 mL of initial solution used) by shaking, then centrifuging
for 5 min at 7500g (4°C). Air-dry the pellet for 5–10 min (do not over dry, be-
cause it will be more difficult to dissolve), then dissolve in 50–100 μL of DEPC-
treated water.
9. The yield and purity of the RNA preparation can be determined by measuring the
optical density on a spectrophotometer. Take an aliquot of RNA (1–2 μL), dilute
in RNase-free TE, and measure the spectrophotometric absorbance at 260 and
280 nm. The OD A260:A280 ratio should be approx 1.8 to 2.0. Total RNA yields
fall in the range of 5 to 15 μg from 1 × 106 mammalian cells and can be calculated
using the formula: RNA isolated (μg/mL) = OD260nm × dilution factor × 40 μg/
mL. Samples can be stored at –70°C.
10. Treating RNA samples with DNase I, add:
a. 1 μg RNA preparation in 8 μL DEPC-treated water.
b. 1 μL 10X DNase I buffer (100 mM Tris-HCl pH 7.5; 25 mM MgCl 2; and
5 mM CaCl2).
Molecular Diagnostics of Supravalvular Aortic Stenosis 153

c. 1 μL DNase I (1 U).
Incubate for 15 min at room temperature. Add 1 μL stop solution (50 mM EDTA)
and inactivate by heating at 70°C for 5 min. Cool on ice. Heating also denatures
hairpins in the RNA, so the RNA can be used directly in reverse transcription.
Alternatively, samples can be stored at –70°C.

3.5.6. RT-PCR of Complementary DNA

SuperScript III RT may be used to synthesize first-strand complementary
DNA (cDNA) from a total RNA preparation. The first-strand cDNA synthesis
reaction can be primed using random hexamers, oligo(dT), or gene-specific prim-
ers. We use oligo(dT)20 as a more specific priming method. This hybridizes to 3'
poly(A) tails, which are found in most eukaryotic mRNAs. First-strand synthesis
can also be specifically primed with a 3'-terminus gene-specific primer PCR
primer; however, oligo(dT) produces an RT-PCR product more consistently and
is our method of choice. In the second step, PCR is performed in a separate tube
using primers specific for ELN. The primers are designed so that they span exon–
intron boundaries to allow specific PCR amplification only from the cDNA tem-
plate and not from any residual contaminating genomic DNA. Some of primer
sequences designed from the ELN cDNA sequence that we have used success-
fully are included in Table 1 (see Note 2).
3.5.7. First-Strand cDNA Synthesis
1. The following procedure can to convert 1 pg to 5 μg of total RNA into first-
strand cDNA. In a 0.5-mL sterile tube add:
a. x μL of total RNA (maximum 5 μg).
b. 1 μL of 50 μM oligo(dT)20 primer, or 2 μM gene-specific primer.
c. 1 μL of 10 mM dNTP mix.
d. DEPC-treated water to 10 μL.
Incubate at 65°C for 5 min, then place on ice for at least 1 min.
2. Prepare the following cDNA synthesis reaction mix:
a. 2 μL of 10X RT buffer.
b. 4 μL of 25 mM MgCl2.
c. 2 μL of 0.1 M dithiothreitol.
d. 1 μL of 40 U/μL RNase Inhibitor (RNaseOUT).
e. 1 μL of 200 U/μL SuperScript III RT.
Recombinant RNase Inhibitor (RNaseOUT) is included to prevent degradation
of target RNA caused by ribonuclease contamination of the RNA preparation.
3. Add 10 μL of cDNA Synthesis Mix to each RNA plus primer mixture, mix, and
collect by brief centrifugation. Incubate for 50 min at 50°C.
4. Inacivate the enzyme by heating at 85°C for 5 min. Cool the tubes on ice.
5. Add 1 μL of RNase H and incubate for 20 min at 37°C. Removing the RNA template
from the cDNA:RNA hybrid molecule by digestion with RNase H after first-strand
synthesis increases the sensitivity of the PCR step (especially for long templates).
The cDNA synthesis reaction can be stored at –20°C or used directly for PCR.
154 Tassabehji and Urban

3.5.8. Amplification of Target ELN cDNA

The cDNA prepared may be amplified directly using PCR. Two microliters
of cDNA can be used for PCR, however, for some targets, adding more tem-
plate may be required to increase the product yield. cDNA prepared from a
normal control individual should be tested alongside the SVAS sample to aid
the identification of aberrantly spliced cDNA or differences in levels of ELN
gene expression. A ubiquitously expressed housekeeping gene, such as human
β-ACTIN can be included as an internal control to allow semiquantitative analy-
sis of the ELN transcript. Using the β-ACTIN gene primers (see Table 1), a
353-bp RT-PCR product is produced, which can be used as an internal indica-
tor of normal transcript levels in the tissue tested.
1. Prepare a PCR mixture for each control reaction. For each control reaction, add
the following to a 0.2-mL tube on ice:
a. DEPC-treated water 38.1 μL
b. 10X PCR buffer without Mg2+ 5 μL
c. 50 mM MgCl2 1.5 μL
d. 10 mM dNTP mix 1 μL
e. 10 μM sense primer 1 μL
f. 10 μM antisense primer 1 μL
g. cDNA 2 μL
h. 5 U/μL Taq DNA polymerase 0.4 μL
i. Final volume 50 μL
2. Mix the contents of the tube. Centrifuge briefly to collect the reaction components.
3. Place reaction mixture in preheated (94°C) thermal cycler. Perform an initial
denaturation step: 94°C for 2 min followed by 35 cycles of:
a. 94°C for 15 s.
b. 55°C for 30 s.
c. 72°C for 1 min (increase for larger product, 1 min/1 kb of sequence).
d. Final extension at 72°C for 10 min.
After completion, maintain reactions at 4°C.
4. Analyze 10 μL of each sample with a DNA ladder on a 2% agarose gel using
ethidium bromide staining to visualize the RT-PCR products. Aberrant ELN splic-
ing or exon deletions or insertions will be observed as DNA bands that migrate
differently compared with the normal control. Reduced ELN expression can be
measured semiquantitatively with radioactively labeled probes, using protocols
described elsewhere (9,10).
5. RT-PCR products can also be analyzed by direct sequencing with the BigDye
cycle sequencing kit, using the RT-PCR primers.

4. Notes
1. If desired, the quality of the PCR products may be assessed by agarose gel elec-
trophoresis before DHPLC analysis. In our experience, such quality control, fol-
Molecular Diagnostics of Supravalvular Aortic Stenosis 155

lowed by reamplification of weak or failed PCR products, may significantly re-

duce the instrument time needed for complete mutation analysis.
2. ELN cDNA Genbank accession number: NM_000501. All nucleotide sequences
cited here can be accessed from the Entrez Nucleotide database available at the
following web address: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
db=Nucleotide&cmd=search&term=Z24075+.

Acknowledgments
We thank Marc W. Crepeau for technical assistance. This work was sup-
ported by The Wellcome Foundation (MT) and, in part, by grant HL073703
(ZU) from the National Heart Lung and Blood Institute, the National Institutes
of Health.

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Extracellular Matrix Assembly and Structure (Yurchenko, P. D., Birk, D. E, and
Mecham, R. P., eds.), Academic, San Diego, CA, pp. 281–314.
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gene and alternative splicing of elastin mRNA: implications for human disease.
Am. J. Med. Genet. 34, 81–90.
3. Tassabehji, M., Metcalfe, K., Donnai, D., et al. (1997) Elastin: genomic structure
and point mutations in patients with supravalvular aortic stenosis. Hum. Mol.
Genet. 6, 1029–1036.
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stenosis. Circulation 24, 1311–1318.
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supravalvular aortic stenosis. Am. J. Dis. Child. 108, 341–347.
6. Li, D. Y., Toland, A. E., Boak, B. B., et al. (1997) Elastin point mutations cause
an obstructive vascular disease, supravalvular aortic stenosis. Hum. Mol. Genet.
6, 1021–1028.
7. Metcalfe, K., Rucka, A. K., Smoot, L., et al. (2000) Elastin: mutational spectrum
in supravalvular aortic stenosis. Eur. J. Hum. Genet. 8, 955–963.
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Boyd, C. D. (1999) Supravalvular aortic stenosis: a splice site mutation within the
elastin gene results in reduced expression of two aberrantly spliced transcripts.
Hum. Genet. 104, 135–142.
9. Urban, Z., Michels, V. V., Thibodeau, S. N., et al. (2000) Isolated supravalvular
aortic stenosis: functional haploinsufficiency of the elastin gene as a result of
nonsense-mediated decay. Hum. Genet. 106, 577–588.
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genetic and molecular dissection of a complex mutation in the elastin gene. Hum.
Genet. 109, 512–520.
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11. Urban, Z., Riazi, S., Seidl, T. L., et al. (2002) Connection between elastin
haploinsufficiency and increased cell proliferation in patients with supravalvular
aortic stenosis and Williams-Beuren syndrome. Am. J. Hum. Genet. 71, 30–44.
12. Curran, M. E., Atkinson, D. L., Ewart, A. K., Morris, C. A., Leppert, M. F., and
Keating, M. T. (1993) The elastin gene is disrupted by a translocation associated
with supravalvular aortic stenosis. Cell 73, 159–168.
13. Ewart, A. K., Jin, W., Atkinson, D., Morris, C. A., and Keating, M. T. (1994)
Supravalvular aortic stenosis associated with a deletion disrupting the elastin gene.
J. Clin. Invest. 93, 1071–1077.
14. Olson, T. M., Michels, V. V., Urban, Z., et al. (1995) A 30 kb deletion within the
elastin gene results in familial supravalvular aortic stenosis. Hum. Mol. Genet. 4,
1677–1679.
15. Tassabehji, M., Metcalfe, K., Karmiloff-Smith, A., et al. (1999) Williams syn-
drome: use of chromosomal microdeletions as a tool to dissect cognitive and
physical phenotypes. Am. J. Hum. Genet. 64, 118–125.
16. Tassabehji, M., Metcalfe, K., Hurst, J., et al. (1998) An elastin gene mutation
producing abnormal tropoelastin and abnormal elastic fibres in a patient with auto-
somal dominant cutis laxa. Hum. Mol. Genet. 7, 1021–1028.
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cutis laxa with severe lung disease: sythesis and matrix deposition of mutant
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lotype-association studies map intracranial aneurysm to chromosome 7q11. Am.
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133–134.
Chipping 157

9
“Chip”ping Away at Heart Failure

J. David Barrans and Choong-Chin Liew

Summary
Studies in the field of microarray technology have exploded onto the scene to delve into the
unknown underlying mechanisms and pathways in molecular disease. Diseases of the cardio-
vascular system, particularly those with unexplained molecular etiologies, such as heart fail-
ure, have more recently been investigated using array technology. Our laboratory has sought to
examine gene expression profiles of human heart failure using a 10,000+ element cardio-
vascular-based complementary DNA microarray constructed in-house, termed the
“CardioChip.” Our studies have identified panels of genes, such as those encoding sarcomeric
and cytoskeletal proteins, stress proteins, and Ca2+ regulators, that are differentially expressed
in disease conditions as compared with samples from nonfailing hearts. Microarrays are effec-
tive tools for examining molecular portraits of the cardiovascular disease condition.
Key Words: Microarray; heart failure; cardiomyopathy; genomics; cardiovascular disease.

1. Introduction
Heart failure resulting from cardiomyopathy is a major cause of morbidity
and mortality in North America. Typically, cardiomyopathy is diagnosed in at
least four forms, including dilated (DCM), hypertrophic (HCM), restrictive,
and arrythmogenic cardiomyopathy. DCM, the most common form of cardi-
omyopathy, is characterized by a dilated left atrium and ventricle and thin ven-
tricular walls, as compared with a normal heart (1). By contrast, HCM
predominantly involves myocyte hypertrophy, leading to a thickening of the
posterior wall of the left ventricle to meet metabolic demands of the body. In
both cases, cardiac output and efficiency are compromised, leading to a gradual
and eventual demise of the cardiac tissue.
Although DCM and HCM share common clinical endpoints, the same can-
not be said about the molecular mechanisms involved in each condition
(reviewed in ref. 2). The study of the molecular mechanisms underlying the
development and progression of this syndrome has been rather challenging.
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

157
158 Barrans and Liew

Much of the difficulty arises from the sometimes indistinct boundaries between
primary, causative events or processes and more secondary phenomena result-
ing from appropriate or inappropriate physiological adaptations to primary
events.
The early 21st century has seen the rise of genomic technologies that exam-
ine the entire genome of an organism. Although techniques such as positional
cloning (whereby genes are characterized according to their chromosomal
locations) had been earlier used to a limited extent, genomics truly came into
widespread use during the long and arduous Human Genome Project and simi-
lar projects in other organisms. Although these projects have looked at the
collection of genes present in respective organisms, they typically do not offer
insight into gene expression at first blush; thus, other studies making use of
expressed sequence tags sought to examine which genetic transcripts were
turned on and turned off in various conditions, leading to or preventing disease
manifestation. The investigation of gene expression has become particularly
important in the cardiovascular sciences, either alone or in combination with
environmental stimuli. The concept of cardiovascular genomics began in ear-
nest in the late 1980s and early 1990s, with the construction and sequencing of
a fetal heart complementary DNA (cDNA) library in our laboratory (3–8).
However, large-scale endeavors of this type have been time-consuming, labo-
rious, and prohibitively expensive to most laboratory establishments.
Since the mid-1990s, studies in genomics have turned to microarray tech-
nology (9). Although simple in their theory and design—essentially a high-
throughput Southern blot on a very small scale—microarrays have
revolutionized the examination of global gene expression. The excitement in
the scientific community regarding the prospects of microarrays spawned an
exponential increase in the number of articles in the literature dealing with
microarrays, because this technology represents a reductive method, whereby
complex gene expression patterns can be distilled to identify specific genes or
chromosomal locations involved in a given disease state. Initial studies in yeast
revealed unique gene expression profiles between different chromosomes,
using a glass slide spotted with clones derived from yeast genomic DNA (10).
Since then, the use of microarrays to examine global gene expression has seen
an exponential increase, most profoundly in cancer, e.g., melanoma (11); hepa-
tocellular carcinoma (12); osteosarcoma (13); breast cancer (14); gastric carci-
noma (15,16); and lymphoma (16–19). DNA microarrays are a highly sensitive
(detection limit is 1 in 100,000 for cDNA microarrays and 1 in 300,000 for
oligonucleotide arrays, relative to messenger RNA (mRNA) abundance
[20,21]) and high-throughput approach for expression profiling. As with other
technology, microarrays (and microarray science, in general) have been evolv-
ing at a rapid pace. Early versions used nylon membranes as a solid base, mim-
Chipping 159

icking those used by traditional blotting strategies (20,22). Today, the most
widely used DNA microarrays come in two main platforms, although with
slight variations. One uses the photolithographic synthesis of
oligodeoxynucleotides directly onto silicon chips, more commonly manifested
in the Affymetrix GeneChip®. The other uses a robotic or ink-jet printer style
system to spot cDNA (polymerase chain reaction [PCR] products or plasmids)
onto coated (usually poly-L-lysine or γ-amino polysilane) standard glass
microscope slides (23–26). In both cases, individual or duplicate spots on the
array represent individual genes. Photolithography, a technology borrowed
from the semiconductor industry, was implemented with DNA synthesis into
the microarray field by Fodor and colleagues at Affymetrix. In this process of
cyclic coupling and deprotection, a photomask is used to reveal a defined region
on a glass wafer. Photoprotected DNA bases are sequentially added to the chip,
enabling the preparation of a first-order oligonucleotide microarray directly on the
chip. The reduction of sample handling and the use of synthetic reagents are impor-
tant advantages for ensuring high chip-to-chip fidelity. Eleven probe sets on the
GeneChip are assigned to each gene, represented by at least a 25-base oligomer
derived from strategic sections of the gene. With the ability to represent more than
38,000 distinct transcripts on a single chip, this microarray attempts to give an
extremely robust genetic platform for global expression profiling from genes all
across the genome, especially for humans and mouse species.
On a cDNA array, DNA spots from unique genes are placed in a grid-like
fashion directly onto the surface of the slide. Current technologies allow for
the placement of several picoliters each of more than 10,000 full-length ele-
ments in an area of less than 1 cm2. Fluid can be deposited in one of three or
more methods. Schena and Brown pioneered the addition of yeast genes using
a “quill pen” (23,27). In this approach, a prepared DNA sample (e.g., a PCR
product) is loaded into a spotting nib by capillary action, and a small volume is
transferred to a solid surface by physical contact between the pin and the solid
substrate. After the first spotting cycle, the nib (or set of nibs) is washed and a
second sample is loaded and deposited. Another technique (used in our labora-
tory) incorporates the principles of surface tension by suspending a portion of
liquid into a ring. A conjoining pin mechanism pokes into, but does not dis-
rupt, the ring of liquid and touches the slide at a precise location. A variation
on the drop system of microarrays is the use of a modified ink-jet printer,
designed at a critical point in the infancy of spotted-array technology, when
overzealous investigators turned to less expensive and more practical methods
to participate in large-scale gene expression endeavors. In this approach, a
DNA sample is loaded into a miniature nozzle equipped with a piezoelectric
fitting (or other form of propulsion), which is used to expel a precise amount of
liquid from the jet onto the slide.
160 Barrans and Liew

Regardless of the system, comparisons of gene expression between any two

samples can be performed. Typically, the two mRNA pools of interest are
oligo-dT primed and labeled with fluorescent tags (e.g., Cy3 or Cy5) and
hybridized independently (oligo array) or simultaneously to a single array
(cDNA on glass slides). A fluorescent scanner then reads the chip or slide (after
appropriate washing and so on) to generate a visual image representing the
signals obtained from the two fluorescent tags. The ratio between the two sig-
nals for each spot is calculated, and differences in signal intensity are represen-
tative of differences in expression levels between the two transcript populations
for each gene. Each type of microarray has its advantage, but there are also
several downsides. Despite coming down in price, commercial oligonucleotide-
based arrays have been hampered by prohibitive initial set up costs and the fact
that two nonreusable chips are typically required for each experiment. cDNA
microarrays are less costly to produce only if the required number of cDNA
clones are readily available; there is also the issue of sample cross-contamina-
tion if appropriate wash steps are not addressed. The Affymetrix GeneChip is
currently a popular platform of choice for the oligo-array consumer consider-
ing the vast number of genes on the array, but its closed reagent system and
strict patent-related issues restrict its usefulness in novel gene discovery.
Greater flexibility with chip designs and clones on hand benefit cDNA array
use; however, the current method for labeling, hybridization, and image analy-
sis is a veritable hodgepodge of protocols provided in the literature and through
on-line user groups. This lack of standardization has hampered the progress of
acceptance by more cautious members of the scientific community, as wit-
nessed by an apparent overflow of review articles on microarrays and the rela-
tively few manuscripts contributing original data.
Although microarray use has been successfully applied to conditions such as
cancer (18), its penetration into the cardiovascular sciences was not as vigorous
at the outset. Initial studies with the GeneChip and cDNA arrays have exam-
ined gene expression after myocardial infarction (28) and in DCM (29,30). In
the first study, approx 7000 clones from a rat left ventricle cDNA library were
spotted and hybridized with labeled heart RNA samples from different times
after myocardial infarction. In the second study, two human left ventricle free-
wall samples from patients with DCM were compared with normal hearts and
analyzed using the Affymetrix Hu6800® GeneChip. In both cases, the gene for
atrial natriuretic peptide (among other genes) was significantly upregulated in
diseased hearts, confirming previous evidence (31–34). Both of these studies
provided an important initial basis for subsequent microarray studies in cardio-
vascular disease, which had been lacking in the field. This has led to subse-
quent gene expression studies of diverse cardiac conditions, including cardiac
Chipping 161

hypertrophy (35–37), DCM (38), end-stage heart failure (39), fibrosis (40), and
response to left ventricular assist device implantation (41).
Our laboratory has taken advantage of our vast previously acquired resources
and has constructed what we think is the first ever custom-made cardiovascu-
lar-based cDNA microarray, which we term the CardioChip (42,43). Its practi-
cality and flexibility has allowed us to conceptualize the molecular events
surrounding end-stage heart failure. We have used our CardioChip to explore
gene expression in end-stage DCM and HCM relative to normal heart function
(42,43). RNA was extracted from the left ventricular free wall of seven patients
undergoing transplantation, and from five samples from nonfailing hearts.
More than 100 transcripts were consistently differentially expressed in DCM
more than 1.5-fold. Not surprisingly, the gene for atrial natriuretic peptide was
found to be upregulated in DCM (19-fold compared with samples from
nonfailing hearts; p < 0.05). In addition, we found differences in transcripts
encoding numerous sarcomeric and cytoskeletal proteins, stress response pro-
teins, and transcription/translation regulators. Downregulation was most
prominently observed with cell-signaling channels and mediators, particularly
those involved in Ca2+ pathways. We also observed a selection of genes that
were differentially expressed between HCM and DCM (including calsequestrin,
lipocortin, and lumican), indicating that, despite similar clinical endpoints, heart
failure resulting from HCM and DCM occurs through different molecular path-
ways (44). Among both upregulated and downregulated transcripts, were novel,
uncharacterized cDNAs, which serve as the basis for further investigation.
Complementing our microarray analysis was verification of expression using
quantitative real-time reverse transcriptase PCR (RT-PCR). Our studies pro-
vided preliminary molecular profiles of DCM and HCM using the largest hu-
man heart-specific cDNA microarray of the day. In recent years, we have
developed molecular portraits to predict pathways and etiology of such dis-
eases as heart failure and Chagas’ cardiomyopathy (45–47).
The protocol outlined in this chapter illustrates one embodiment of methods
for determining gene expression using cDNA microarrays typical of the meth-
ods used in our laboratory. Although other methods exist, and may prove ben-
eficial to the individual user, we have found that this regimen has offered the
most consistent results.

2. Materials
1. TRIzol® buffer.
2. Diethylpyrocarbonate (DEPC)-treated water.
3. Oligo-dT.
4. 200 mM dNTP.
5. First-strand buffer.
162 Barrans and Liew

6. Cy3- and Cy5-dUTP.

7. Reverse transcriptase (SuperScript®).
8. 0.5 M NaOH.
9. 10 mM EDTA.
10. 0.5 M Tris-HCl, pH 7.0.
11. Gel exclusion chromatography column.
12. DIG EasyHyb® hybridization solution (Roche).
13. Yeast tRNA (10 mg/mL).
14. Human Cot1 DNA.
15. Poly-dA.
16. Salmon sperm DNA (10 mg/mL).
17. HybriSlips® (Sigma-Aldrich, St. Louis, MO).
18. 1X sodium chloride-sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS).
19. 50-mL conical tubes.

3. Methods
3.1. PCR Products
In the process of our large-scale sequencing project, PCR products were
generated from human fetal and adult heart, familial hypertrophic cardiomy-
opathy heart, and vascular phage cDNA libraries, as described previously (5–
7,48). After sequence-similarity searching using BLAST (49) in the
non-redundant database and database of ESTs, an annotated database of clones
was compiled. Table 1 illustrates the categorical distribution of the PCR prod-
ucts used on the CardioChip.
3.2. PCR Product Purification and Construction of 10,368-Element
cDNA Microarray
Rescue individual clones from phage (λ ZAP) into phagemid vector (for 3'-
end sequencing and further experimental analysis, e.g., protein expression).
1. Amplify phagemids by PCR (T3 and T7 forward and reverse primers, respec-
tively), in 96-well microplates (Corning).
2. Visualize inserts on a 1% agarose minigel.
3. Randomly assign clones to individual wells of a 96-well microplate (Corning).
4. Purify 50 μL of each PCR product with 5 μL of 3 M ammonium acetate and 125
μL of 95% ethanol at –20°C overnight.
5. The next day, centrifuge the plates at 4000 rpm for 30 min at 4°C.
6. Decant the supernatant. After two washes with 50 μL of 70% ethanol, air-dry the
resulting DNA pellets.
7. Resuspend pellets in 20 μL of 3X SSC.
To construct the CardioChip, spot 108 of the microplates (containing 10,368
nonredundant PCR products) onto CMT-UltraGAPS® amino-silane-coated
Chipping 163

Table 1
Categorical Distribution of the 10,368 Expressed Sequence Tags (ESTs)
on the CardioChip

Category of EST Number of clones on array (% of total)

Known, matched genea 4002 (38.6)
Matched other EST in dbESTb 1818 (17.5)
Unmatched, putative novel ESTc 4356 (42.0)
Bacterial clones (negative controls) 192 (1.8)
aIncludes matches to full-length hypothetical proteins in the non-redundant database
of GenBank.
bIncludes matches to human genome sequences in the non-redundant database of

GenBank.
c Includes matches to sequences in the unfinished high-throughput genomic

sequences database of GenBank.

glass microarray slides (Corning) using a GMS 417 arrayer (Affymetrix, Santa
Clara, CA), and postprocess the arrays, as previously described (11).
3.3. Fluorescent Probe Labeling and Hybridization
Extract total RNA from tissue samples using TRIzol reagent (Gibco BRL-
Life Technologies), according to the manufacturer’s protocol (see Note 1). We
used samples of unique normal human adult heart (left ventricular free wall of
five nonfailing human adult hearts, rejected as donors because of infection)
and of DCM heart (explanted hearts from patients undergoing transplantation).
3.3.1. Label Probes and Hybridize to Microarray Slides (see Notes 2–4)
1. Suspend 10 μg of each total RNA species in 8 μL DEPC-treated water.
2. Add 2 μL oligo-dT15–18, incubate at 65°C for 2 min.
3. Add reaction mixture to each sample:
a. 4 μL first-strand buffer.
b. 1 μL dNTP (total concentration = 200 μM).
c. 4 μL Cy3- or Cy5-dUTP stock (Amersham).
d. 1 μL SuperScript RT.
4. Incubate at 42°C for 2 h, adding an additional 1 μL RT to each sample after 1 h.
5. Stop reaction with 5 μL of 0.5 M NaOH and 5 μL of 10 mM EDTA for 5 min,
then neutralize with 0.5 M Tris-HCl.
6. Remove excess label by gel exclusion chromatography (ProbeQuant G-50 ®,
Amersham), according to the manufacturer’s protocol.
7. Mix the two probes of interest (one with Cy3 and one with Cy5).
8. Reduce to a volume of 10 μL using a speed vacuum.
9. Combine with 30 μL of hybridization solution (stock solution containing the fol-
lowing as blocking agents):
164 Barrans and Liew

a. 100 μL DIG EasyHyb hybridization solution (Roche).

b. 5 μL of 10 mg/mL yeast tRNA.
c. 5 μL human Cot1 DNA.
d. 5 μL poly-dA.
e. 5 μL of 10 mg/mL salmon sperm DNA.
10. Add probe mixture to microarray slide and cover with cover slip.
11. Hybridize slide in a sealed dry chamber in a 37°C water bath overnight.
3.3.2. Slide Scanning (see Notes 5 and 6)
1. The next day, wash the slides in a slide-washing basin, first with 1X SSC to
remove the cover slip (HybriSlips; Sigma), then with three successive washes of
1X SSC/0.1% SDS for 15 min each at 50°C, followed by a rinse with 1X SSC.
2. Remove excess fluid on the slides by placing them into individual 50-mL conical
tubes and centrifuging at 500 rpm for approx 2 min.
3. Scan the slides using an appropriate microarray scanner, first at 635 nm (for Cy5),
then at 532 nm (for Cy3).

3.4. Data Processing (see Notes 7–11)

1. Superimpose the Cy3 and Cy5 scans for each slide. Turn the gain to the maxi-
mum value.
2. Place a grid on the superimposed image, ensuring that the grid locators com-
pletely cover the illuminated spots.
3. Obtain values corresponding to the level of fluorescent intensity for each spot
and import to an Excel® spreadsheet.
4. Subtract the local background from the fluorescent value of each spot to obtain a
net value.
5. Determine median ratio for each spot (calculated as the ratio of the median fluo-
rescence from each pixel, minus the background, of Cy5 to Cy3). Submit this
expression data to hierarchical clustering analysis.

3.5. Verification of Candidate Gene Expression Using Quantitative

Real-Time RT-PCR (see Notes 12 and 13)
1. Design forward and reverse primers for the selected genes, including an internal
control.
2. Take 100 ng of total RNA per reaction and prepare the quantitative RT-PCR
solution:
a. 50 μL total volume containing 1X SYBR® Green PCR Master Mix.
b. 0.25 U/μL Multiscribe® RT (Applied BioSystems, Foster City, CA).
c. 0.4 U/μL RNase inhibitor.
d. 10 pmoles of each forward and reverse primer.
3. Perform the reactions in a 96-well format, with the following cycling parameters:
30 min at 48°C, and 40 cycles of 30 s at 94°C and 1 min at 60°C.
Chipping 165

4. Notes
1. RNA quality is an important limiting factor in conducting a microarray experi-
ment. Always run the sample on a formaldehyde gel to check the integrity of the
RNA; clear 28S, 18S, and 5S bands should be visible with no genomic DNA
contamination. Check the optical density of the sample at 260 nm/280 nm to
ensure a ratio of at least 1.8.
2. Labeling, overnight hybridization, washing, and scanning MUST be performed
in reduced light, i.e., as close to dark conditions as possible. Increased light expo-
sure will bleach the dyes and impair proper signal generation from the spots on
the array.
3. One method for verifying the integrity of the hybridization method is by reverse
labeling. Take the same samples and reverse the fluorescent dye used in the first
experiment (i.e., if the DCM heart samples were labeled with Cy3 and samples
from nonfailing hearts with Cy5 in the first experiment; for the second experi-
ment, label samples from DCM hearts with Cy5 and samples from nonfailing
hearts with Cy3). Ideally, the ratios of each spot should be inverse—e.g., spot A
with a DCM to nonfailing ratio of 2.5 in the first experiment should have a
nonfailing to DCM ratio of 0.4 in the second experiment. However, we noted that
this phenomenon typically occurs with genes that are more vastly expressed in
one sample than in the other, and when each set of hybridizations is performed at
least three times, preferably more.
4. To assess the intersample variation, a parallel labeling against each of the samples
can be performed with human universal reference RNA, and hybridized together.
The universal RNA acts as a common reference to which any future sample can
be compared.
5. To ensure that uniform spotting on the array has occurred, one slide out of the lot
was tested by staining with a 1:10,000 dilution of SYBR Green I (Applied
Biosystems), which detects double-stranded DNA. The slide was scanned in the
Cy3 channel (532 nm) and visualized using ScanAlyze (M. Eisen, Stanford Uni-
versity, CA) and PhotoShop (Adobe, San Jose, CA). Aberrant spots or regions of
inconsistencies on the slide were flagged, and, as necessary, the spotting process
was repeated.
6. Scanning of Cy5 and Cy3 channels was performed using the GMS 418 Array
Scanner (Affymetrix). Cy5 is more sensitive, so it should be scanned first.
7. Raw scanned images were processed using ScanAlyze 2.44 microarray image
analysis software (M. Eisen, available at: http://rana.lbl.gov, Stanford Univer-
sity, CA).
8. To account for incomplete hybridization on each spot, in our analysis, we only
included those spots in which at least 50% of the pixels (within the defined area
of the spot) displayed a fluorescence at least 1.5 times higher than background in
all experiments. Spots whose net fluorescent value did not exceed the mean value
obtained from the 192 bacterial negative-control spots were excluded.
166 Barrans and Liew

9. Another, older method for normalizing spot intensity is to use a scatterplot. The
level of normalization required is based on the deviation of signal from the mean
Cy3 signal. The factor by which the Cy3 fluorescence signal is reduced can be
determined by plotting the raw net signals from each channel on a scatterplot.
The slope of the resulting trend line is used as a multiplying factor against the
Cy3 fluorescence value of each spot. The resulting slope has a value of 1.0 and,
thus, proper ratios can be calculated.
10. To assess the reproducibility of hybridization results and assess intraassay varia-
tion, one can examine the correlation of the median ratio values for each filtered
spot on the array from at least three replicate experiments (i.e., using the same
RNA sample divided into three separate aliquots).
11. Hierarchical cluster analysis and/or intensity filtering was also performed, using
commercially available software, such as GeneSpring v6.1 (Silicon Genetics,
Redwood City, CA).
12. In 96-well format, for each gene of interest, single quantitative RT-PCR reac-
tions were performed on each individual DCM heart mRNA sample (n = 7) and
each nonfailing adult heart mRNA sample (n = 5). As an internal control, primers
for glycerol phosphate dehydrogenase were also designed and amplified in paral-
lel with the genes of interest.
13. Primers were designed online (http://alces.med.umn.edu/rawprimer.html), veri-
fied for complementarity (http://www.basic.northwestern.edu/biotools/
oligocalc.html), and searched against the public database to confirm unique am-
plification products (http://www.ncbi.nlm.nih.gov).

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Molecular Diagnostics of CPVT 171

10
Molecular Diagnostics of Catecholaminergic
Polymorphic Ventricular Tachycardia Using Denaturing
High-Performance Liquid Chromatography
and Sequencing

Alex V. Postma, Zahurul A. Bhuiyan, and Hennie Bikker

Summary
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an arrhythmogenic dis-
ease characterized by adrenergic-induced arrhythmias in the form of bidirectional and PVT.
CPVT is a distinct clinical entity associated with a high mortality rate of up to 50% by the age
of 30 yr. Recently, the molecular diagnostics of this disease have become increasingly impor-
tant because underlying mutations can be found in more than 60% of the identified CPVT
patients. Along with the fact that treatment with β-blockers has a favorable outcome in
CPVT patients, and given the risk of sudden death, the identification of causative muta-
tions in CPVT is important because it can greatly augment early diagnosis and subsequent
preventive strategies. In this chapter, we describe the molecular diagnostics, as performed in
our lab, of the three genes known to be involved in CPVT, the cardiac ryanodine receptor gene,
the cardiac calsequestrin gene, and the inwardly rectifying potassium channel KCNJ2.
Key Words: CPVT; RYR2; CASQ2; KCNJ2; DHPLC; sequencing.

1. Introduction
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare
arrhythmogenic disease characterized by syncopal events and sudden cardiac
death at a young age (1). CPVT is a distinct clinical entity associated with a
high mortality rate of up to 50% by the age of 30 yr. Its key features include
childhood onset of syncope and collapse triggered by exercise and other stress-
ful scenarios, with reproducible polymorphic and/or bidirectional ventricular
tachycardia demonstrated during exercise testing and catecholamine infusion.
Cardiac investigations show no evidence of structural heart disease, and the
resting 12-lead electrocardiogram is unremarkable, including the QT interval.
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

171
172 Postma et al.

Cases have been reported throughout the world, and both sexes seem to be
susceptible. Recently, the molecular diagnostics of CPVT has become increas-
ingly important because underlying mutations can be found in more than 60%
of the identified CPVT patients (2,3). Along with the fact that treatment with
β-blockers has a favorable outcome in CPVT patients, and given the risk of
sudden death, the identification of causative mutations in CPVT is important
because it can greatly augment early diagnosis and subsequent preventive strat-
egies. In this chapter, we describe the molecular diagnostics, as performed in
our lab, of the three genes currently known to be involved in CPVT.
1.1. Autosomal-Dominant CPVT, the Cardiac Ryanodine Receptor
Many cases of CPVT are familial, and the first extensive report with a defi-
nite linkage analysis was published by Swan et al., and showed linkage of
CPVT with chromosome 1q42-43 (4). This report was followed by publica-
tions that associated mutations in a gene from the 1q42-43 region, the cardiac-
specific ryanodine receptor type 2 (RYR2), with CPVT (1,5,6). Ryanodine
receptor channels are intracellular Ca 2+-release channels that form a
homotetrameric membrane-spanning calcium channel on the sarcoplasmic
reticulum. The RyR2 gene is located on chromosome 1q42 and consists of 105
exons, which translate into 15 kb of complementary DNA. RYR2 encodes a
protein of 4967 amino acids, making it the largest known ion channel to date.
At present, approx 50 mutations have been reported in more than 52 families
(1,2,5–8). The various mutations cluster within four regions in the RyR2 pro-
tein: the N-terminal side; around the binding site of FKBP12.6, a protein that
stabilizes the RyR2 channel (9); the calcium binding site; and the channel-
forming transmembrane domains.
1.2. Autosomal-Recessive CPVT, the Cardiac Calsequestrin Gene
In contrast to the majority of CPVT patients, who have an autosomal-domi-
nant mode of inheritance (RYR2), two studies have recently demonstrated a
recessive form of CPVT (3,10). The affected patients of these four families all
shared an area on chromosome 1p13-21. Subsequently, homozygous mutations
in the cardiac calsequestrin gene (CASQ2) located in that region were found to
underlie this recessive form of CPVT. Strikingly, the heterozygous carriers of
the mutations were devoid of any clinical symptoms or electrocardiographic
anomalies. The phenotypes of the recessive CASQ2 CPVT patients seem more
severe compared with the RyR2 CPVT patients. The CASQ2 gene consists of
11 exons and encodes a protein that serves as the major Ca2+ reservoir within
the sarcoplasmic reticulum lumen of cardiac myocytes. However, although
CASQ2 mutations are often autosomal recessive, some reports indicate that
Molecular Diagnostics of CPVT 173

autosomal-dominant inheritance with reduced penetrance can be part of the

clinical spectrum of CASQ2 CPVT (3).
1.3. Overlapping Diseases: Andersen and CPVT, the KCNJ2 Gene
Mutations of the KCNJ2 gene are known to be causative in Andersen syn-
drome (AS), a disease characterized by potassium-sensitive periodic paralysis,
dysmorphic features, and PVT (11). However, mutations in KCNJ2 result in a
pleiotropy of phenotypic AS variations, including all, some, or a single charac-
teristic of AS. Moreover, there is evidence that KCNJ2 only produces CPVT
characteristics with a very low penetrance of prominent dysmorphic features,
suggesting that some AS patients may present as CPVT patients (12,13). These
“overlap” patients have syncope, exercise-induced PVT, and a normal QTc
interval. However, in contrast to CPVT, they can also exhibit polymorphic
ventricular beats in the resting electrocardiogram. The KCNJ2 gene is a back-
ground ion channel involved in maintaining the membrane potential of
cardiomyocytes during diastole. It is located on chromosome 17q23.1-q24.2
and consists of a single coding exon.
1.4. Molecular Diagnostics of CPVT
It is clear that there is a strong genetic component in CPVT, and, currently,
underlying mutations are found in approx 60% of patients with CPVT. De-
pending on the clinical presentation of the disease and the family history, the
appropriate genes can be screened for in CPVT patients. Because the causative
genes differ so much in size, the diagnostics for CPVT are challenging. The
main gene involved in CPVT, RYR2, has 105 exons, CASQ2 has 11 exons, and
KCNJ2 has 1 exon. Thus, the strategies for the genetic screening of patients
with CPVT depend on the size of the genes involved, the equipment available,
and the cost effectiveness. Our lab currently uses denaturing high-performance
liquid chromatography (DHPLC) analysis for the RYR2 and the CASQ2 genes,
and sequence analysis for the KCNJ2 gene. In Subheading 3., we outline the
various techniques we use to screen CPVT patients for the genes of interest. In
our laboratory, patients with a CPVT diagnosis are screened first for RYR2,
subsequently for CASQ2, and finally for KCNJ2, this order is based on the
prevalence of mutations.

2. Materials
2.1. Polymerase Chain Reaction
1. 10X polymerase chain reaction (PCR) buffer (Roche).
2. 5X PCR buffer. For 1 mL:
a. 250 μL of 1 M Tris-HCl, pH 9.0.
174 Postma et al.

b. 140 μL of 0.5 M (NH4)SO4.

c. 100 μL dimethylsulfoxide.
d. 75 μL Tween-20.
e. 435 μL ddH2O.
3. 25 mM MgCl2 (Applied Biosystems [ABI]).
4. dNTPs, 1.25 mM for each NTP (Amersham Pharmacia).
5. 20 pmol/μL primers (see Note 1).
6. Super Taq (HT Biotechnology).
7. 5 mM betaine (Sigma).
8. Strip tubes/caps (VWR).
9. 96-well plate (Biozym).

2.2. Sequencing
1. BigDye Terminator v3.0 (ABI).
2. 5X sequencing buffer (supplied with BigDye Terminator v3.0) (ABI).
3. 5 mM betaine (Sigma).
4. Strip tubes/caps (VWR).

2.3. Gel Electrophoresis Analysis

1. Agarose.
2. 1X Tris-acetate-EDTA (TAE):
a. 0.04 M Tris-acetate.
b. 0.001 M EDTA, pH 8.0.
3. Ethidium bromide (10 mg/mL).
4. 10X loading buffer (25 mL):
a. 6.25 g Ficoll 400.
b. 0.5 mL of 0.5 mM EDTA.
c. 0.25 mL of 10% sodium dodecyl sulphate.
d. 0.0625 g Orange G (Merck).
e. Add ddH2O to bring up to 25 mL.

2.4. Denaturing High-Performance Liquid Chromatography

1. 0.1 M triethylamine acetate (pH 7.0) (Transgenomic).
2. Acetonitrile (Transgenomic) (see Note 2).

2.5. Equipment
1. Thermocycler.
2. Gel electrophoresis device.
3. Gel image-capture device, Eagle-eye II (Stratagene).
4. ABI PRISM® DNA Analyzer (ABI).
5. Computer with sequence analysis software (ABI) and WAVE Maker TM software
(Transgenomic).
6. DHPLC-WAVETM system (Transgenomic).
Molecular Diagnostics of CPVT 175

3. Methods
3.1. Direct Sequence
3.1.1. PCR Reaction
1. Amplify genomic DNA for sequence analysis in 20 μL reaction mixtures con-
taining:
a. 3.0 μL of 25 ng/μL genomic DNA.
b. 4.0 μL of 5X PCR buffer.
c. 1.2 μL of 25 mM MgCl2.
d. 2.25 μL of 1.25 mM dNTPs.
e. 0.4 μL of each 20 pmol/μL primer.
f. 0.1 μL Super Taq (HT Biotechnology).
g. 4.0 μL of 5 mM Betaine.
h. 4.65 μL ddH2O (see Note 3).
2. Perform PCR using an initial denaturing step of 94°C for 3 min, followed by 35
cycles of the following touch-down PCR protocol: denaturation at 94°C for 45 s,
annealing at 66 to 52°C (see Note 4) for 45 s, and extension at 72°C for 1 min.
3. Store the product mixture at 4°C until further use.
3.1.2. Gel Electrophoresis Analysis
1. The PCR products are tested on an agarose gel to determine the outcome and
specificity of the reaction. Single, crisp bands indicate a successful PCR product
that can be used for subsequent sequence analysis.
2. Prepare a 1.5% (w/v) agarose gel with 1X TAE, with 5 μL of 10 mg/mL ethidium
bromide added to each 100 mL of gel solution. Run the electrophoresis in a 1X
TAE buffer.
3. Add 1 μL of 10X loading buffer to a sample of 5 μL of each PCR product, and
load the reaction mixture onto the agarose gel. Use a stock ladder (100-bp ladder)
to determine the size of the products.
4. Perform electrophoresis at 100 V/100 mA; running time depends on product size
and gel length.
5. Capture the gel image (photograph or computer) under long-wave UV to deter-
mine the result of the PCR. If the PCR was successful, sequence the sample.

3.1.3. Sequencing Reaction

1. Assemble the sequencing reaction (10 μL total volume) by adding 3.0 μL of PCR
product diluted 1:5 to a strip tube containing:
a. 1.0 μL BigDye Terminator v3.0.
b. 1.0 μL of sequencing primer (2 pmol/μL).
c. 2.0 μL 5X sequencing buffer.
d. 2.0 μL 5 mM betaine.
e. 1.0 μL ddH2O (see Notes 3 and 5).
2. Denature the DNA initially by incubating the reaction mixture at 94°C for 2 min.
176 Postma et al.

3. Perform cycle sequencing with 24 cycles of denaturation at 96°C for 10 s, primer

annealing at 50°C for 5 s, and primer extension at 60°C for 4 min; and with a
single, final extension step at 60°C for 10 min (see Note 6).
4. Store the product mixture at 4°C until loading onto the capillary DNA sequencer.

3.2. Denaturing High-Performance Liquid Chromatography

3.2.1. PCR Reaction
1. Amplify genomic DNA for DHPLC analysis in 50-μL reaction mixtures contain-
ing:
a. 2.0 μL of 25 ng/μL genomic DNA.
b. 5.0 μL of 10X DHPLC-PCR buffer (Roche).
c. 3.0 μL of 25 mM MgCl2.
d. 8.0 μL of 1.25 mM dNTPs.
e. 1.0 μL of each 20 pmol/μL primer.
f. 0.1 μL Super Taq (HT Biotechnology).
g. 30 μL ddH2O (see Note 7).
2. Perform PCR using an initial denaturing step of 94°C for 3 min, followed by 35
cycles of the following touch-down PCR protocol: denaturation at 94°C for 45 s,
annealing at 66 to 52°C for 45 s, and extension at 72°C for 1 min (see Note 4).
3. Store the product mixture at 4°C until further use.
3.2.2. Gel Analysis of PCR Products
1. PCR products for subsequent DHPLC analysis are checked using agarose gels in
the manner described in Subheading 3.1.3. Only PCR products with single, crisp
bands are to be used in the DHPLC analysis (see Note 8).

3.2.3. DHPLC Analysis

1. For each amplicon, the PCR product of wild-type DNA (healthy control) has to
be mixed with the patient’s product at equimolar ratios (see Note 9); subse-
quently, the resulting mix is subjected to a 5 min, 95°C denaturing step in a PCR
machine, followed by a gradual reannealing from 95°C to room temperature dur-
ing 1 h. This ensures the formation of equimolar ratios of homoduplex and het-
eroduplex species. The mixed products can be stored at 4°C for several weeks, or
used immediately.
2. The temperatures needed for successful resolution of heteroduplex molecules are
determined by running amplicon-specific melting curves and by using the
DHPLC melting algorithm WAVE Maker of the WAVE instrument. Melting
curves are determined as follows: the elution time of a specific fragment under
standard conditions is determined. This specific gradient is then tested for the
same PCR product for temperatures ranging from 48 to 70°C, and retention time
vs temperature are graphed to yield a fragment-specific melting curve. The opti-
mal analysis temperature is defined by a maximal decrease of retention time in a
minimal temperature range. However, the complexity of the melting curve may
Molecular Diagnostics of CPVT 177

need between one and four different temperatures for fragment analysis. On av-
erage, three different temperatures to cover the entire DNA fragment of interest
are necessary (see Note 10). The chosen temperatures are stored by the software
and can be reused for subsequent samples for the same amplicon.
3. The (mixed) samples are loaded into the DHPLC machine and covered with a
(96-well) rubber mat to avoid evaporation of the products. It is advisable to also
use a negative control (water control of the PCR) and a positive control (a known
aberration in the amplicon examined) during each DHPLC run. Enter whether
you are using strips or plates into the DHPLC software and use an injection vol-
ume of 8 μL per (mixed) DNA sample per temperature.
4. The (mixed) samples are separated at a flow rate of 0.9 mL/min by means of a
linear acetonitrile gradient. Generally, analysis takes approx 4 min/sample,
including column regeneration and re-equilibration to starting conditions. The
column mobile phase consists of a mixture of 0.1 M triethylamine acetate (pH
7.0) (buffer B) with 25% acetonitrile (buffer A).
5. Subsequently, the DHPLC is run with the optimal temperatures and gradients,
and the results are stored for analysis.

3.3. Sequence Variation Identification by DNA Analysis

Whether sequence variations of aberrant DHPLC samples will be deter-
mined or variation in a patient’s sequence will be directly identified, the meth-
ods for finding sequence variations remain the same. Always sequence samples
from at least two different individuals, i.e., a confirmed healthy control DNA
sample sequenced together with DNA samples of the patient(s) of interest.
After the sequencing run on the ABI PRISM 310 DNA Analyzer (or similar
machine), trim and reanalyze the sequence traces of all of the sequences with
the ABI Sequence Analysis software. In this way, poor quality bases can be
removed and the sequencing signal can be boosted. Subsequently, the ABI
Factura program is used to mark and annotate sequence variations and areas of
low signal quality. The final step is to align the cleaned-up sequences. For this,
we use the ABI Sequence Navigator program. After importing eight sequences
into the program (including a healthy control), “Clustal alignment” with the
default settings will provide the best alignment. If necessary, sequences per-
formed with a reverse primer can also be imported and converted to inversed
complementary sequences to complete the alignment (see Note 11). After the
alignment, we let the program mark all of the differences in a given position
using the option “create shadow/compute ambiguity sequences.” This marks
all of the places in the alignment with possible differences, including homozy-
gous mutations or polymorphisms (Fig. 1). Similar options for marking ambi-
guity in sequences are available in the ABI Auto Assembler program. We
subsequently display the alignments at the points of interest (places with ambi-
guity) and determine the source of the ambiguity (Fig. 1). In case of a possible
178 Postma et al.
Molecular Diagnostics of CPVT 179

mutation, polymorphism, or disruption of the reading frame, screenshots are

taken for archiving, and the sequence of interest can be printed. It is important
to understand that sequence variations can always arise from the PCR tech-
nique itself and, therefore, aberrant sequences need to be validated by amplify-
ing control DNA and patient DNA in a additional subsequent PCR reaction.
Moreover, it is important to check whether the aberrant sequence is truly a
mutation, or a (rare) polymorphism. In general, an aberration is labeled as a
mutation if it is absent from more than 200 control alleles. However, the cau-
sality of any given mutation depends on DNA analysis in family members,
coupled to the clinical history and expression analysis. This approach and good-
quality sequences provide a balance between speed of analysis and accuracy.
We use the sequencing techniques for various exons of CASQ2 (see Note 12)
and all of the KCNJ2 samples. After identifying a possible mutation, it is im-
perative to finish screening the remaining exons as well.
3.4. Sequence Variation Identification by DHPLC Analysis
The main reason to perform DHPLC analysis is that it is a fast and accurate
method for screening for mutations. Samples resulting in aberrant patterns al-
ways have to be sequenced to determine the nature of the sequence variation.
Even if the DHPLC pattern resembles a pattern of a known polymorphism for
the amplicon examined, sequencing is still necessary, because this does not
exclude the possibility that a mutation close to the polymorphism is masked, or
that an unknown mutation causes a similar pattern. DHPLC is used to filter out
the wild-type sequences to decrease the amount of patient samples to be
sequenced. It is important to analyze the patient’s samples at each temperature
indicated by the WAVE maker software, because some sequence aberrations
can only be seen at one specific temperature. To obtain a reliable analysis, a
second researcher should always check the DHPLC results. DHPLC samples
are compared at each temperature, and any aberrant patterns are marked and
printed for archiving purposes (Fig. 2). Subsequently, the sequence analysis on
the aberrant samples can be performed directly from the PCR product loaded
in the DHPLC machine using the methods described in Subheading 3.2.3. It is
important to understand that amplicons with numerous sequence variations will
severely hamper a reliable DHPLC analysis. Therefore, DHPLC analysis is
only performed on amplicons that do not contain frequent polymorphisms (see

Fig. 1. (opposite page) Example of a clustal alignment of sequences in which any

ambiguity between sequences is marked with an asterisk; in the lower panel, a close-
up view of the ambiguity is displayed. Note that up to eight sequences can be aligned
and analyzed at the same time.
 18
0
180

Fig. 2. Examples of aberrant DHPLC profiles caused by the presence of (A) no, one, or two polymorphisms in exon 43 of
RYR2, and (B) a known mutation, E4076K, in exon 90 of RYR2.
Po

st

ma
Molecular Diagnostics of CPVT 181

Note 12). We use DHPLC analysis for the majority of the CASQ2 samples and
all of the RYR2 samples. After identifying a possible mutation, it is imperative
to finish screening the remaining exons as well.

4. Notes
1. Primers were designed with a target melting temperature of 60°C. It is important
to design the forward and reverse primer in introns as far upstream or down-
stream as necessary, because this will ensure that any sequence variations around
the splice sites and branch sites are included in the analysis. Make sure that the
chosen primers do not overlap with single-nucleotide polymorphisms. Moreover,
it is important to keep in mind that accurate DHPLC analysis is only possible ±50
bp downstream or upstream from any given primer. Primers for RYR2 are avail-
able from Tiso et al. (5); primers for CASQ2 and KCNJ2 are available from the
authors on request.
2. Acetonitrile is a hazardous chemical and can penetrate the skin, therefore, cau-
tion is warranted when replacing the containers; always use gloves. Moreover,
the waste product of the DHPLC machine also contains acetonitrile and it is,
therefore, recommended to place a fume hood above the waste container to cap-
ture any hazardous fumes.
3. Betaine is used in the PCR and sequencing steps to reduce self-coiling of GC-
rich areas and to lower melting temperatures; in our experience betaine has sub-
stantial beneficial effects on all PCR/sequence reactions.
4. In a PCR touch-down protocol, the annealing temperature is lowered (propor-
tionally) for each successive cycle; the first cycle is performed at the first tem-
perature indicated in the protocol and is subsequently lowered each cycle until
the last temperature mentioned is reached at the end of the final cycle.
5. Sequence reactions can be purified using spin columns or gel filtration, however,
in our experience, a dilution of 1:5 of the PCR product works equally well, and
saves time and costs. If the dilution of a PCR product produces unusable results
during sequencing, one can always revert to other methods of purification.
6. If the product is GC rich, it might help if the temperature of the annealing step of
the sequencing reaction is raised, for instance from 50°C to 55°C or even 58°C.
7. When using DHPLC in patient analysis, it is crucial to use PCR reaction buffers
that do not contain solvent or detergents (found in most PCR buffers), such as
dimethylsulfoxide, glycerol, Tween-20, or betaine. These products can damage
the columns of the DHPLC machine; therefore, PCR buffers without such prod-
ucts should be used. However, if these products are necessary for a specific PCR,
the PCR products can be filtered by column purification and subsequently used
in the DHPLC.
8. PCR products for subsequent DHPLC analysis need to be specific; any double
bands or smears on gel analysis point to a PCR with side products. These side
products will interfere with the DHPLC analysis by producing incorrect patterns
and might even mask real polymorphisms or mutations.
182 Postma et al.

9. Homozygous mutations are difficult to detect in a DHPLC because aberrant ho-

mozygous patterns might differ only slightly, or even not at all, compared with
homozygous normal alleles. Mixing of wild-type DNA with patient DNA results
in heteroduplexes that are easier to detect. However, in case of a clear family
history with autosomal-dominant inheritance (most of the CPVT cases) one could
take the risk to analyze patient DNA without mixing with wild-type DNA to
speed analysis.
10. A set of random samples plus a positive control is to be used for the initial opti-
mization of the PCR amplicons of interest. The DHPLC conditions are adjusted
so that the elution profile of the positive control is different from the wild-type
sample. When no positive control is available, conditions are considered to be
optimal at the temperature and corresponding gradient immediately before a sig-
nificant decrease in the retention time of the amplicon and/or an excessive broad-
ening of the peak, indicating excess denaturation. Useful temperatures are typically
located in the range of 50 to 75% of the helical fraction for the amplicons ana-
lyzed.
11. Initially unidirectional sequencing per patient is used (i.e., only a forward primer).
If aberrant sequences are found, a new PCR is performed, and, in the subsequent
sequence reaction, both the forward and reverse primers are used.
12. Direct sequencing is warranted for CASQ2 exons 1, 7 (contains a poly T tail in
the 5' intron; therefore, a reverse primer is recommended), 8, 9, and 10 because
they contain numerous polymorphisms.

References
1. Priori, S. G., Napolitano, C., Tiso, N., et al. (2001) Mutations in the cardiac
ryanodine receptor gene (hRyR2) underlie catecholaminergic polymorphic ven-
tricular tachycardia. Circulation 103(2), 196–200.
2. Priori, S. G., Napolitano, C., Memmi, M., et al. (2002) Clinical and molecular
characterization of patients with catecholaminergic polymorphic ventricular ta-
chycardia. Circulation 106(1), 69–74.
3. Postma, A. V., Denjoy, I., Hoorntje, T. M., et al. (2002) Absence of calsequestrin
2 causes severe forms of catecholaminergic polymorphic ventricular tachycar-
dia. Circ. Res. 91(8), e21–26.
4. Swan, H., Piippo, K., Viitasalo, M., et al. (1999) Arrhythmic disorder mapped to
chromosome 1q42-q43 causes malignant polymorphic ventricular tachycardia
in structurally normal hearts. J. Am. Coll. Cardiol. 34(7), 2035–2042.
5. Tiso, N., Stephan, D. A., Nava, A., et al. (2001) Identification of mutations in
the cardiac ryanodine receptor gene in families affected with arrhythmogenic
right ventricular cardiomyopathy type 2 (ARVD2). Hum. Mol. Genet. 10(3),
189–194.
6. Laitinen, P. J., Brown, K. M., Piippo, K., et al. (2001) Mutations of the cardiac
ryanodine receptor (RyR2) gene in familial polymorphic ventricular tachycar-
dia. Circulation 103(4), 485–490.
Molecular Diagnostics of CPVT 183

7. Bauce, B., Rampazzo, A., Basso, C., et al. (2002) Screening for ryanodine recep-
tor type 2 mutations in families with effort-induced polymorphic ventricular
arrhythmias and sudden death: early diagnosis of asymptomatic carriers. J. Am.
Coll. Cardiol. 40(2), 341–349.
8. Postma, A. V., Denjoy, I., Kamblock, J., et al. (2005) Catecholaminergic poly-
morphic ventricular tachycardia: RYR2 mutations, bradycardia, and follow-up
of the patients. J. Med. Gen. 42, 863–870.
9. Meissner, G. (2002) Regulation of mammalian ryanodine receptors. Front.
Biosci. 7, d2072–2080.
10. Lahat, H., Pras, E., Olender, T., et al. (2001) A missense mutation in a highly
conserved region of CASQ2 is associated with autosomal recessive catechola-
mine-induced polymorphic ventricular tachycardia in Bedouin families from Is-
rael. Am. J. Hum. Genet. 69(6), 1378–1384.
11. Plaster, N. M., Tawil, R., Tristani-Firouzi, M., et al. (2001) Mutations in Kir2.1
cause the developmental and episodic electrical phenotypes of Andersen’s syn-
drome. Cell 105(4), 511–519.
12. Andelfinger, G., Tapper, A. R., Welch, R. C., et al. (2002) KCNJ2 mutation
results in Andersen syndrome with sex-specific cardiac and skeletal muscle phe-
notypes. Am. J. Hum. Genet. 71(3), 663–668.
13. Donaldson, M. R., Jensen, J. L., Tristani-Firouzi, M., et al. (2003) PIP2 binding
residues of Kir2.1 are common targets of mutations causing Andersen syndrome.
Neurology 60(11), 1811–1816.
Mutation Detection in Archival Tissue 185

11
Mutation Detection in Tumor Suppressor Genes
Using Archival Tissue Specimens

Aristotelis Astrinidis and Elizabeth Petri Henske

Summary
Tuberous sclerosis complex (TSC) is a neurocutaneous syndrome characterized by seizures,
mental retardation, and benign tumors of many organs, including the brain, kidneys, skin, retina,
and heart. TSC is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The
genes follow the two-hit model for tumorigenesis, with germline mutations inactivating one
allele and somatic mutations inactivating the remaining wild-type allele. Allelic loss (also called
loss of heterozygosity [LOH]) in the 9q34 and 16p13 regions has been found in many tumor
types from TSC patients. Cardiac rhabdomyomas are frequently found in infants with TSC.
Because rhabdomyomas often spontaneously regress, access to fresh tissue is limited. In this
chapter, we present methodology for detection of genetic inactivation of TSC1 and TSC2 in
paraffin-embedded archival tissues. The template DNA is obtained either by direct scraping of
tissue or after laser capture microdissection. LOH analysis is performed after polymerase chain
reaction amplification of microsatellite markers in the 9q34 and 16p13 regions and denaturing
polyacrylamide gel electrophoresis. Mutation detection is performed using single-strand con-
formation polymorphisms on mutation detection enhancement gels. Finally, variant bands are
amplified and analyzed by direct sequencing.
Key Words: Tuberous sclerosis complex (TSC); TSC1; TSC2; tumor suppressor genes;
rhabdomyomas; laser capture microdissection (LCM); loss of heterozygosity (LOH); single-
strand conformation polymorphisms (SSCP); direct sequencing; variant bands.

1. Introduction
Rhabdomyomas, which are the most common pediatric cardiac neoplasm,
are frequently associated with tuberous sclerosis complex (TSC) (1). TSC is an
autosomal-dominant syndrome characterized by seizures, mental retardation,
autism, and benign tumors of the brain, heart, kidney, and skin (2,3). Muta-
tions in the TSC1 or TSC2 tumor suppressor genes cause TSC (4,5) and pul-
monary lymphangioleiomyomatosis (6,7). According to Knudson’s two-hit
hypothesis for tumorigenesis, two mutational events are necessary for tumor
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

185
186 Astrinidis and Henske

initiation; the first is a germline or somatic mutation, in familial or sporadic

cases, respectively (8). The second event affects the remaining wild-type allele
of the tumor suppressor gene and is usually a deletion of a chromosomal region,
which is termed allelic loss or loss of heterozygosity (LOH). However, it is not
unusual for the second hit to be a smaller mutation, such as a nonsense or
missense mutation.
Rhabdomyomas arise during fetal development, and usually spontaneously
regress during early childhood (9). Therefore, surgical resection is usually
avoided, access to tissue (particularly fresh tissue) is very limited, and rela-
tively little is known about their pathogenesis. This chapter focuses on the
methods for genetic analysis of the TSC1 and TSC2 genes using archival, par-
affin-embedded tissue specimens. Template DNA can be obtained either by
direct scraping from tissue sections or after laser capture microdissection
(LCM). Two types of genetic analyses are described: LOH using microsatellite
markers, and mutational analysis using single-strand conformation polymor-
phisms (SSCP) followed by direct sequencing. Although the methodology
refers to the TSC1 and TSC2 genes, it can be applied in any tumor suppressor
gene.
The complexity of the TSC1 and TSC2 genes, with 21 and 41 coding exons,
respectively, and the absence of obvious mutational hot spots in either gene,
make screening for mutations challenging. All mutations in TSC1 cause pre-
mature protein termination (nonsense or frameshift mutations), whereas, in
TSC2, there are also missense mutations (10–13). LOH has been found in 60%
of renal angiomyolipomas (14,15), and in pulmonary lymphangioleio-
myomatosis (6,16,17). LOH in TSC tumors is more frequent in the TSC2 gene
region of chromosome 16p13 (18), than in the TSC1 region (9q34).

2. Materials
1. Xylene.
2. Harry’s modified hematoxylin solution.
3. Eosin Y solution.
4. Histology slide extraction buffer: 50 mM KCl, 10 mM Tris-HCl, pH 8.3, 1.5 mM
MgCl2, 100 μg/mL bovine serum albumin, 0.45% v/v Tween-20, 0.45% v/v
Nonidet P-40.
Sterilize by filtering, aliquot, and store at –20°C. Before using, add proteinase K
at a final concentration of 1 mg/mL.
5. PixCell II LCM microscope, and CapSure transfer caps (Arcturus Biosciences,
Mountain View, CA).
6. 10X TK buffer: 500 mM Tris-HCl, pH 8.9, 10 mM NaCl, 20 mM EDTA, 5% v/v
Tween-20.
Sterilize by filtering, aliquot, and store at –20°C. Before using, add proteinase K
at a final concentration of 2 mg/mL.
Mutation Detection in Archival Tissue 187

7. Taq DNA polymerase, 10X polymerase buffer, and 50 mM MgCl2.

8. dNTP mix: 10 mM of each dATP, dCTP, dGTP and dTTP.
9. α[32P]-dCTP, 3000 Ci/mmol, 10 mCi/mL.
10. 10 μM oligonucleotide primers for the microsatellite markers (Invitrogen,
Carlsbad, CA), and for each of the exons of TSC1 and TSC2.
11. Mineral oil.
12. Vertical polyacrylamide gel unit (30-cm height, 38-cm width) with 0.4-mm spac-
ers and shark tooth-type comb.
13. Siliconizing solution (i.e., Sigmacoat; Sigma, St. Louis, MO).
14. 10X Tris-borate-EDTA (TBE) buffer: 0.89 M Tris-borate, pH 8.3, 0.02 M EDTA.
15. 40% acrylamide gel solution: 38% w/v acrylamide, 2% w/v bis-acrylamide (N,N'-
methylenebisacrylamide).
Filter and store at 4°C in tinted bottle.
16. Urea.
17. 10% w/v ammonium persulfate. Store in aliquots at –20°C.
18. TEMED.
19. 2X denaturing loading buffer. Store in aliquots at –20°C: 50% formamide, 0.1%
bromophenol blue, 0.1% xylene cyanol.
20. 3MM Whatman chromatography paper.
21. 2X mutation detection enhancement (MDE) gel solution (Cambrex, East Rutherford, NJ).
22. Agarose gel electrophoresis unit.
23. Polymerase chain reaction (PCR) purification kit (i.e., Qiagen, Valencia, CA).
24. Gel extraction kit (i.e., Qiagen).
25. Tris-HCl-EDTA (TE) buffer: 10 mM Tris-HCl, pH 8.0, 1 mM EDTA.
26. Self-stick fluorescent labels.

3. Methods
The methods below describe in detail:
1. The extraction of DNA either directly from the histology slide, or from LCM
material.
2. LOH analysis using microsatellite markers.
3. SSCP to detect variant bands.
4. Direct sequencing of variant bands to detect mutations or polymorphisms.
5. Analysis of LOH and SSCP/direct sequencing results.

3.1. Extraction of DNA From Archival Tissue Specimens

Archival, paraffin-embedded tissue can be used for the extraction and
amplification of DNA (see Note 1). If the tissue under investigation is homog-
enous and clearly defined, direct scraping and extraction can be used. If the
tissue of interest is small or the cells of interest are mixed with normal cells, a
microdissection procedure can be used. From the several microdissection meth-
ods available, we use the LCM, which was developed by the National Insti-
tutes of Health (19) and marketed by Arcturus Biosciences Inc.
188 Astrinidis and Henske

3.1.1. Preparation of Hematoxylin and Eosin-Stained Slides

1. Cut 5- to 7-μm-thick sections and mount on microscopy slides. Use uncoated
slides for LCM.
2. Remove paraffin by dipping slides twice in xylene for 2 min.
3. Rehydrate tissue by dipping for 2 min in decreasing ethanol concentrations: twice
in 100% ethanol, once in 95% ethanol, and once in 70% ethanol. Rehydrate com-
pletely twice in dH2O for 2 min.
4. Dip slide in hematoxylin solution for 10 s.
5. Rinse slide twice in dH2O (three dips).
6. Dip slide for 2 min in 70 and 95% ethanol, consecutively.
7. Dip slide in eosin Y (five dips).
8. Wash slide twice in 95% ethanol for 2 min.
9. Dehydrate slide in 100% ethanol for 2 min.
10. Air-dry slide. Do not allow excessive drying if slides are to be used for LCM.
3.1.2. Scraping of Tissue Directly Into DNA Histology Slide Extraction
Buffer
1. Use a hematoxylin and eosin-stained section to identify the area to be used for
DNA extraction. Mark the area of interest on an adjacent unstained slide with a
fine-tip permanent marker.
2. Using a clean razor blade, remove all excess paraffin from the unstained slide.
3. Scrape the tissue from the area of interest, avoiding normal tissue.
4. Using a sterile microbiological loop, transfer the tissue into histology slide ex-
traction buffer (~150 μL/cm2 of tissue, see Note 2).
5. Vortex briefly and incubate at 65°C overnight.
6. Heat inactivate proteinase K at 95°C for 10 min.
7. Spin briefly, aliquot extracted DNA, and store at –20°C.
3.1.3. Use of LCM to Obtain Tissue
In LCM, a microscope is used to facilitate the visualization of lightly stained
tissue sections. A transparent cap with a polymer (capturing film) rests on top of
the tissue section under the objective lens. The user can fire a laser beam, which
melts and attaches the polymer to the underlying tissue. The precision of LCM
has allowed researchers to capture single cells from tissue sections (see Note 3).
1. Prepare 1X TK buffer by a 1:10 dilution of 10X TK buffer in dH2O.
2. Perform LCM on a lightly hematoxylin and eosin-stained uncoated slide.
3. If capturing more than 100 cells, add 50 μL of 1X TK buffer on top of the CapSure
cap. Cap a 0.5-mL microcentrifuge tube using the tool provided by the manufac-
turer. Invert the tube so that the extraction solution is always in contact with the
captured cells. Incubate at 55°C overnight.
4. If capturing less than 100 cells, use a sterile scalpel to excise the area of transfer
film containing the captured cells. Using sterile forceps, transfer the film into a
Mutation Detection in Archival Tissue 189

0.2-mL PCR tube, add 10 to 20 μL of 1X TK buffer, and incubate at 55°C over-

night.
5. Spin tubes briefly. Heat inactivate proteinase K at 95°C for 10 min.
6. Store extracted DNA at –20°C.

3.2. PCR Amplification for LOH and SSCP Analysis

Because the fixatives used in archival tissue damage nucleic acids, it is dif-
ficult to amplify targets larger than 300 bp, and it is advisable to choose or
design primers that will amplify DNA fragments smaller than 200 bp. For the
TSC1 genomic region (chromosomal location 9q34), we use the D9S1198 and
D9S1199 microsatellite markers. For the TSC2 genomic region (16p13), we
use D16S291, D16S418, D16S475, D16S663, and Kg8. The primer informa-
tion for the TSC1 and TSC2 exons has been previously published (20,21). Nor-
mal DNA adjacent to the tumor analyzed must always be included in the study
to provide positive controls for the presence of heterozygosity and/or the nor-
mal SSCP pattern. The PCR products are radiolabeled by direct incorporation
of 32P-dCTP in the reaction, resolved in polyacrylamide gels, and visualized
after autoradiography (see Note 4).
1. Dilute DNA samples extracted directly from pathology slides 1:10 to 1:100 in
dH2O. DNA after LCM must not be diluted. Use 2 μL of DNA sample per reaction.
2. In a 0.2-mL PCR tube (or 96-well PCR plate for multiple samples), set up a 10-μL
PCR reaction according to Table 1.
3. Overlay PCR reactions with 10 μL mineral oil.
4. Perform the amplification using the following cycling conditions: 95°C for 5
min, 30 cycles of (95°C for 30 s; 55°C for 30 s; and 72°C for 30 s), 72°C for 5
min (see Note 5).
5. Store the samples at –20°C until analyzed.

3.3. LOH Analysis Using Microsatellite Markers

LOH analysis is performed after PCR amplification of highly polymorphic
microsatellite markers that are close to the gene of interest. Microsatellite mark-
ers in unrelated chromosomal locations are used as negative controls. The PCR
products are resolved in denaturing polyacrylamide gels.
3.3.1. Preparation of Denaturing Polyacrylamide Gel
1. Wash the glass plates of the vertical electrophoresis unit thoroughly and dry.
2. Under a fume hood, apply 0.5 to 1 mL of siliconizing solution onto a small piece
of tissue paper and smear on the inner surface of the back glass plate. Remove
traces of siliconizing solution by washing the glass plate with dH2O. Wipe and
allow to air-dry (see Note 6).
3. Wash the inner surface of the front glass plate with 70% ethanol. Wipe and allow
to air-dry.
190 Astrinidis and Henske

Table 1
PCR Reaction for LOH and SSCP Analysis

Final concentration Volume (mL)

10X PCR buffer 1X 1.0
50 mM MgCl2 1.5 mM 0.3
10 mM dNTP mix 0.2 mM 0.2
10 μM forward primer 1.5 μM 1.5
10 μM reverse primer 1.5 μM 1.5
DNA 2.0
10 μCi/μL of α[32P]-dCTP 0.1 μCi/μL 0.1
dH2O 3.0
5 U/μL of Taq polymerase 0.2 U/μL 0.4
Total 10.0

4. Assemble the unit and lay flat, back plate facing up. Clean the comb with etha-
nol, and dry.
5. Prepare gel solution by mixing 5 mL of 10X TBE, 7.5 mL of 40% acrylamide gel
solution, and 21 g of urea, in a final volume of 50 mL (see Note 7).
6. Add 350 μL of 10% ammonium persulfate and mix.
7. Add 20 μL TEMED and mix.
8. Using a 50-mL syringe, pour the acrylamide gel solution between the two glass
plates. Gently tap the top glass plate to avoid formation of air bubbles. Fill the
unit with gel solution to the top.
9. Insert the straight edge of the comb between the two glass plates, approx 5 mm
from the edge of the glass plate. Clamp the two glass plates together using three
large paper clamps (see Note 8).
10. Let gel polymerize for 1 h.
11. Remove the clamps. Remove the comb and clean it.
3.3.2. Electrophoresis and Autoradiography
1. Use 1X TBE as the running buffer. Prerun the gel at 65W for 15 min, until the gel
temperature is 55°C (see Note 9).
2. Add an equal volume of 2X denaturing loading buffer into each PCR reaction.
3. Denature DNA by heating at 99°C for 5 min. Immediately put in ice for 2 min.
4. Stop the prerun and flush the gel surface with running buffer. Insert the comb
between the two glass plates, so that the shark teeth are buried 1 mm in the poly-
acrylamide gel.
5. Load 4 μL of the denatured samples.
6. Perform the electrophoresis at 55W, maintaining the gel temperature at 55°C,
until the bromophenol blue front reaches the bottom of the gel.
Mutation Detection in Archival Tissue 191

7. Stop the electrophoresis and disassemble the unit. Lay the glass plates flat, back
plate on top. Gently separate the glass plates by inserting a spatula between them.
Place a 3MM Whatman paper on top of the gel. Allow the 3MM Whatman paper
to stick for a few minutes, and slowly lift one end of the filter paper. Cover the
gel with plastic wrap, place in gel drier, and dry under vacuum at 80°C for 1 h.
8. Perform autoradiography at –80°C, using intensifying screens.

3.4. Mutational Analysis Using SSCP

SSCP is based on the ability of single-stranded DNA molecules to migrate
in nondenaturing polyacrylamide gels. The mobility of those molecules
depends on the DNA sequence; single nucleotide changes can greatly affect
the mobility, resulting in mobility shifts between the test and wild-type DNA.
Although SSCP is not a very sensitive mutation detection method (70–80%
detection rate of mutant DNA species), it is simple and fairly cost effective
when analyzing large number of samples.
3.4.1. Preparation of SSCP Gel
1. Follow steps 1–4 of Subheading 3.3.1.
2. Prepare gel solution by mixing 3 mL of 10X TBE and 12.5 mL of 2X MDE gel
solution, in a final volume of 50 mL.
3. Add 200 μL of 10% ammonium persulfate and mix.
4. Add 20 μL of TEMED and mix.
5. Follow steps 8–11 of Subheading 3.3.1.
3.4.2. Electrophoresis
1. Add an equal volume of 2X denaturing loading buffer in each PCR reaction.
2. Heat at 99°C for 5 min, then snap-chill on ice for 5 min.
3. Flush the surface of the SSCP gel with running buffer (1X TBE). Insert the comb
so that the shark teeth are buried 1 mm in the polyacrylamide gel.
4. Load 4 μL of sample in each well.
5. Perform electrophoresis at 100 to 160V for 16 to 24 h (see Note 10).
Follow Subheading 3.3.2., steps 7 and 8.

3.5. Direct DNA Sequencing

SSCP analysis is indicative of the presence of a nucleotide change in the test
DNA. In many instances, false-positive results and complex banding patterns
arise from DNA molecules that have more than one stable three-dimensional
conformation. To exclude the possibility that the variant band is caused by an
error during DNA amplification, a second, independent, confirmation of the
SSCP result is needed. Finally, direct sequencing is used to identify the exact
nucleotide change. Direct sequencing can be performed after PCR amplifica-
tion of DNA extracted from tissue sections or LCM material, or from variant
bands.
192 Astrinidis and Henske

3.5.1. Extraction of DNA From Variant Bands

1. Line up the autoradiography with the dried SSCP gel over a light box (see Note 11).
2. Mark the region of the gel corresponding to a variant band with a fine-tipped
marker.
3. Cut the filter paper and gel containing the variant band, allowing a 2-mm margin
on each side.
4. Immerse the cutout filter paper/gel in 100 μL dH2O for 1 h.
5. Aspirate as much liquid as possible, and store gel at –20°C.
3.5.2. Amplification and Purification of DNA for Direct Sequencing
1. Use DNA from scraped paraffin-embedded tissue, LCM, or from a variant band.
2. Set up a 50-μL PCR reaction according to Table 2.
3. Overlay the reaction with 20 μL mineral oil.
4. Use the optimized cycling conditions for the specific exon.
5. Resolve one-tenth (5 μL) of the PCR reaction in an 1% agarose/0.5X TBE verti-
cal gel.
6. If PCR product does not have nonspecific bands, use a PCR purification kit to
purify DNA from buffer, dNTPs, primers, and enzyme. Elute in the smallest pos-
sible amount of TE buffer or dH2O.
7. If PCR product has nonspecific bands, resolve the remaining PCR reaction on an
agarose gel, excise the appropriate gel slice, and purify using a gel purification
kit. Elute in the smallest possible amount of TE buffer or dH2O.
8. Perform direct sequencing in the purified PCR product with the primers used for
amplification.

3.6. Analysis of LOH and SSCP/Direct Sequencing Results

3.6.1. Reading an LOH Gel
LOH is observed as an absence of an allelic band in the tumor sample, com-
pared with the presence of both allelic bands in the normal sample for het-
erozygous markers. In some instances, normal DNA can contaminate the tumor
sample. In this case, the observed LOH is not complete. Because smaller DNA
fragments are favored during a PCR amplification reaction, LOH is harder to
demonstrate for the smaller of the two alleles of a heterozygous marker.
3.6.2. Distinguishing Mutations From Polymorphisms After DNA
Sequencing
Some of the variations observed in the TSC1 or TSC2 genes are caused by
common polymorphisms. These are easy to identify because they occur in high
frequencies (>0.05) in the general population. Frameshifting and nonsense
mutations are considered disease-causing mutations, because they both result
in premature termination of protein synthesis. Missense mutations are harder
to classify as disease-causing or rare polymorphisms. If the mutation is identi-
Mutation Detection in Archival Tissue 193

Table 2
PCR Reaction for Direct Sequencing Analysis

Final concentration Volume (mL)

10X PCR buffer 1X 5.0
50 mM MgCl2 1.5 mM 1.5
10 mM dNTP mix 0.2 mM 1.0
10 μM forward primer 1.5 μM 7.5
10 μM reverse primer 1.5 μM 7.5
DNA 5.0
dH2O 20.5
5 U/μL of Taq polymerase 0.2 U/μL 2.0
Total 50.0

fied in normal DNA, the researcher can test normal DNA from other members
of the family. A disease-causing mutation will segregate with the affected indi-
viduals of a large pedigree. Parental DNA can be particularly informative in
patients with TSC whose parents are unaffected. Approximately 60% of TSC
patients represent new germline mutations. In these cases, the disease-causing
mutation will not be present in parental DNA. However, in complex disorders,
such as TSC, extensive clinical evaluation may be needed to exclude a diagno-
sis in the parents.

4. Notes
1. In addition to the tissue of interest, DNA from normal cells must also be obtained.
The normal DNA is essential for LOH, and may be needed for SSCP studies to
distinguish between germline and somatic mutations. Peripheral blood lympho-
cytes are a good source of high quality normal DNA, although any normal tissue
can be used, including microdissected normal cells adjacent to the tumor.
2. This amount of buffer is critical. Using too much or too little buffer will impair
the DNA amplification.
3. Slide preparation and staining will greatly affect the conditions (pulse duration
and power of laser beam) for successful capture. It is preferable to stain the slide
and perform the capture the same day. If LCM is to be performed on another day,
the slides can be stored in a desiccator. However, storing for long periods is not
indicated, because the tissue tends to adhere more strongly to the glass slide. If
the cells are resistant to capture, try increasing the power and duration of the
laser pulse. If the cells of interest are morphologically indistinguishable from the
surrounding cells, immunohistochemically stained slides with a marker specific
to the cells of interest can be used.
4. We regularly use 1 to 2.5 μL of extracted DNA in a standard 10-μL PCR reac-
tion. It is advisable to optimize PCR conditions, using as low as 0.5 ng of high-
194 Astrinidis and Henske

quality template (i.e., genomic DNA from peripheral blood or cultured cells).
Because the amount of template DNA per reaction is very small (especially for
LCM-extracted DNA), take additional precautions to prevent cross contamina-
tion. Always include a dH2O control PCR reaction. When setting up PCR reac-
tions, use aerosol-barrier tips and a designated set of automatic pipettors.
5. The annealing temperature (55°C) must be optimized for each oligonucleotide
pair. PCR conditions that are optimal for other sources of high-quality DNA may
need reoptimization when amplifying archival DNA. In some instances, the an-
nealing temperature is significantly lower (5–10°C) for archival DNA. If nonspe-
cific DNA fragments are present that cannot be removed after optimization, a
“hot-start” technique should be used. It is best to amplify and analyze multiple
patients at the same time, so that it is easier to identify the alleles and banding
patterns during LOH and SSCP analyses, respectively.
6. Siliconizing solutions are volatile and toxic. They should be applied in a fume
hood. After siliconization, do not wash this plate with ethanol. It is best if the
same glass plate is siliconized each time. Some researchers use bonding solu-
tions for the opposite (front) glass plate, but we find that unnecessary.
7. Urea dissolves better in warm solution. However, the acrylamide solution must
be allowed to cool at room temperature before adding ammonium persulfate and
TEMED, otherwise, rapid polymerization will occur.
8. Clamping the two glass plates together is necessary for appropriate and uniform
gel thickness, and eliminates cross contamination of samples during loading. The
acrylamide solution polymerizes within 30 to 45 min, but the gel should not be
used for an additional 2 h. The gel can be stored at 4°C overnight, but it must be
equilibrated at room temperature for at least 2 h before use.
9. The wattage of the electrophoresis depends on the gel surface. The wattages sug-
gested are for 30 × 38-cm gels. Gel temperature should be maintained at 50°C to
60°C during the electrophoresis of samples.
10. Single-stranded DNAs are better resolved in low-voltage runs. Increasing the
voltage excessively will increase the temperature of the gel and destroy the three-
dimensional conformations of the single-stranded DNA. Several conditions can
affect the mobility of single-stranded DNAs and the ability of SSCP to distin-
guish between wild-type and mutant molecules. Two of the conditions commonly
used are: the addition of 10% glycerol in the nondenaturing gels, and electro-
phoresis at 4°C. In the latter case, equilibrate the gel and running buffer tempera-
ture at 4°C for at least 2 h before loading.
11. Use fluorescent labels during autoradiography for easy orientation.

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their association with tuberous sclerosis. Arch. Dis. Child. 68, 367–370.
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sensus conference: revised clinical diagnostic criteria. J. Child. Neurol. 13, 624–628.
3. Gomez, M., Sampson, J. R., and Whittemore, V. H. (1999) Tuberous Sclerosis
Complex, 3rd ed, Oxford University Press, New York.
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4. The European Chromosome 16 Tuberous Sclerosis Consortium. (1993) Identifica-

tion and characterization of the tuberous sclerosis gene on chromosome 16. Cell
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the tuberous sclerosis gene TSC1 on chromosome 9q34. Science 277, 805–808.
6. Carsillo, T., Astrinidis, A., and Henske, E. P. (2000) Mutations in the tuberous
sclerosis complex gene TSC2 are a cause of sporadic pulmonary
lymphangioleiomyomatosis. Proc. Natl. Acad. Sci. USA 97, 6085–6090.
7. Sato, T., Seyama, K., Fujii, H., et al. (2002) Mutation analysis of the TSC1 and
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sclerosis. Acta. Paediatr. 85, 928–931.
10. Jones, A. C., Shyamsundar, M. M., Thomas, M. W., et al. (1999) Comprehensive
mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families
with tuberous sclerosis. Am. J. Hum. Genet. 64, 1305–1315.
11. Niida, Y., Lawrence-Smith, N., Banwell, A., et al. (1999) Analysis of both TSC1
and TSC2 for germline mutations in 126 unrelated patients with tuberous sclero-
sis. Hum. Mutat. 14, 412–422.
12. van Slegtenhorst, M., Verhoef, S., Tempelaars, A., et al. (1999) Mutational spec-
trum of the TSC1 gene in a cohort of 225 tuberous sclerosis complex patients: no
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cohort of 224 tuberous sclerosis patients indicates increased severity of TSC2,
compared with TSC1, disease in multiple organs. Am. J. Hum. Genet. 68, 64–80.
14. Carbonara, C., Longa, L., Grosso, E., et al. (1994) 9q34 loss of heterozygosity in a
tuberous sclerosis astrocytoma suggests a growth suppressor-like activity also for
the TSC1 gene. Hum. Mol. Genet. 3, 1829–1832.
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and Kwiatkowski, D. J. (1995) Loss of heterozygosity in the tuberous sclerosis
(TSC2) region of chromosome band 16p13 occurs in sporadic as well as TSC-
associated renal angiomyolipomas. Genes Chromosomes Cancer 13, 295–298.
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Henske, E. P. (1998) Evidence that lymphangiomyomatosis is caused by TSC2 muta-
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19. Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., et al. (1996) Laser capture mi-
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(1999) Mutation of the 9q34 gene TSC1 in sporadic bladder cancer. Oncogene 18,
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Methods to Diagnose Friedreich Ataxia 197

12
Friedreich Ataxia

Detection of GAA Repeat Expansions and Frataxin Point

Mutations

Massimo Pandolfo

Summary
Friedreich ataxia (FA) is an autosomal-recessive disease primarily characterized by pro-
gressive neurological disability. A significant proportion of patients also present with a hyper-
trophic cardiomyopathy, which may, in some cases, cause premature death. FA is caused by
insufficient levels of the protein, frataxin, which is involved in mitochondrial iron metabolism.
All patients carry at least one copy of an intronic GAA triplet-repeat expansion that interferes
with frataxin transcription. Normal chromosomes contain up to 35 to 40 GAA triplets in an Alu
sequence localized in the first intron of the frataxin gene; FA chromosomes carry from approx
70 to more than 1000 GAA triplets. The molecular diagnosis of FA is, therefore, based on the
detection of this expansion, which is present in homozygosity in more than 95% of the cases.
The remaining patients are heterozygous for the GAA expansion and carry a frataxin point
mutation as the other pathogenic allele. The expanded GAA triplet repeat may be detected by
polymerase chain reaction (PCR) amplification followed by agarose gel electrophoresis analy-
sis. In our hands, carefully performed PCR testing, in particular, if fragment detection is
enhanced by hybridization with a GAA oligonucleotide probe, is as effective in identifying
patients and carriers as is Southern blot analysis of genomic DNA, and allows a more accurate
sizing of the repeat. Furthermore, in the case of smaller expansions, the amplified fragment
may be directly sequenced to identify very rare nonpathogenic variant repeats, such as
GAAGGA. Sequence analysis of the five coding exons of the frataxin gene should be per-
formed in clinically affected individuals who are heterozygous for an expanded GAA repeat to
identify point mutations.
Key Words: Ataxia; neurodegenerative diseases; cardiomyopathies; expanded triplet
repeats; mutation analysis; polymerase chain reaction; Southern blot; DNA sequencing.

From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

197
198 Pandolfo

1. Introduction
Friedreich ataxia (FA) is an autosomal-recessive disease characterized by
progressive neurological disability, cardiomyopathy, and increased risk of dia-
betes mellitus. The disease, which currently has no treatment, affects roughly 2
to 3 in 100,000 people. Because of a founder effect of the main responsible
mutation, the disease only affects individuals of European, North African,
Middle Eastern, and Indian origins. In most cases, the neurological symptoms
dominate the clinical picture, however, a significant proportion of patients have
their life shortened because of heart disease. In addition, rare patients have
disease onset with symptoms and signs of cardiomyopathy.
1.1. Clinical Presentation
The typical onset of FA is around puberty (1–6), but it may be earlier (7,8).
After the gene was mapped and identified, it became clear that late-onset cases
exist, even in late adult life (late-onset FA) (9,10). The typical presentation at
onset is with gait instability or generalized clumsiness. Among nonneurological
manifestations, scoliosis, often considered to be idiopathic, may precede the
onset of ataxia. Rare patients (5%) are diagnosed with idiopathic hypertrophic
cardiomyopathy and treated as such for up to 2 to 3 yr before neurological
symptoms appear (1–4).
1.2. Neurological Signs and Symptoms
Mixed cerebellar and sensory ataxia characterizes the disease. It begins as
truncal ataxia causing swaying, imbalance, and falls. Subsequently, the ataxic
nature of gait becomes evident, with irregular steps, veering, and difficulty in
turning. With further progression, gait becomes broad based, with frequent
losses of balance, requiring intermittent support. A cane, and then a walker,
becomes necessary. Finally, on average, 10 to 15 yr after onset, patients lose
the ability to walk, stand, and sit without support. Evolution is variable; how-
ever, with mild cases patients are still ambulatory decades after onset. Limb
ataxia appears after truncal ataxia, impairing writing, dressing, and handling
utensils. Ataxia is progressive and unremitting, although periods of stability
are frequent at the beginning of the illness. Dysarthria appears within 5 yr of
clinical onset (1–4), and has a cerebellar character (11,12). Dysphagia, particu-
larly for liquids, appears with advancing disease. Cognitive functions are gen-
erally well-preserved.
Findings at the neurological examination indicate the underlying pathology.
Involvement of the central and peripheral sensory system results in deep sen-
sory loss and abolished reflexes (1,2). Pyramidal tract degeneration causes
extensor plantar responses and progressive muscular weakness, which become
Methods to Diagnose Friedreich Ataxia 199

severe only late in the progression of the disease. Ataxia and not weakness is
the primary cause for loss of ambulation, even when patients become wheel-
chair-bound, they still maintain, on average, 70% of their normal strength in
the lower limbs (13). The relative impact of sensory neuropathy and of pyrami-
dal tract degeneration varies from patient to patient, resulting most often in the
described picture of areflexia associated with extensor plantar responses. How-
ever, sometimes, one component prevails, thus, some patients have retained
reflexes or flexor plantar responses. These are usually milder cases of the dis-
ease. Some involvement of lower motor neurons is common and is revealed by
distal amyotrophy in the four limbs (2). When patients are wheelchair-bound,
disuse atrophy occurs. The typical oculomotor abnormality is fixation instabil-
ity with square-wave jerks (14). Various combinations of cerebellar, vestibu-
lar, and brainstem oculomotor signs may be observed, but gaze-evoked
nystagmus is uncommon and ophthalmoparesis does not occur. Approximately
30% of patients with FA develop optic atrophy, with or without visual impair-
ment (1,2,4,15–17), and 20% have sensorineural hearing loss (18,19). Optic
atrophy and sensorineural hearing loss tend to be associated with each other
and with diabetes (1,20).
1.3. Heart Disease
The cardiomyopathy of FA is most commonly asymptomatic; however, in a
significant minority of patients it may contribute to disability and cause prema-
ture death, particularly in those with earlier age of onset (1–4,21–28). Short-
ness of breath (40%) and palpitations (11%) are the most common first
symptoms (1). As the disease evolves, patients may develop arrhythmias, which
may be fatal, and congestive heart failure. At end-stage disease, the cardiomy-
opathy becomes dilative, with progression of heart failure and eventually car-
diogenic shock and death.
1.4. Other Signs and Symptoms
Approximately 10% of patients with FA develop diabetes mellitus, and 20%
have carbohydrate intolerance. The mechanisms are complex, with β-cell dys-
function (29) and atrophy (30), as well as peripheral insulin resistance (31).
Oral hypoglycemic drugs may initially give adequate control, but insulin even-
tually becomes necessary.
Skeletal abnormalities are common. Kyphoscoliosis may cause pain and
cardiorespiratory problems. Pes cavus and pes equinovarus may further affect
ambulation.
Autonomic disturbances, most commonly cold and cyanotic legs and feet,
become increasingly frequent as the disease advances (32). Parasympathetic
200 Pandolfo

abnormalities, such as decreased heart rate variability parameters have been

reported (33). Urinary problems, usually urgency, are rare.
1.5. Laboratory Investigations
FA causes typical neurophysiological abnormalities. Sensory nerve action
potentials are severely reduced or, most often, lost (34–36). Motor and sensory
(when measurable) nerve conduction velocities are, instead, within or just be-
low the normal range. These findings clearly distinguish an early case of FA
from a case of hereditary demyelinating sensorimotor neuropathy.
Central nervous system magnetic resonance imaging shows a thinned spinal
cord, but no major atrophy of brain structures. Even the cerebellum is appar-
ently normal or only mildly atrophic in more advanced cases (37).
The electrocardiogram shows inverted T waves in essentially all patients
with FA, ventricular hypertrophy in most patients, conduction disturbances in
approx 10% of patients, and, occasionally, supraventricular ectopic beats and
atrial fibrillation (3,4,26,27). The electrocardiogram may vary in time with
occasional normal recordings, however, repeated recordings remain the most-
sensitive test for the FA cardiomyopathy. Echocardiography and Doppler–
echocardiography demonstrate concentric hypertrophy of the ventricles (62%)
or asymmetric septal hypertrophy (29%), with diastolic function abnormalities
(2,38).
Recently, abnormalities in heart and skeletal muscle metabolism have been
detected by phosphorus magnetic resonance spectroscopy, in particular, a
reduced rate of adenosine triphosphate (ATP) synthesis. These abnormalities
are a direct consequence of the primary genetic defect that affects mitochon-
drial function.
1.6. Prognosis
Patients with FA become wheelchair-bound, on average, 15 yr after onset of
symptoms, but the variability is very large (2,8). Early onset and left ventricu-
lar hypertrophy predict a faster rate of progression (8,19). The burden of neu-
rological impairment, cardiomyopathy, and, occasionally, diabetes, shortens
life expectancy (8). Survival may be significantly prolonged with treatment of
cardiac symptoms (particularly arrhythmias), with antidiabetic treatment, and
with preventing and controlling complications resulting from prolonged neu-
rological disability.
1.7. Molecular Genetics
The FA gene (FRDA) (39,40) encodes a small mitochondrial matrix protein,
frataxin, that is highly conserved in evolution. A single frataxin gene is found
in all eukaryotes, including fungi and plants. A homolog, CyaY, is present in
Methods to Diagnose Friedreich Ataxia 201

Gram-negative bacteria and in other prokaryotes, such as Rickettsia

prowazeckii, thought to be related to the hypothetical mitochondrial precursor.
FRDA is expressed in all cells, but at variable levels in different tissues and
during development (41,42). In adult humans, frataxin messenger RNA is most
abundant in the heart, brain, and spinal cord; followed by liver, skeletal muscle,
and pancreas.
Patients with FA have a profound but not complete frataxin deficiency, with
a small residual amount of normal protein. FA is caused by a so-far, unique
mutation mechanism: the expansion of an intronic GAA triplet-repeat sequence
(TRS), for which most patients are homozygous. Smaller expansions allow a
higher residual gene expression (43). Accordingly, the severity and age of onset
of the disease are, in part, determined by the size of the expanded GAA TRS, in
particular, of the smaller allele (20,44). Lengths of the GAA TRS correspond-
ing to pathological FRDA alleles can adopt a triple-helical structure in physi-
ological conditions and can inhibit transcription in vitro and in vivo (45–47).
Approximately 2% of FA chromosomes carrying GAA repeats of normal
lengths have missense, nonsense, or splice-site mutations ultimately affecting
the frataxin coding sequence (Fig. 1) (48).
1.8. Pathogenesis
Structural studies have been carried out on frataxin (49,50) and its bacterial
homolog, CyaY (51), by nuclear magnetic resonance and by crystallography.
These investigations revealed a novel structural motif, called the frataxin fold,
unique to frataxin and CyaY proteins. The structure is compact, overall globu-
lar, containing an N-terminal α-helix, a middle β-sheet region composed of
seven β-strands, a second α-helix, and a C-terminal coil. The α-helices are
folded on the β-sheet, with the C-terminal coil filling a groove between the two
α-helices. On the outside, a ridge of negatively charged residues and a patch of
hydrophobic residues are highly conserved, suggesting that they interact with a
large ligand, probably a protein.
Knockout of the yeast frataxin homologous gene (YFH1) has provided the
first information on frataxin function. Most YFH1 knockout yeast strains,
called Δyfh1, lose the ability to carry out oxidative phosphorylation, cannot
grow on nonfermentable substrates, and lose mitochondrial DNA (52,53). In
ΔYFH1, iron accumulates in mitochondria, more than 10-fold in excess of wild-
type yeast, at the expense of cytosolic iron. Loss of respiratory competence
requires the presence of iron in the culture medium, and occurs more rapidly as
iron concentration in the medium is increased, suggesting that permanent
mitochondrial damage is the consequence of iron toxicity (54). Iron in mito-
chondria can react with reactive oxygen species that form in these organelles
and generate the highly toxic hydroxyl radical through the Fenton reaction with
 202
202

Pan
Fig. 1. Examples of mutation affecting the frataxin coding sequence. The two highlighted missense mutations are associated
dolf
with a mild phenotype. Notice that the missense mutations are clustered after the cleavage site that removes the mitochondrial
targeting N-terminal o
peptide.
Methods to Diagnose Friedreich Ataxia 203

H2O2. The hydroxyl radical causes lipid peroxidation, and protein and nucleic
acid damage. Occurrence of the Fenton reaction in ΔYFH1 yeast cells is sug-
gested by their highly enhanced sensitivity to H2O2 (52).
In Δyfh1 yeast, iron is trapped in mitochondria, and there is a deficit in cyto-
solic iron, causing a marked induction (10- to 50-fold) of the high-affinity iron
transport system on the cell membrane, normally not expressed in yeast cells
that are iron replete (52). Consequently, iron crosses the plasma membrane in
large amounts and further accumulates in mitochondria, engaging the cell in a
vicious cycle. Experimental evidence suggests that frataxin stimulates a flux of
nonheme iron out of mitochondria (54).
Respiratory chain complexes I, II, and III, and aconitase are impaired in
Δyfh1 yeast (55). These enzymes contain iron–sulfur clusters (ISCs) in their
active sites. ISCs are synthesized in mitochondria and are highly sensitive to
free radicals (56). Remarkably, all yeast mutants defective in ISC synthesis
have mitochondrial iron accumulation, apparently caused by defective iron
export out of mitochondria, because it occurs in Δyfh1. Recent data point to a
direct involvement of frataxin in an early step of ISC synthesis (57), through
an interaction with the scaffold protein Isu1, in which the first ISC assembly
takes place, probably facilitating iron incorporation (58). This finding suggests
that frataxin may be a mitochondrial iron chaperone, protecting the iron from
reactive oxygen species and making it bioavailable. Recent data support this
view, suggesting that frataxin also acts as an iron chaperone in heme synthesis
(59) and in the modulation of aconitase activity (60). A much higher affinity of
frataxin for the heme synthesis enzyme, ferrochelatase, than for Isu1 (59) would
explain why heme synthesis is resistant to low frataxin levels and is essentially
unaffected in patients with FA (61). To act as an iron chaperone, frataxin must
have iron-binding properties. Adamec et al. (62) first reported the ability of
yfh1p, when exposed to a high iron concentration (iron to protein ratio of 40:1),
to form a high molecular weight complex containing approx 60 frataxin mol-
ecules and 3000 Fe3+ atoms in a ferritin-like structure; however, the in vivo
relevance of this finding has been controversial. Subsequent studies by the
same group suggested that frataxin has an intrinsic ferroxidase activity and that
it may bind and chaperone Fe2+ at lower iron to protein ratios (63).
Altered iron metabolism, free radical damage, and mitochondrial dysfunc-
tion all occur in patients with FA. Iron deposits are found in myocardial cells
from patients with FA (64). Oxidative stress is revealed by increased plasma
levels of malondialdehyde, a lipid peroxidation product (65), and increased
urinary 8-hydroxy-2'-deoxyguanosine, a marker of oxidative DNA damage
(66). We directly showed increased free-radical production in cultured cells
engineered to produce reduced levels of frataxin (67). In addition, patients’
fibroblasts are sensitive to low doses of H2O2, doses that induce apoptosis at
204 Pandolfo

lower doses than in control fibroblasts (68), suggesting that even nonaffected
cells are in an at-risk status for oxidative stress as a consequence of the primary
genetic defect. FA fibroblasts also show abnormal antioxidant responses, in
particular, a blunted increase in mitochondrial superoxide dismutase triggered
by iron and by oxidants in control cells (69). Mitochondrial dysfunction has
been proven to occur in vivo in patients with FA. Phosphorus magnetic reso-
nance spectroscopy analysis of skeletal muscle and heart shows a reduced rate
of ATP synthesis (70). Finally, and most importantly, the same multiple iron–
sulfur protein enzyme dysfunctions found in ΔYFH1 yeast are found in affected
tissues from patients with FA (55).
1.9. Animal Models
The generation of a frataxin knockout mouse (71) has revealed that homozy-
gous knockout mice die as early as embryonic day 7. To date, viable mouse
models have been obtained through a conditional gene-targeting approach. A
heart and striated muscle frataxin-deficient line and a line with more general-
ized, including neural, frataxin deficiency have been generated (72). These
mice reproduce important progressive pathophysiological and biochemical fea-
tures of the human disease: cardiac hypertrophy without skeletal muscle
involvement in the heart and striated muscle frataxin-deficient line, large sen-
sory neuron dysfunction without alteration of the small sensory and motor neu-
rons in the more generalized frataxin-deficient line, and deficient activities of
complexes I to III of the respiratory chain and of the aconitases in both lines.
Time-dependent intramitochondrial iron accumulation occurs in the heart of
the heart and striated muscle frataxin-deficient line. These animals provide an
important resource for pathophysiological studies and for testing of new treat-
ments. However, they still do not mimic the situation occurring in the human
disease, because conditional gene targeting leads to complete loss of frataxin
in some cells at a specific time in development, whereas FA is characterized by
partial frataxin deficiency in all cells and throughout life. An attempt to closely
mimic the human disease by inserting a GAA TRS into the mouse gene by
homologous recombination has succeeded in generating mice with a partial
reduction in frataxin, but this was not sufficient to induce a pathological phe-
notype (73). Recently, a mouse model recreating the neurological features of
the human disease was obtained using a tamoxifen-inducible Cre recombinase
under the control of a neuron-specific prion protein promoter (74). These mice
present a general locomotor deficit without a defect in muscle strength, begin-
ning at approx 10 wk, and, further, develop a clear progressive ataxia leading
to loss of spontaneous ambulation at approx 1 yr of age. In addition, elec-
tromyographic studies show a significant decrease in sensorimotor reflexes
after sciatic nerve stimulation, indicating that the large myelinated propriocep-
Methods to Diagnose Friedreich Ataxia 205

tive sensory neurons are functionally defective, causing sensory and spinocer-
ebellar ataxia, a distinctive pathological characteristic of FRDA.
1.10. Perspectives for Treatment
The findings presented in Subheading 1.8. paved the way for the develop-
ment of pharmacological treatments. Because of their ability to stimulate oxi-
dative phosphorylation and to act as potent free-radical scavengers, coenzyme
Q derivatives have been considered a promising treatment for FA. Coenzyme
Q10 and its short chain analog, idebenone, have both been clinically tested.
Despite a short-term (3 mo) study showing no effect on heart size or function
(75), several small open-label trials and a single double-blind, placebo-con-
trolled trial concluded that idebenone is able to reduce cardiac hypertrophy in
patients with FA (76–78). Only one study, however, showed some functional
improvement along with heart-size reduction (78). Studies in mouse models of
FA cardiomyopathy also confirmed a positive effect of idebenone on cardiac
size and function and on survival (79). In addition, a positive effect on cardiac
and calf muscle energy metabolism of a cocktail of 400 mg/d of coenzyme Q10
and 2100 IU/d of vitamin E could be demonstrated by 31P-magnetic resonance
spectroscopy in 10 FRDA patients (80). Conversely, thus far, it has not been
possible to document any significant effect of these drugs on neurological
symptoms. Although detection of a modest effect could not be possible with
the design limitations of the clinical trials that have been conducted, pharma-
cokinetic factors may also be involved, because one study indicates that
idebenone levels in the cerebrospinal fluid are very low when the drug is given
at the dosage used in most trials (81).
Newer pharmacological approaches, still at the experimental or preclinical
stages, include modified coenzyme Q derivatives that are targeted to mitochon-
dria (82); other antioxidants; glutathione peroxidase mimetics (83); and a very
promising group of new iron chelators that can reach the mitochondrial com-
partment and possibly act more like iron chaperones (frataxin-like) in remov-
ing iron than traditional chelators do.
Finally, approaches that are being explored in the laboratory and may hold
some promise include gene replacement therapy, protein replacement, and sub-
stances that are able to boost frataxin gene expression, either through a direct
effect or by interfering with the structure adopted by the GAA expansion.
1.11. Molecular Methods for Diagnosing FA
The diagnostic molecular test for FA is aimed to detect the unstable
hyperexpansion of the GAA triplet repeat in the first intron of the FRDA gene,
that is found in 98% of FA chromosomes. Normal alleles contain between 6
and 36 GAA triplets. In whites, two groups of normal alleles are found: short
206 Pandolfo

normal (SN) alleles of less than 12 repeats and long normal (LN) alleles of
more than 12 triplets. SN alleles are present on approx 80% of the chromo-
somes, most contain nine triplets. LN alleles have a broad distribution, with a
median of approx 16 to 18 triplets. Stable LN alleles with more than 27 triplets
are usually interrupted by GAGGAA or GAAGGA hexanucleotide units,
whereas uninterrupted alleles with 34 or more triplets can hyperexpand and
should be considered “premutation” alleles. Alleles found in individuals with
FA are called expanded (E) and have 66 to more than 1500 triplets. E alleles
show meiotic and mitotic instability. Occasionally, alleles in the E range are
stable and nonpathogenic. These are usually less than 150 triplets in size and
contain variant sequences, e.g., GAAGGA repeats. As detailed in Subheading
3.3., sequencing of alleles in this size range, as well as some very long LN
alleles, may be indicated in particular circumstances.
Polymerase chain reaction (PCR) or Southern blot can be used to detect the
expansion (Fig. 2). PCR requires only a small amount of DNA, but high-qual-
ity DNA is extremely important. Ambiguous results, particularly in heterozy-
gote detection, can be resolved by subsequent hybridization of PCR products
with an oligonucleotide probe containing a GAA or CTT repeat. Southern blot
requires more DNA and is less accurate for determining the number of repeats;
however, it has full sensitivity in detecting E alleles at the heterozygous state.

2. Materials
1. Agarose and DNA sequencing gel equipment.
2. Thermocycler for PCR.
3. Oligonucleotide primers.
4. rTth DNA polymerase.
5. dNTP mix, 2 mM each.
6. 10X PCR buffer.
7. 32P-ATP for end labeling of oligonucleotides.

8. 32P end-labeling kit for oligonucleotides.

9. Restriction enzymes.
10. 32P-dCTP for probe labeling.

11. DNA probe-labeling kit.

12. HybondN+ membranes.
13. Whatman filter paper no. 1.
14. 10X saline sodium citrate (SSC): 1.5 M sodium chloride and 0.15 M sodium citrate.
15. 1% sodium dodecyl sulfate.
16. Film, intensifying screens, and cassettes for autoradiography.
17. Dimethylsulfoxide.
18. DNA sequencing kit, including dNTPs, ddNTPs, DNA polymerase, and buffer;
for manual or automated sequencing.
Methods to Diagnose Friedreich Ataxia 207

Fig. 2. (A) PCR analysis of the GAA triplet repeat in the frataxin gene. The two lanes
on the extreme right correspond to normal individuals, all other lanes to Patients with
FA. Notice how several samples generate multiple bands, a sign of somatic instability of
the expanded repeats. (B) PCR analysis of FA carriers. Amplified fragments were blot-
ted and hybridized with a (CTT)10 oligonucleotide probe to enhance sensitivity.

3. Methods
3.1. PCR Analysis
When testing for FRDA carrier status, we routinely perform two different
PCR reactions. The first is a long-range PCR that generates fragments of 1350
+ 3n bp (n being the number of GAA triplets), using the primers 2500F (40)
and 104FGAA (8). This reaction is performed in a final volume of 50 μL, using
200 ng of genomic DNA, 20 pmoles of each primer, a final concentration of
each dNTP of 0.2 mM, 1 U of rTth polymerase, and 5 μL of 10X buffer (as
provided by the polymerase manufacturer). Temperature cycling is: 94°C for 1 h;
followed by 10 cycles of 15 min at 94°C and 3.5 h at 67°C; then by 20 cycles of
15 min at 94°C, 30 min at 66°C, and 3 h at 68°C, with a 20 min increase at each
cycle. In our experience, these PCR conditions are optimal for the detection of
208 Pandolfo

expanded repeats, both in the homozygous and heterozygous state (see Note 1).
The second reaction is optimal for the detection and sizing of repeats in the
normal range. It generates fragments of 451 + 3n bp (n = number of GAA
triplets) using the GAA-F/GAA-R primers (as described in ref. 40). Analysis
of GAA-F/GAA-R PCR products on 2% agarose gels clearly resolves SN from
LN alleles. To maximize sensitivity, we routinely transfer the amplified frag-
ments obtained by 2500F/104FGAA and by GAAF/GAAR PCR to a nylon
membrane (Hybond N+), and hybridize them with an 32P end-labeled (CTT)10
oligonucleotide. Hybridization is for 3 h at 42°C, followed by two 5 h washes
at room temperature, first with 2X SSC, then with 0.1X SSC.
3.2. Southern Blot Analysis
The Southern blot method (44) involves digestion of genomic DNA with the
BsiHKAI enzyme, which yields a 2.4-kb target DNA fragment (see Note 2).
Ten micrograms of genomic DNA are digested by BsiHKAI (New England
Biolabs), electrophoresis is performed in 0.9% agarose gel, the gels are blotted
on HybondN+ membranes (Amersham), and the samples are hybridized with a
32P-radiolabeled 463-bp genomic fragment containing exon 1 of the frataxin

gene. This fragment can be obtained by PCR amplification from genomic DNA
using the forward primer, CAAGTTCCTCCTGTTTAG, and the reverse
primer, CCGCGGCTGTTCCCGG. Blots are washed in 0.2X SSC and 0.1%
sodium dodecyl sulfate twice at room temperature and twice at 60°C, and ex-
posed for autoradiography at –80°C with an intensifying screen.
3.3. Sequencing of the Frataxin Intronic Repeat
Sequencing of the frataxin intronic repeat may be useful whenever it is
important to differentiate small pathogenic E alleles from very long, nonpatho-
genic variant repeats or potentially unstable from stable LN alleles (see Note
3). Most cases involve diagnosis of carrier status; occasionally, for the small E
alleles, diagnosis of FA may be involved. Pathogenic alleles contain uninter-
rupted stretches of more than 66 GAA triplets, unstable LN alleles have unin-
terrupted stretches of more than 34 GAA triplets.
GAA-F/GAA-R amplification products are purified from NuSieve gels using
the QIAquick Gel Extraction Kit (Qiagen), and directly sequenced using the
Sequenase PCR Product Sequencing Kit (USB). Because of the presence of a
poly-A stretch preceding the GAA repeat, which interferes with the sequenc-
ing reaction, samples are sequenced on the opposite (CTT) strand, using the
GAA-R primer.
3.4. Detection of Frataxin Point Mutations
Frataxin point mutations should be searched in ataxic individuals who are
heterozygous for an E and a normal allele at the GAA repeat (Fig. 2). No patient
Methods to Diagnose Friedreich Ataxia 209

with point mutations in both frataxin alleles has been found thus far, probably
because the complete or quasi-complete loss of frataxin function that would fol-
low is incompatible with life, as indicated by the knockout mouse model (71).
No mutation in the frataxin coding sequence could be identified in up to
40% of heterozygous patients with a GAA expansion in some series (48). Some
of these cases may be bona fide FA cases and have mutations deep into introns
or in regulatory sequences. Some, however, may have a different disease and
carry a GAA expansion by chance, given its high frequency (1 in 90 people) in
whites.
Carrier testing by point mutation analysis is currently limited to family mem-
bers of individuals with known point mutations. The frequency of frataxin point
mutations is approx 1 in 40 GAA expansions (48), thus, exclusion of the
expansion leaves a 1 in 4000 risk of being a carrier. This risk may vary in
different populations, for example, it is close to 0 in French Canadians, because
all FRDA patients with this ancestry have two expanded GAA repeats, and
higher in individuals from the Naples, Italy region, where the I154F mutation
is relatively frequent (40,48). Testing for a locally prevalent point mutation
may, in this case, be added to expansion analysis when determining carrier
status.
The following intronic primers are used to amplify the five frataxin exons
from genomic DNA (50–100 ng) (Note 4 [40,48]):
Exon 1 (240 bp): forward, AGCACCCAGCGCTGGAGG; reverse, CCG
CGGCTGTTCCCGG
Exon 2 (168 bp): forward, AGTAACGTACTTCTTAACTTTGGC; reverse,
AGAGGAAGATACCTATCACGTG
Exon 3 (227 bp): forward, AAAATGGAAGCATTTGGTAATCA; reverse,
AGTGAACTAAAATTCTTAGAGGG
Exon 4 (250 bp): forward, AAGCAATGATGACAAAGTGCTAAC; reverse,
TGGTCCACAATGTCACATTTCGG
Exon 5a (223 bp): forward, CTGAAGGGCTGTGCTGTGGA; reverse,
TGTCCTTACAAACGGGGCT
Amplifications for exons 2, 3, 4, and 5a consist of 30 cycles of: 1 min at
94°C, 1 min at 55°C, and 1 min at 72°C. To amplify the highly GC-rich exon 1,
the annealing temperature is raised to 68°C and 10% dimethylsulfoxide is
added to the reaction.
Amplified fragments are gel purified and directly sequenced on both strands
using the same forward and reverse primers.
Some mutations can be confirmed by restriction enzyme-based assays (48) .
Mutations affecting the ATG initiation codon and the H183 codon disrupt an
NlaIII restriction site (CATG/). D122Y and the L156P changes create new
restriction sites for RsaI (GT/AC) and for HaeIII (GG/CC), respectively.
158delC and 158insC mutations in exon 1 are resolved on sequencing gels of
210 Pandolfo

TaqI digestion products of exon 1 PCR fragments, yielding 54- and 56-bp
labeled fragments, respectively (48). Other mutations can be detected using
allele-specific oligonucleotide hybridization or allele specific amplification
(48) (Note 5).

4. Notes
1. PCR detection of GAA expansions is fast, sensitive, effective, and requires little
genomic DNA. We used this method in approx 800 molecular tests for FA or for
carrier status. One possible source of error when interpreting the results of a PCR
test comes from the observation that some individuals seem to be carriers of a
large expansion along with either a small and a large normal allele, or an allele in
the normal range and a small expansion (up to 120–150 triplets). In some cases,
several apparently fully expanded bands are visible, particularly when the gel is
overloaded. These larger bands represent heteroduplex molecules formed during
the PCR coamplification of repeats of different length. This phenomenon must
be taken into account when performing the molecular test to detect FRDA carri-
ers to avoid false-positive results. We recommend always performing the two
PCR reactions when testing for the FRDA GAA expansion, and to add Southern
blot analysis of genomic DNA if any uncertainty is left by the PCR results.
2. Southern blot analysis is used by many diagnostic labs because it allows a clear,
usually unquestionable detection of expanded repeats in affected subjects as well
as in heterozygous carriers. Disadvantages are mainly related to the need for
larger amounts of genomic DNA, and the time consuming and more complex
protocol, particularly at a time when genomic Southern blotting is performed less
frequently and technical personnel may not be familiar with this technique.
Another disadvantage is the difficulty of accurately sizing expanded bands, par-
ticularly when they are close to the normal range.
3. Sequencing the expanded repeat is technically challenging. The best results are
obtained by sequencing the CTT strand, in which DNA polymerase slippages are
less likely to occur. The occurrence of interruptions in the GAA repeated
sequence, such as GAAGGA, GGGA, GAAA, and similar variants, is particu-
larly important to distinguish shorter pathogenic repeats, mostly or entirely com-
posed of uninterrupted GAA, from similar-size nonpathogenic repeats, mostly
composed of variant repeats, e.g., GAAGGA hexanucleotides. Fortunately, such
variant sequences are less likely to cause DNA polymerase slippages, and, there-
fore, easier to sequence.
4. The sequencing of frataxin exons and the neighboring intronic sequence offers
no special difficulty except for exon 1, which is highly GC rich. Some laborato-
ries perform preliminary analyses to select exons to sequence, such as single-
strand conformation polymorphism or denaturing high-performance liquid
chromatography. In our experience, given the small number of fragments to ana-
lyze and the limited number of tests to perform for this rare disorder, there is no
clear advantage compared with directly sequencing all fragments, which is what
we routinely do. In addition, single-strand conformation polymorphism and
Methods to Diagnose Friedreich Ataxia 211

denaturing high-performance liquid chromatography are less sensitive for the GC-
rich exon 1, therefore, this exon must be sequenced anyway.
5. There have been reported cases of genomic deletions involving the frataxin gene.
Affected subjects carrying this type of mutation are always compound heterozy-
gotes for the GAA expanded repeat. Separate PCR amplification of each exon in
these cases may give a normal result, because the frataxin coding sequence is
complete and normal on the chromosome with the GAA expansion. If such a case
is suspected, as in a clinically affected individual who is heterozygous for the
GAA expanded repeat and has a normal frataxin coding sequence, either quanti-
tative PCR or genomic Southern blot analysis should be performed on each exon.
This is usually done in specialized research laboratories.

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Heart Defects in Alagille Syndrome 217

13
The Cardiovascular Manifestations of Alagille Syndrome
and JAG1 Mutations

Elizabeth Goldmuntz, Elizabeth Moore, and Nancy B. Spinner

Summary
Alagille syndrome is an autosomal-dominant disorder characterized by hepatic, cardiac,
ocular, skeletal, and facial abnormalities. The disease gene, Jagged1 (JAG1), was identified by
molecular analyses of chromosomal alterations involving chromosome 20p. Total gene dele-
tions (3–7%) and intragenic mutations (70%) of JAG1 have been identified in Alagille patients.
Identifying JAG1 mutations is challenging, given its size of 26 exons. Methods to identify both
whole-gene deletions and intragenic mutations of JAG1 are described in detail, including fluo-
rescence in situ hybridization (FISH), conformation-sensitive gel electrophoresis (CSGE), and
complementary DNA (cDNA) sequencing.
Key Words: Alagille syndrome; congenital heart disease; JAG1; fluorescence in situ
hybridization; mutation detection; conformation-sensitive gel electrophoresis; peripheral pul-
monary stenosis; tetralogy of Fallot.

1. Introduction
Alagille, or arteriohepatic dysplasia, syndrome is a multisystem, autosomal-
dominant disorder independently described by two investigators more than 30
yr ago (1,2). The original clinical diagnostic criteria required the demonstra-
tion of bile duct paucity on liver biopsy in addition to three of the five follow-
ing characteristics: cholestatic liver disease, cardiac anomalies, skeletal
anomalies, ocular abnormalities, and characteristic facies. Typical skeletal
anomalies included butterfly vertebrae, and typical eye anomalies included
posterior embryotoxon. Renal anomalies were also commonly reported.
Approximately 5 to 10% of patients were found to have abnormal karyotypes
involving the short arm of chromosome 20, thereby defining a probable dis-
ease locus. Additional molecular analyses identified the smallest region of
overlap, and candidate gene analyses identified mutations in affected patients

From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

217
218 Goldmuntz et al.

in a gene mapping to the disease locus, called JAG1 (3,4). Therefore, the dis-
ease gene for Alagille syndrome is now known to be JAG1.
1.1. Cardiovascular Manifestations of Alagille Syndrome
As noted, Alagille syndrome is characterized in part by cardiac anomalies.
Earlier reports had demonstrated that the right side of the heart, including the
pulmonary arterial bed, was most commonly affected. We recently reviewed a
large cohort of patients with Alagille syndrome who were tested for JAG1
mutations in our center to better define the cardiovascular phenotype of this
disorder and to identify any genotype–phenotype correlations (5). This study
demonstrated that 93% of patients with Alagille syndrome had some cardio-
vascular anomaly, ranging from a murmur consistent with peripheral pulmo-
nary stenosis (PPS; mild changes) to tetralogy of Fallot with pulmonary atresia
(severe defects). Overall, 76% of the cohort had PPS; 35% of the cohort had
PPS in isolation, whereas the rest (41%) had PPS in conjunction with other
cardiac anomalies. Right-sided cardiac defects were most common (55% of
entire cohort), but left-sided cardiac abnormalities were also seen (7%). Mul-
tiple other anomalies (14%), including septal defects (10%), were identified as
well. In this study, there was no correlation between the type and location of
JAG1 mutation and cardiac phenotype.
1.2. JAG1 Mutations in Congenital Heart Disease
Because a cardiovascular phenotype seems to be so highly penetrant in
Alagille syndrome, many questioned whether patients with cardiac defects in
the absence of hepatic disease could have JAG1 mutations. Inspection of pedi-
grees and individuals harboring a JAG1 mutation demonstrated marked clini-
cal variability. In these families, some individuals carrying a JAG1 mutation
had very mild features or a “microform” of Alagille syndrome, whereas others
with the same mutation manifested all of the features of Alagille syndrome
(3,6). Moreover, some patients predominantly manifested a cardiac phenotype
with no overt hepatic involvement.
Subsequent reports highlight the potential contribution of JAG1 mutations
to the molecular genetic basis of congenital heart disease (7–9). Krantz and
colleagues (7) identified two patients with congenital heart disease and no
apparent liver disease who were found to have JAG1 mutations. The first
patient had tetralogy of Fallot and butterfly vertebrae, and, after karyotyping,
was found to have a 20p12 deletion encompassing JAG1. The second patient
had branch pulmonary artery stenosis, and, on closer inspection, typical facial
features of Alagille syndrome, posterior embryotoxon, and mild hepatic alter-
ations. Her family history was significant for four generations of presumably
Heart Defects in Alagille Syndrome 219

affected individuals. The mother (with similar features of the proband) and the
proband were found to share a protein truncating mutation. More recently,
Eldadah and colleagues (8) reported an extensive pedigree with apparently iso-
lated heart disease, including tetralogy of Fallot and PPS. The affected mem-
bers of this family did not have hepatic involvement, and were found to have a
unique missense mutation. Finally, Le Caignec and colleagues (9) reported a
family with eight affected members with typical types of cardiac defects seen
in Alagille syndrome (posterior embryotoxon and deafness); the affected mem-
bers of this family had a missense mutation of JAG1 but no hepatic manifesta-
tions. These reports suggest that JAG1 mutations are etiological for a subset of
patients with congenital heart disease, and should be considered, particularly
in cases of familial right-sided defects. Studies are ongoing in our laboratory to
identify the cardiac population at risk for JAG1 mutations in the absence of
hepatic or familial disease.
1.3. Additional Vascular Manifestations of JAG1 Mutations
Additional extracardiac vascular anomalies have been reported in the litera-
ture in patients with Alagille syndrome, including cases with abdominal aortic
coarctation, renal and visceral arterial stenoses, intracranial arterial anomalies,
and Moyamoya. A recent retrospective analysis found that 9% (25/268) of a
large cohort with Alagille syndrome had either extracardiac vascular anoma-
lies or events (10). Vascular accidents accounted for 34% of the mortality in
this cohort, exceeding the reported mortality from either congenital heart (21%)
or hepatic (10%) disease in this series. The findings of extracardiac vascular
anomalies are consistent with the embryonic pattern of expression of JAG1 in
mice and humans (11,12). Thus, additional extracardiac vascular anomalies
are common in this disorder and present a significant risk for mortality and
morbidity.
1.4. JAG1 and Mutations in Alagille Syndrome
JAG1 consists of 26 exons and encodes the Jagged1 protein, a cell-surface
protein that functions as one of five ligands for the four human Notch recep-
tors. The Notch signaling pathway has been implicated in several human dis-
eases (13) and is critical to developmental cell-fate decisions (14). The Jagged1
protein has a single-pass transmembrane domain, a small intracellular domain,
and a larger extracellular domain that consists of a signal peptide; a highly
conserved region, known as the DSL region (DSL stands for Delta, Serrate,
and Lag-2, the name of the Notch ligands in Drosophila and Caenorhabditis
elegans); 16 epidermal growth factor-like repeats; and another conserved
region, called the cysteine-rich region.
220 Goldmuntz et al.

To date, more than 300 Alagille syndrome patients have been screened for
JAG1 mutations. Approximately 60 to 70% of the mutations seem to arise de
novo, whereas the rest are transmitted in a family. Although published reports
find a JAG1 mutation in 65 to 70% of those patients screened, recent studies in
our laboratory now identify a mutation in more than 90% of patients with a
definitive clinical diagnosis of Alagille syndrome (15–17). The mutations in
JAG1 include total gene deletions (3–7% of mutations) and intragenic muta-
tions. The intragenic mutations are protein truncating (frameshift and nonsense
mutations account for ~70% of mutations), splicing (~10%), and missense
(~10%) mutations. Thus, Alagille syndrome seems to result from
haploinsufficiency of Jagged1 protein. The mutations are distributed across
the entire gene, with no significant hot spots. Therefore, screening this large
gene presents a technical challenge.
1.5. Testing for JAG1 Mutations
Because of the enormous clinical variability of patients with JAG1 muta-
tions, identifying the cardiac patient with a JAG1 mutation or a microform of
Alagille syndrome is important to offer appropriate testing and genetic coun-
seling to families. Although additional research to help identify the at-risk car-
diac patient is still underway, currently, suspicion for a JAG1 mutation should
be raised when a family history of right-sided cardiac defects or transient he-
patic dysfunction is reported, even if the patient at hand does not meet the
complete clinical criteria for Alagille syndrome. Clinical genetic testing for
JAG1 mutations by sequencing the entire coding region is now available. The
techniques by which whole gene deletions (FISH) or coding mutations (CSGE)
are identified in our laboratory are described in detail in this chapter. JAG1 is
composed of 26 exons that occupy 35,000 kb of genomic DNA on chromo-
some 20 in band 20p12. The total gene deletions can be detected by cytoge-
netic or molecular cytogenetic techniques (FISH), and, in practice, FISH using
a bacterial artificial chromosome (BAC) probe that contains JAG1 is a straight-
forward assay for deletions. A second probe is used that serves as a control to
positively identify chromosome 20, and the control probe can be fluorescently
labeled in one color, with the JAG1-containing probe labeled in a second color
to facilitate screening (Fig. 1).
The majority of Alagille syndrome-associated JAG1 mutations are intragenic
mutations, and these can be identified by analyzing the sequence of amplified
regions of JAG1 for sequence variation. It is possible to sequence the 26 exons
of JAG1 to look for mutations, but this approach is quite expensive as a first
pass. In our laboratory, we use the technique of CSGE to provide a relatively
rapid and sensitive screening technique to identify sequence variations. CSGE
is a method for screening heteroduplex DNA molecules. The method uses an
Heart Defects in Alagille Syndrome 221

Fig. 1. Metaphase spread showing FISH using a probe containing the JAG1 gene
(that maps to the short arm of chromosome 20 at band 20p12), and a control probe that
maps to the bottom of the long arm of chromosome 20. The chromosome on the right
is normal, with one JAG1 signal and one control signal, whereas the chromosome on
the left has the control probe, but not the JAG1-containing BAC.

acrylamide gel matrix that includes 1,4 bis (acrolyl) piperazine (BAP) to
crosslink, with ethylene glycol and formamide as mildly denaturing solvents.
This environment enhances the differences in mobility shown by sequence
mismatches in DNA heteroduplexes, so that variations as small as single nucle-
otide polymorphisms can be detected (18). We screen a group of 25 patients at
one time, and analyze the gene exon by exon. DNA from any patient whose
DNA demonstrates a gel shift on electrophoresis is then sequenced for that
exon to confirm the sequence (Fig. 2). CSGE scanning provides a powerful,
cost-efficient method to scan genes with high sensitivity and specificity. How-
ever, we have found that CSGE identifies mutations in approx 70% of patients.
As a follow-up to CSGE scanning, patients with a definitive diagnosis of
Alagille syndrome, in whom no mutation is identified by CSGE, are targeted
for further analysis, which is either direct sequencing of the 26 exons from
genomic DNA, or sequencing of the 5.5-kb Jagged1 messenger RNA, which
has been made into more stable cDNA.
222 Goldmuntz et al.

Fig. 2. Example of band with aberrant mobility on CSGE gel. Multiplex analysis of
JAG1 exons 13, 14, 15, and 21 (from top to bottom). First lane contains molecular
weight markers, followed by PCR samples from five patients with Alagille syndrome.
Note the aberrant band in exon 14 (*) in the fourth patient.

2. Materials
2.1. Fluorescence In Situ Hybridization
1. BACs are purchased from Children’s Hospital Oakland Research Center. RP11-
829A12 is an 183,891-bp BAC that contains the JAG1 gene. The control BAC,
RP11-15M15, maps to 20q.
2. Luria Bertani (LB) broth: NaCl (10 g), tryptone (10 g), yeast extract (5 g), dH2O
(1 L).
Adjust pH to 7.0. Autoclave the LB broth and allow it to cool to room temp-
erature. Using good aseptic technique, add 20 μg/mL of chloramphenicol
(see Note 1).
3. LB agar: NaCl (10 g), tryptone (10 g), yeast extract (5 g), agar (10 g), dH2O (1 L).
Adjust pH to 7.0 Autoclave the LB Agar and allow it to cool to 45°C in a water
bath. Using good aseptic technique, add 20 μg/mL of chloramphenicol. Pour 20 to
Heart Defects in Alagille Syndrome 223

25 mL of agar into 60-mm plates and allow the agar to completely solidify (see
Notes 1 and 2).
4. Fix solution: methanol (75 mL), acetic acid (25 mL), dH2O (250 mL), 1–2 trays of
ice cubes.
5. 2X sodium saline citrate (SSC) (0.3 M NaCl, 0.003 M Na Citrate, pH 7.0) and
0.05% Tween-20: 2X SSC (50 mL), Tween-20 (25 mL).
6. 0.4% SSC: 2X SSC (200 mL), sterile dH2O (48.8 mL).

2.2. Mutation Detection

2.2.1. Polymerase Chain Reaction
1. 2 mM dNTP mix: 100 mM dATP (10 mL), 100 mM dCTP (10 mL), 100 mM dTTP
(10 mL), 100 mM dGTP (10 mL), sterile dH2O (460 mL).
2.2.2. Conformation-Sensitive Gel Electrophoresis
1. 40% Acryl:BAP: Acrylamide 40% solution (500 mL), BAP (2.02 g), sterile dH2O
(5 mL).
Stir for 30 to 40 min, filter through a 0.2-μm nylon filter, and store at 4°C in the
dark. Make fresh monthly (see Note 3).
2. 20X TTE: trizma base (108 g), taurine (36 g), EDTA (2 g).
Dissolve in 200 mL of dH2O by stirring on low heat. Adjust the volume to 500 mL
and filter through a 0.22-μm nylon filter. Store at room temperature.
3. Loading dye: 30% Glycerol, 0.25% Bromophenol blue, 0.25% Xylene Cyanol FF,
in 0.5X TTE buffer.
4. Staining buffer: 0.5X TTE, 0.1 mL/mL Ethidium bromide (10 mg/mL) (see Note 4).
5. 15% gel solution: 40% Acryl:BAP (75 mL), 20X TTE buffer (5 mL), deionized
formamide (30 mL), ethylene glycol (20 mL), sterile dH2O (68 mL), TEMED
(114 mL), 10% ammonium persulfate (APS) (2 mL) (see Note 5).
2.2.3. cDNA Sequencing
1. Complete media: RPMI-1640 (389 mL), fetal bovine serum (100 mL), L-glutamine
(200 mM) (10 mL), penicillin/streptomycin (100X) (1 mL) (see Note 6).
2. Cycloheximide media: Cycloheximide (50 mg), complete media (50 mL) (see
Note 7).
3. Diethylpyrocarbonate (DEPC)-treated water: water is treated with 0.1% v/v DEPC
and autoclaved to inactivate ribonuclease (RNase) in solution.

3. Methods
3.1. Fluorescence In Situ Hybridization
1. Streak LB agar plate (containing 20 μg/mL of chloramphenicol) with the
Escherichia coli-containing BAC RPII-829A12 (this BAC contains the JAG1
gene). Incubate overnight at 37°C.
224 Goldmuntz et al.

2. A single colony from the plate is used to inoculate 10 mL of LB broth containing

20 μg/mL of chloramphenicol. Incubate at 37°C overnight.
3. Take 1 mL of the overnight broth and inoculate 100 mL of LB broth containing 20
μg/mL of chloramphenicol. Incubate at 37°C overnight. The remaining 9 mL can
be frozen in 30% glycerol at –80°C for future use.
4. Centrifuge at 5858g for 15 min at 4°C.
5. Isolate DNA (Purgene DNA Isolation Kit, Gentra).
a. Add 3 mL of cell lysis solution and mix well.
b. Incubate at 80°C until cells are lysed (see Note 8).
c. Cool the sample to room temperature.
d. Add 2 mL of protein precipitation solution and vortex. Incubate on ice for
5 min and vortex until white precipitate forms.
e. Centrifuge at 805g for 10 min.
f. Pour supernatant into a clean 15-mL tube containing 3 mL of 100% isopro-
panol.
g. Gently rock the tube back and forth until you see strands of white DNA.
h. Using a sterile glass rod, transfer the DNA to a clean tube.
i. Add 3 mL of 70% ethanol.
j. Centrifuge at 805g for 1 min.
k. Drain for 30 min. Make sure all ethanol has evaporated.
l. Add 500 μL of DNA hydration solution.
m. Incubate overnight at room temperature. Add sterile dH2O if the DNA it does
not go into solution well (see Note 9).
6. Determine the DNA concentration by running on a 1.5% agarose gel with a quan-
titative DNA marker. Polymerase chain reaction (PCR) can be performed to con-
firm that Jagged 1 is present in the BAC DNA (see Subheading 2.2.1.).
7. Probes can be fluorescently labeled with a commercially available Nick Transla-
tion Kit (32-801300; Abbott).
8. Place clean slides into fix solution for 1 min.
9. Use a Pasteur pipet to mix the cell pellet.
10. Remove slide from fix solution and allow slides to drain briefly at a 45° angle.
11. Hold slide over steam from a hot water bath for 3 s.
12. Hold pipet parallel to slide and place six drops from the cell pellet evenly along
the slide.
13. Place slides on a slide warmer at 45°C to evaporate any excess fluid.
14. After most of fluid has evaporated, hold the slide over steam for 3 s, and then
either incubate the slide overnight at room temperature or incubate the slide in an
oven at 90°C for 1 h.
15. Place slides on the slide warmer at 45°C.
16. Add 10 μL of probe (RPII-829A12, JAG1) and 10 μL of a control (RPII-15M15,
maps to 20q) in several drops. Probes should be labeled with different fluoro-
chromes.
17. Place a coverslip (22 × 40 mm) on the slide, without creating air bubbles between
the slide and the coverslip. If there are air bubbles, press gently on the coverslip.
18. Incubate slides on a hot plate at 75°C for 3 min.
Heart Defects in Alagille Syndrome 225

19. Seal the coverslip to the slide by generously adding rubber cement around the
edges of coverslip.
20. Incubate overnight in a humidified chamber at 37°C.
21. Remove slides from the chamber and remove rubber cement and coverslip (do not
let slides dry out).
22. Incubate slides in 0.4% SSC for 2 min at 73°C.
23. Wash slide in 2X SSC/0.05% Tween at room temperature for 30 s to 1 min.
24. Remove slide, and allow it to drain briefly (do not allow slide to dry).
25. Add 10 μL of DAPI (Abbott), a counterstain that permits visualization of the chro-
mosome, in several drops along the center of the slide.
26. Place a coverslip (24 × 50 mm) on the slide without creating air bubbles. Press
gently on the slide if there are any air bubbles.
27. Visualize using a fluorescent microscope.

3.2. Mutation Detection

3.2.1. Polymerase Chain Reaction
1. Table 1 has a list of primers, MgCl2 concentrations, and PCR cycles for screening
all 26 exons of the JAG1 gene.
2. Place 5 μL of patient DNA [25 ng/μL] into a sterile 0.5-μL PCR tube.
3. Add the following to the PCR tube containing the patient DNA.
PCR reaction:
a. 11.2 μL-X sterile dH2O.
b. 2.5 μL 10X buffer.
c. X (1 μL or 1.5 μL) 25 mM MgCl2 (Table 1).
d. 2.5 μL dNTP mix.
e. 2.5 μL Dimethylsulfoxide.
f. 0.5 μL 20 μM Forward primer (Table 1).
g. 0.5 μL 20 μM Reverse primer (Table 1).
h. 0.3 μL Amplitaq gold.
4. Vortex the tube and centrifuge briefly.
5. Place the samples into a thermocycler, programmed according to Table 1.
6. To determine whether amplification has been successful, DNA bands can be
visualized by running the samples on a 1.5% agarose gel stained with ethidium
bromide and illuminated with UV light (see Note 10).
7. PCR products can be used for CSGE, or purified for sequencing.
3.2.2. Confirmation-Sensitive Gel Electrophoresis
1. Heating PCR products at 98°C for 5 min and then at 68°C for 30 min creates
heteroduplexes.
2. Assemble plates as follows:
a. Wash glass plates with hot tap water, rinse with dH2O and ethanol, and dry
with lint-free tissue paper.
b. Gel slick (see Note 11) should be added occasionally to large plates to prevent
the gel from sticking during disassembly. Add gel slick, wipe it evenly across
the plate, and let dry. Once dry, buff the gel slick off.
 Table 1 Primer Pairs for CSGE 22
Exon Product Annealing
6
Exon Forward primer sequence Reverse primer sequence size (bp) size (bp) [MgCl2] temperature

Jag1 exon 01 5'CAG CGG CGA CGG CAG CAC C 3' 5'AGA GGA CGG CTG GGA GGG A 3' 81 204 1.5 mM 62°C/30 s
Jag1 exon 02 5'CGC CAC CTC TAT ACT CGA AG 3' 5'CCA GGC GCG GGT GTG AG 3' 306 469 1 mM 50°C/1 min
Jag1 exon 03 5'GTG GGG TAT TCT GGG AGG 3' 5'GCA AGA GGT GGC AGA AAT 3' 51 254 1 mM 50°C/1 min
Jag1 exon 04 5'GGC TGC AAT GTG AAT ATT A 3' 5'TCC CAC CCC ACC TGA GAT A 3' 255 452 1 mM 50°C/1 min
Jag1 exon 05 5'GGA ATT TGC AGA CTT TAA TGC AA 3' 5'CAC AAT AAA GTC AGT TCC TC 3' 61 229 1 mM 50°C/1 min
Jag1 exon 06 5'ATG AGC CTT GGG AGT CTA C 3' 5'AAA CCC ACA CAG CAT TCA A 3' 131 388 1.5 mM 50°C/1 min
Jag1 exon 07 5'GGC TAG AAA CAT GGT GGG T 3' 5'ATC TTT GGA AGC TAT TTT C 3' 120 295 1.5 mM 50°C/1 min
Jag1 exon 08 5'GGA GGT AAC GGT GTG CAG GCA TC 3' 5'ACC TCT CCC CAG CGT GGT ATC TT 3' 114 236 1 mM 60°C/20 sa
Jag1 exon 09 5'GGA TCT AAT TGT CAG ATG GAT 3' 5'CCA CAC GCT CGT CTT CTG 3' 115 256 1 mM 50°C/1 min
Jag1 exon 10 5'TTC CAA GGT GGG GGA GAT 3' 5'CCT GAC CAC TCC CTC TCA AA 3' 114 300 1.5 mM 55°C/1 min
Jag1 exon 11 5'CAC CCA GCG TAA TAA CCT T 3' 5'CTA GTG TCG CAC AAA TCT 3' 47 262 1.5 mM 50°C/1 min
Jag1 exon 12 5'TGA AGC CCT GTG TTT GTG GAA TAC 3' 5'GAA AAG TAA AGG GAA GCG GAG GAG 3' 174 354 1 mM 60°C/1 min
226

Jag1 exon 13 5'GTT TTA CTC TGA TCC CTC 3' 5'CAA GGG GCA GTG GTA GTA AGT 3' 151 273 1 mM 50°C/1 min
Jag1 exon 14 5'GAA TGC CGC ATC TGT GGG TG 3' 5'AGG CTG GGG AGC ACT GGT C 3' 165 263 1 mM 60°C/20 sa
Jag1 exon 15 5'AGG AGG GAG CCA TGA AAA CTG C 3' 5'CAA CAT GAC CCA TAC ATC CCA GAG 3' 114 250 1.5 mM 54°C/30 s
Jag1 exon 16 5'GCC TGT CGT GAA TGG TCC TGG A 3' 5'CCA CAG AAG ACA GAG GGA AG 3' 124 231 1 mM 55°C/1 min
Jag1 exon 17 5'GCT ATC TCT GGG ACC CTT 3' 5'CCA CGT GGG GCA TAA AGT T 3' 114 192 1 mM 50°C/1 min
Jag1 exon 18 5'CCT CCA GAC TGT TTC TGG ATA 3' 5'GCA AGT CCC CAA GGG TGT CA 3' 117 244 1 mM 50°C/1 min
Jag1 exon 19 5'GGC TAA GAC CGC TTT CCC TGT T 3' 5'ACG ATA GTG GAT GAG TGC TGG CTT 3' 28 128 1 mM 60°C/1 min
Jag1 exon 20 5'CAT GTG AGT GAT TGG CAG C 3' 5'CAG CTG GAG GAG AGA GAT C 3' 86 298 1 mM 55°C/1 min
Jag1 exon 21 5'CAT TGC CAC ACA CCA TCA GTC 3' 5'CGC TCA CCC CAG AAG ACC CAT 3' 114 209 1.5 mM 60°C/20 sa
Jag1 exon 22 5'CAA AGA ATT GAA CCC CGA TCC 3' 5'GCT GGC AGC TTA GCA GGC ATG 3' 110 250 1 mM 50°C/1 min Gol
Jag1 exon 23 5'ATG GCT GCC GCA GTT CA 3' 5'CAC CAT TCA AAA AAA AAA CAA AGG 3' 234 409 1 mM 50°C/1 mi dm
Jag1 exon 24 5'GCC TCA AAG AGA ACA TCT CAG 3' 5'AAC CGA ACT GCC TTG CCA TCG 3' 132 262 1 mM 55°C/1 min
unt
Jag1 exon 25 5'GCA GAC ACA GAT TGT CGA 3' 5'CCC TCG ACC TGA TGG CTT TA 3' 156 378 1.5 mM 56°C/30 s
z
Jag1 exon 26 5'TCT TGG AGA GTT AAT TGG TTT TGT GC 3' 5'GAC AGT TTA AAG AAC TAC AAG CCC TCA GA 3' 455 525 1 mM 50°C/1 min

Cycle: initital, 94°C/5 min; 36 cycles of (denature, 94°C/30 s; annealing, 50°C/1 min; and extension, 72°C/30 s); and hold, 72°C/10 min.
aCycle: Initital, 94°C/5 min; 36 cycles of (denature, 94°C/20 s; annealing, 60°C/20 s; and extension, 72°C/20 s); and hold, 72°C/3 min.

et
al.
Heart Defects in Alagille Syndrome 227

c. Place 1-mm spacers between the plates, flush on each side.

d. Place tape around the edges of the glass to prevent leaking. Clamps can also
be placed along the edges to help prevent leaking.
e. Add the 15% gel solution between the plates with a 25-mL pipet. Do not create
air bubbles. Tap lightly on the glass to remove any air bubbles (see Note 12).
f. Insert comb and add excess gel to the sides of the comb to prevent gel shrink-
age. Make sure comb is pushed all the way in and use a clamp to hold the
comb in place (see Note 13).
g. Let the gel polymerize for 2 h before use or for 30 min before wrapping for
overnight storage at 4°C. For overnight storage, place paper towels soaked
with dH2O along the comb and wrap with plastic wrap to keep the gel from
drying out.
h. Remove the tape from around the gel. Gently remove the comb from the gel
without damaging the wells.
3. Attach plates to gel apparatus and add running buffer (0.5X TTE).
4. Rinse wells with running buffer, using a 20-mL syringe.
5. Prerun gel at 40 W for 15 min.
6. Rinse wells again with running buffer (see Note 14).
7. Mix 2 μL of PCR product with 1 μL of loading buffer.
8. Quickly load samples, using gel-loading tips to prevent diffusion of samples into
the wells (see Note 15).
9. Run gel at 40 W for 6 to 8 h.
10. Detach the plates from apparatus and pry the plates apart, leaving the gel on the
smaller plate.
11. Pour staining buffer on the gel (still attached to the plate) and soak for 10 min.
Pour dH2O on the gel and let soak for 10 min. Drain gel.
12. Apply a piece of Whatman 3 paper to the gel and remove the gel from the plate.
Gel is now attached to paper.
13. Visualize the bands on the gel with a UV lamp (see Note 10). Take a photograph of the gel.
14. Purify PCR products from the samples with multiple bands and submit for
sequencing (see Note 16).

3.2.3. cDNA Sequencing

1. Split cells (lymphoblastoid cell line or fibroblast cell line) into two flasks. Add
fresh complete media until the volume reaches 20 to 25 mL.
2. Remove the complete media from one flask, with a pipet, being careful not to
remove any cells (see Note 17). Remove as much media as possible without dis-
turbing the cells. Add 25 mL of cycloheximide media. Do not do anything to the
second flask (it will be a negative control).
3. Incubate for 6 hours.
4. Centrifuge at 453g for 10 min.
5. Remove the supernatant and add 1 mL of TRIzol®. Mix well and transfer to
1.5-mL tubes.
228 Goldmuntz et al.

6. Freeze tubes at –80°C. To isolate RNA (see Note 18), thaw frozen samples at
room temperature for 5 min.
7. Add 200 μL of chloroform and shake tubes vigorously.
8. Incubate at room temperature for 2 to 3 min.
9. Centrifuge at 4°C for 15 min at 13,400g.
10. Transfer the colorless upper layer to a new tube and add 500 μL of isopropanol to
each tube. Incubate at room temperature for 10 min.
11. Centrifuge at 4°C for 10 min at 13,400g.
12. RNA should be in pellet form. Carefully remove supernatant. Add 1 mL of 75%
ethanol to tube. Use DEPC-treated water to dilute ethanol.
13. Vortex the sample.
14. Centrifuge at 4°C for 5 min at 5100g.
15. Carefully remove supernatant and allow the tubes to air-dry for 10 to 15 min.
Make sure that all ethanol has evaporated before proceeding to the next step.
16. Add 50 μL of DEPC-treated water to dissolve pellets.
17. Store RNA at –80°C.
18. RNA is reverse transcribed into cDNA using reverse transcription (RT)-PCR
(Invitrogen, Superscript First-Strand Synthesis System for RT-PCR).
19. PCR can be performed on the cDNA for sequencing.
20. Table 2 has a list of primers, MgCl2 concentrations, and PCR cycles for screen-
ing all five regions of the JAG1 cDNA.
21. Place 2 μL of cDNA into a sterile 0.5-μL PCR tube.
22. Add the following to the PCR tube containing cDNA.
PCR reaction:
a. 14.2 μL-X sterile dH2O.
b. 2.5 μL 10X buffer.
c. X (1 μL or 1.5 μL) 25 mM MgCl2 (Table 2).
d. 2.5 μL dNTP mix.
e. 2.5 μL Dimethylsulfoxide.
f. 0.5 μL 20 μM Forward primer (Table 2).
g. 0.5 μL 20 μM Reverse primer (Table 2).
h. 0.3 μL Amplitaq gold.
23. Place the samples into a thermocycler, programmed according to Table 2.
24. Bands can be visualized by running the samples on a 1.5% agarose gel stained
with ethidium bromide and illuminated with UV light.
25. PCR products should be purified and submitted for sequencing.

4. Notes
1. It is important to let the LB Broth or agar cool before adding the chloramphenicol.
2. Store LB Agar plates inverted at 4°C. Plates are inverted to prevent moisture
from accumulating on the agar surface.
3. Caution: acrylamide is a neurotoxin and BAP is irritating to the eyes and skin, so
handle with care.
4. Caution: ethidium bromide is a carcinogen.
 He
art

De
fec
ts

Table 2 in
PCR Primers for cDNA Screening Ala
gill
Annealing
e
Region Forward primer sequence Reverse primer sequence [MgCl2] temperature Exons per region Product size (bp)

A 5' CGC TCT TGA AAG GGC TTT TGA AAA GTG GTG 3' 5' CAT CCA GCC TTC CAT GCA A 3' 1 mM 50°C/1 min exons 1–3 and part of exon 4 800
B 5' CAC TTT GAG TAT CAG ATC CGC GTG A 3' 5' CGA TGT CCA GCT GAC AGA 3' 1.5 mM 58.8°C/1 min Part of exon 4 through exon 13 1200 Syn
C 5' CGG GAT TTG GTT AAT GGT TAT 3' 5' GGT ACC AGT TGT CTC CAT 3' 1.5 mM 55°C/1 min Part of exon 12-part of exon 18 1000 dro
D 5' GGA ACA ACC TGT AAC ATA GC 3' 5' GGC CAC ATG TAT TTC ATT GTT 3' 1.5 mM 55°C/1 min exon 18 –23 and part of exon 24 825 me
E 5' GAA TAT TCA ATC TAC ATC GCT T 3' 5' CTC AGA CTC GAG TAT GAC ACG A 3' 1 mM 52°C/30 sa part of exon 24 through exon 26 756

Cycle: initial, 94°C/5 min; 36 cycles of (denature, 94°C/30 s; annealing, 50°C/1 min; and extension, 72°C/30 s); and hold, 72°C/10 min.
aCycle: initial, 94°C/5 min; 36 cycles of (denature, 94°C/30 s; annealing, 52°C/30 s; and extension, 72°C/30 s); and hold, 72°C/10 min.
230 Goldmuntz et al.

5. Add TEMED and APS immediately before pouring the gel. Adding TEMED and
APS will cause the gel to polymerize. Do not add TEMED and APS before you
are ready to pour the gel.
6. Make complete media fresh weekly and store at 4°C. L-Glutamine degrades over
time.
7. Make cycloheximide media fresh for each use.
8. Solution will appear clear when cells are lysed. You may need to vortex the cells
a few times during incubation.
9. If the sample has a hazy appearance, do not dilute the sample. You can place
samples at –80°C overnight and centrifuge to clarify the solution.
10. Caution: UV light can be damaging to eyes and skin.
11. Gel slick is a glass-plate coating that prevents gels from adhering to electro-
phoresis plates.
12. Air bubbles make it difficult to visualize band shifts.
13. Comb must be clamped down to prevent them from shifting as the gel polymer-
izes. If the comb shifts, the wells will not form properly and the samples will not
run correctly.
14. It is critical that wells be clean so that the PCR products run into the gel at the
same time.
15. It is important that all samples enter the gel at the same time. Diffused samples
can appear band shifted.
16. PCR products from samples with blurry bands should also be purified and
sequenced. A blurry appearance of bands could be two bands very close together.
17. Lymphoblastoid cells will settle in the bottom of the flask.
18. Make sure to work in an area that is RNase free. Also make sure that the tubes
and pipets are RNase-free. If you are not careful, RNase can degrade your RNA.
Areas and equipment can be treated with RNase Away spray (Gentra) to remove
any RNase contamination.

References
1. Watson, G. H. and Miller, V. (1973) Arteriohepatic dysplasia: familial pulmonary
arterial stenosis with neonatal liver disease. Arch. Dis. Child. 48, 459–466.
2. Alagille, D., Odievre, M., Gautier, M., and Dommergues, J. P. (1975) Hepatic
ductular hypoplasia associated with characteristic facies, vertebral malformations,
retarded physical, mental, and sexual development, and cardiac murmur. J.
Pediatr. 86, 63–71.
3. Li, L., Krantz, I. D., Deng, Y., et al. (1997) Alagille syndrome is caused by muta-
tions in human Jagged1, which encodes a ligand for Notch1. Nat. Genet. 16, 243–
251.
4. Oda, T., Elkahloun, A. G., Pike, B. L., et al. (1997) Mutations in the human
Jagged1 gene are responsible for Alagille syndrome. Nat. Genet. 16, 235–242.
5. McElhinney, D. B., Krantz, I. D., Bason, L., et al. (2002) Analysis of cardiovas-
cular phenotype and genotype-phenotype correlation in individuals with a JAG1
mutation and/or Alagille syndrome. Circulation 106, 2567–2574.
Heart Defects in Alagille Syndrome 231

6. Yuan, Z. R., Kohsaka, T., Ikegaya, T., et al. (1998) Mutational analysis of the
Jagged 1 gene in Alagille syndrome families. Hum. Mol. Genet. 7, 1363–1369.
7. Krantz, I. D., Smith, R., Colliton, R. P., et al. (1999) Jagged1 mutations in patients
ascertained with isolated congenital heart defects. Am. J. Med. Genet. 84, 56–60.
8. Eldadah, Z. A., Hamosh, A., Biery, N. J., et al. (2001) Familial tetralogy of Fallot
caused by mutation in the Jagged1 gene. Hum. Mol. Genet. 10, 163–169.
9. Le Caignec, C., Lefevre, M., Schott, J. J., et al. (2002) Familial deafness, congeni-
tal heart defects, and posterior embryotoxon caused by cysteine substitution in the
first epidermal-growth-factor-like domain of jagged 1. Am. J. Hum. Genet. 71,
180–186.
10. Kamath, B. M., Spinner, N. B., Emerick, K. M., et al. (2004) Vascular anomalies in
Alagille syndrome: a significant cause of morbidity and mortality. Circulation 109,
1354–1358.
11. Loomes, K. M., Underkoffler, L. A., Morabito, J., et al. (1999) The expression of
Jagged1 in the developing mammalian heart correlates with cardiovascular dis-
ease in Alagille syndrome. Hum. Mol. Genet. 8, 2443–2449.
12. Jones, E. A., Clement-Jones, M., and Wilson, D. I. (2000) JAGGED1 expression
in human embryos: correlation with the Alagille syndrome phenotype. J. Med.
Genet. 37, 658–662.
13. Gridley, T. (2003) Notch signaling and inherited disease syndromes. Hum. Mol.
Genet. 12 Spec No 1, R9–13.
14. Artavanis-Tsakonas, S., Rand, M. D., and Lake, R. J. (1999) Notch signaling: cell
fate control and signal integration in development. Science 284, 770–776.
15. Spinner, N. B., Colliton, R. P., Crosnier, C., Krantz, I. D., Hadchouel, M., and
Meunier-Rotival, M. (2001) Jagged1 mutations in alagille syndrome. Hum. Mutat.
17, 18–33.
16. Ropke, A., Kujat, A., Graber, M., Giannakudis, J., and Hansmann, I. (2003) Iden-
tification of 36 novel Jagged1 (JAG1) mutations in patients with Alagille syn-
drome. Hum. Mutat. 21, 100.
17. Wathen, D. M., Moore, E. C., Kamath, B. M., et al. (2005) Jagged1 (JAG1) muta-
tions in alagille syndrome: increasing the mutation detection rate. Hum. Mutat. (in
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18. Ganguly, A. (2002) An update on conformation sensitive gel electrophoresis. Hum.
Mutat. 19, 334–342.
Molecular Dissection of Tetralogy of Fallot 233

14
Array Analysis Applied to Malformed Hearts

Molecular Dissection of Tetralogy of Fallot

Silke Sperling

Summary
Microarray technology as a method for large-scale gene expression analysis has entered
into widespread use in the field of cardiovascular research. This chapter summarizes the appli-
cation of arrays to study gene expression profiles of congenital heart diseases, in particular the
molecular portrait of tetralogy of Fallot.
The sections of this chapter correspond to the several distinct steps of microarray experi-
ments. A general introduction to the method, and information on the selection of arrays and
preparation of labeled complementary DNA samples are given. A specific focus of the chapter
is the experimental design and data analysis.
Key Words: Microarray; cDNA array; experimental design; gene expression profiling; te-
tralogy of Fallot; congenital heart diseases.

1. Introduction
Recently, complementary DNA (cDNA) microarray technology has entered
into widespread use to understand gene expression, and the technology is tan-
talizing in the possibilities it presents. In light of this excitement, some per-
spective is in order, to ensure well-designed and accomplished experiments.
This chapter summarizes the application of cDNA arrays to study gene expres-
sion profiles of congenital heart disease (CHD) focusing on tetralogy of Fallot
(TOF).
CHDs are the clinical manifestation of anomalies in heart development,
which is a complex process requiring the precise integration of cell type-spe-
cific gene expression and morphological development; both are intertwined in
their regulation by transcription factors. Although studies of heart develop-
ment in fish, frog, mice, chicken, flies, and worms have begun to unravel how
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

233
234 Sperling

morphogenesis and hierarchies of developmental control are exerted, the basic

mechanism for CHD in human is still incompletely defined. The rarity of large
CHD human families and the incomplete penetrance of CHD as a phenotype
have limited the usefulness of linkage analysis in identifying causative genes.
The genetics of CHD points to the existence of powerful disease modifiers
because wide phenotypic spectra are seen in patients harboring identical dis-
ease alleles.
The application of cDNA arrays as a large-scale technology for the simulta-
neous analysis of thousands of genes permits the identification of specific gene
expression profiles of the various stages of cardiac development. Moreover,
the comparison of gene expression patterns between human normal and con-
genital malformed hearts or among different types of CHDs will identify dif-
ferentially expressed genes that may point to the molecular mechanisms
involved in normal and CHD states, and perhaps provide new insights for the
discovery of novel molecular targets for diagnostics and therapeutics.
Any microarray experiment involves several distinct stages. First, there is
the design of the experiment. The researcher must decide on the source of RNA
to be hybridized to the arrays, on the set of genes to be represented on the
arrays, and on the number of replicative hybridizations to be performed. Sec-
ond, the wet-lab experiments, including RNA isolation, labeling, and array
hybridization, follow. Third, the array data are processed and analyzed to se-
lect differentially expressed genes, to identify patterns within the data, and to
interpret the resulting molecular portraits. The sections of this chapter corre-
spond roughly to these three steps and focus on specific considerations for the
molecular dissection of TOF in humans. Regarding the recent developments of
commercially available gene expression analysis arrays, this chapter provides
an overview on the general technique, with hands-on information, and explains,
in detail, the specific considerations for the analysis of CHDs.
Generally, cDNA arrays are a measurement tool with cDNA (the probes) of
known sequence immobilized in an orderly arrangement of tens to hundreds of
thousands of unique DNA molecules. Labeled cDNA samples (the targets) are
simultaneously hybridized to the array and the signal intensity from the bound
target is quantified. There are many unknown quantities in this process; how-
ever, the basic principle is as follows: for a given sequence spotted on the
array, the quantity of the corresponding transcript of the sample hybridized is
measured using the intensity of the fluorescence or radioactive signal, which
should be proportional to the quantity of the corresponding transcript. Finally,
the obtained transcript quantities for each gene within each sample are
bioinformatically and statistically analyzed with respect to the hypothesis that
drive the experiment. The main advantage of the application of cDNA arrays
compared with other quantitative methods, such as real-time polymerase chain
Molecular Dissection of Tetralogy of Fallot 235

Fig. 1. Molecular dissection of tetralogy of Fallot (TOF). Schematic representation

of molecular portraits for the normal right and left ventricle (norRV and norLV) as
well as for the diseases stages of TOF and a variety of cardiac malformations (RVdis)
sharing the feature of right ventricular hypertrophy in response to pressure overload in
the TOF cases. The characteristic changes of gene expression in each tissue and dis-
eases can be extracted by comparing the molecular portraits.

reaction (PCR), is the simultaneous analysis of thousands of genes within very

small samples. Using large-scale arrays, we are able to analyze more than two-
thirds of the entire set of human transcripts with samples as small as 8 μg of
total RNA for one assay (1).
The concept for the analysis of gene expression profiles in the setting of
TOF in human is outlined in Fig. 1. This concept focuses on the study of dis-
ease-specific transcriptome changes in patients with TOF and on the dissection
of the molecular portrait corresponding to the primary dys-development and
the molecular portrait associated with the secondary hemodynamic changes
because of the heart malformation. For such a study, the analysis of the
transcriptome of the right ventricle (RV) of patients with TOF, as well as of
patients showing a variety of cardiac malformations but sharing the common
cardiac adaptation feature of the RV (RV hypertrophy [RVH]), should be en-
visaged. To further distinguish the diseased from the normal ventricular por-
trait, normal samples of at least the RV should be profiled as well.

2. Materials
2.1. Patient and Sample Collection
To allow for the selection of a balanced patient population enabling the sepa-
ration of disease- or tissue-specific expression patterns, we collected 150
samples of human ventricular and atrial cardiac tissue. For the storage of all
general, clinical, and sample collection information, we set up a relational da-
tabase with an Internet interface. The overall clinical characterization included
250 features of hemodynamical, morphological, and therapeutical information.
The sample collection and laboratory information section contained surgical or
236 Sperling

interventional conditions (e.g., patient temperature and cardiac arrest) of the

sample retrieval as well as timing and cardiac localization.
2.2. DNA Microarrays
In our study we used “Human Unigene Set-RZPD 2” cDNA arrays (nylon
membrane arrays) from the German Resource Center for Genome Research,
Berlin, Germany.
Other sources of premade human DNA arrays are GeneChips® (Affymetrix,
Santa Clara, CA), BD Atlas Arrays (BD Biosciences Clontech, Palo Alto, CA),
ResGen (Invitrogen, Hunstville, AL), Agilent (Agilent Technologies, Palo
Alto, CA), sciTRACER Cardio Vascular 725 (Scienion, Berlin, Germany), and
several other resources. Custom-made arrays are also available from some of
these suppliers.
2.3. RNA Isolation, Labeling, Hybridization, and Signal Detection
We used TRIzol® reagent for RNA isolation, pd(T)12–18 oligonucleotides
for reverse transcription to cDNA, and α-33P-dCTP for labeling. For signal
detection, we scanned our arrays using a Fuji Film Bas-1800 reader (Fuji photo
film).
Finally, the material for labeling, hybridization, and signal detection strongly
depends on the arrays used, and the majority of array suppliers purchase the
material along with their arrays. For example, the oligonucleotide arrays
GeneChip or cDNA arrays sciTRACER are hybridized with biotin-labeled or
Cy3/Cy5-labeled targets, respectively.
2.4. Data Analysis Tools and Array Databases
A selection of software packages for the analysis of array data follows:
1. SAM Software, Stanford University (Stanford, CA http://www-stat.stanford.edu/
~tibs/SAM).
2. R, Bioconductor project, http://www.bioconductor.org.
3. TM4, TIGR Institute for Genomic Research (Rockville, MD, http://www.tigr.org/
software/tm4).
4. GeneSpring, Silicon Genetics (Redwood City, CA, http://www.silicongenetics.com).
Public repositories for array data follow:
5. GEO—Gene Expression Omnibus, National Center for Biotechnology Informa-
tion (Bethesda, MD, http://www.ncbi.nlm.nih.gov/geo).
6. ArrayExpress, European Molecular Biology Laboratory–European Bioinformatics
Institute (Cambridge, UK, http://www.ebi.ac.uk/arrayexpress).
Molecular Dissection of Tetralogy of Fallot 237

3. Methods
3.1. Selection of Samples
The questions that can be answered by the array experiment mainly depend
on the sample selection regarding the studied phenotype and cardiac localiza-
tion of the obtained sample. Focusing on the analysis of TOF, we compared
samples from patients with TOF with samples from a variety of CHD cases
also sharing the feature of RVH caused by pressure overload as the cardiac
adaptation to their aberrant disease state. In addition, we compared these dis-
eased hearts with normal hearts. For our study, we chose right ventricular
samples of the CHD patients and samples from all four cardiac chambers as
well as the interventricular septum of normal hearts. Furthermore, we profiled
right atrial samples of patients with single atrial or ventricular septal defects
(see Note 1). In general, to consider known confounding factors, such as age
and gender, the number of collected samples needs to widely exceed the num-
ber of samples finally chosen for the experiment. Moreover, all clinical fea-
tures should be assembled in a detailed and sufficiently searchable way. The
selected patient populations should represent a tight range of those factors on
which the analysis will focus (in our study TOF, RVH, and tissue specificity)
and a wide range of all other clinical factors known or unknown as confound-
ing factors, for which no stringent selection can be achieved, e.g., because of
natural sample limitation (see Note 2).
3.2. Selection of cDNA Array
The various types of cDNA arrays currently available for gene expression
profiling differ mainly in their basic source for the DNA probes on the array
and in the array platform. Either each probe is individually synthesized on a
rigid surface (usually glass) (2), or presynthesized probes (oligonucleotides or
PCR products) are attached to the array’s platform (usually glass or nylon mem-
branes) (3,4). Although the in situ probe synthesis method requires sophisti-
cated and expensive robotic equipment, the method of attaching presynthesized
cDNA probes (usually 100–5000 bases long) to a solid surface, such as glass or
nylon membrane, is affordable for academic research laboratories, and many
institutions have developed core facilities for the in-house manufacture of custom
glass slide cDNA arrays.
For our genome-wide array study of CHD in human, we used the nylon mem-
brane Human Unigene Set 2 arrays from the RZPD (http://www.rzpd.de). In
total, 61 arrays were used, each represented by 3 Hybond N+ membranes con-
taining PCR products (600–1200 bases long) of 74,695 different IMAGE
238 Sperling

clones, spotted in duplicate, representing 34,000 Unigene clusters and approx

20,000 genes annotated by Ensembl.
3.3. Experimental Design
Statistics is often thought to concern only the analysis of observational or
experimental data. However, experimental design is one of the oldest subfields
of statistics. The experimental design affects many things: the analysis that
will be possible, the question that will be answerable, and the quality of the
results (5). Although a good design does not guarantee a successful experiment,
a suitably bad design guarantees a failed experiment, no results, or useless re-
sults. Many experimental designs for gene expression profiling experiments
are possible. However, no matter what the purpose of the experiment, a suffi-
cient number of measurements must be obtained for statistical analysis of the
data, either through multiple measurements of homogeneous samples (replica-
tion) or through multiple sample measurements (e.g., across subjects or time).
This is because many genes will show considerable changes in expression lev-
els between two experimental conditions, without the changes being signifi-
cant. These false-positive results arise from chance occurrences caused by
uncontrolled biological variance as well as experimental and measurement er-
rors. Experimental errors include variations in the sample retrieval procedure
(surgical probes vs catheter biopsies can lead to different cell sample types),
and the treatment and handling of RNA during extraction and subsequent pro-
cessing. For example, if large frozen samples are reduced to smaller pieces for
the RNA isolation procedure, this should be done without thawing, because a
change of gene expression profiles could be caused if samples encounter a tem-
perature shift, even for a short time. In addition, the protocols for RNA isola-
tion and cDNA preparation should be standardized for all samples and should
preferably be performed by a single person, e.g., cDNA preparation either with
random or oligo d(T) priming. On the other hand, biological variance is some-
times more difficult to control (see Subheading 3.1.). On top of these sources
of errors, the quality of DNA array data can vary depending on the type of array
and the array manufacturing methods and quality.
With these considerations in mind, we used the experimental design pre-
sented in Subheading 3.1. for our gene expression-profiling study. Our study
consisted of 55 cardiac samples and 1 control sample that were hybridized to
61 array sets, each consisting of 3 array subsets, thus, all together, we had 183
arrays. Except for the control sample, the gene expression profile of each
sample was measured only once. The smallest statistical analysis group con-
sisted of four different samples and two measurements per gene, because those
were represented in duplicates on the arrays.
Molecular Dissection of Tetralogy of Fallot 239

On the biological side, we classified our samples according to the disease

state, tissue type, gender, and age. On the experimental side, our selected gene
set was represented on three different arrays and, for manufacturing reasons,
we had to use two different lots of array sets produced from PCR products of
different production dates. Furthermore, the hybridizations were performed in
two different hybridization ovens. To minimize the influence of the experi-
mental errors, we put together groups of four samples that were hybridized
simultaneously in the same oven at one time. Two hybridization sessions were
carried out per week. Each sample received a hybridization group number,
which allowed for later statistical analysis of any of the factors. Considering
the fact that each sample was hybridized three times (one array subset each
time), we randomly distributed the different hybridizations through the overall
experimental time of 14 consecutive weeks to avoid a possible influence of
training time. The same researcher performed all procedures of our experi-
ment, and all solutions were prepared in advance for the entire experimental
period. In addition, a large control RNA batch was intermittently used as an
experimental hybridization control. An example of our hybridization groups
for a 3-wk period is given in Table 1.
3.4. RNA Isolation, cDNA Synthesis, Labeling, Hybridization,
and Signal Detection
Our procedure used for radioactive labeling and nylon membrane arrays is de-
scribed as follows. Total RNA of all cardiac tissues and control HEK 293 cells was
extracted using TRIzol reagent, according to the standard protocol. Labeling was
performed by reverse transcription of 8 μg of total RNA with AMV-reverse tran-
scriptase in the presence of pd(T)12–18 and α-33P-dCTP (see Note 3). Unincorpo-
rated nucleotides were removed using ProbeQuant G-50 micro columns, and cDNA
was added to the hybridization solution, together with salmon sperm DNA, pla-
centa DNA, and pd(A)40 (see Note 4). Hybridizations were performed at 65°C for
16 h. After washing, arrays were exposed for 24 h to phosphor-imaging plates and
scanned subsequently to obtain signal intensities (see Note 5).
3.5. Data Processing and Further Analysis
Before one can determine the differential gene expression profiles between
two samples or conditions obtained, one first needs to ascertain that the data
are comparable. That is, one should use a method to normalize the data sets for
sources of experimental and biological variations, such as those discussed in
Subheading 3.3. However, with few exceptions, the sources of these variations
have not been measured and characterized within the experiment. Normaliza-
tion methods attempt to correct for the following variables:
240 Sperling

Table 1
Experimental Designa
Disease Tissue type Sex Age Array subset Array batch Hyb-group Week

ASD RA m y 1 1 1a 1
ASD RA m o 1 1 1a 1

VSD RA m y 1 1 1a 1

Normal RA f o 1 1 1a 1

RVdis RV m y 1 1 1b 1

RVdis RV m y 1 1 1b 1

TOF RV m y 1 1 1b 1

Normal RV m o 1 1 1b 1

RVdis RV m y 1 2 2a 1

TOF RV m o 1 1 2a 1

TOF RV f y 1 1 2a 1

Normal RV m o 1 2 2a 1

Normal RA f o 1 1 2b 1

Normal RV m o 1 1 2b 1

Normal LV m o 1 1 2b 1

Normal IVS m o 1 1 2b 1

ASD RA m y 2 1 3a 2

ASD RA m o 2 1 3a 2

VSD RA m y 2 1 3a 2

Normal RA f o 2 1 3a 2

ASD RA f y 2 1 3b 2

ASD RA f o 2 1 3b 2

TOF RA m o 2 1 3b 2

control 2 1 3b 2

RVdis RV m y 2 1 4a 2

RVdis RV m y 2 1 4a 2

TOF RV m y 2 1 4a 2

Normal RV m o 2 1 4a 2

Normal RA f o 2 1 4b 2

Normal RV m o 2 1 4b 2

Normal LV m o 2 1 4b 2

Normal IVS m o 2 1 4b 2

ASD RA f y 3 1 9a 5

ASD RA f o 3 1 9a 5

TOF RA m y 3 1 9a 5
control 3 1 9a 5

Normal RA f o 3 1 9b 5

Normal LA f o 3 1 9b 5

Normal RV f o 3 1 9b 5

(continued)
Molecular Dissection of Tetralogy of Fallot 241

Table 1 (continued)

Disease Tissue type Sex Age Array subset Array batch Hyb-group Week

Normal LV m o 3 1 9b 5
ASD RA m y 3 1 10a 5
VSD RA m y 3 1 10a 5

RVdis RV m y 3 1 10a 5

RVdis RV f o 3 1 10a 5

RVdis RV f o 3 1 10b 5

RVdis RV f y 3 1 10b 5

TOF RV f o 3 2 10b 5

Normal RV f o 3 1 10b 5

aExcerpt of experimental schedule for our array study. Hyb-group,

hybridization group; a or b, assignment for the hybridization oven used;

f, female; m, male; o, old ( 7 years); y, young (<7 years); ASD, atrial
septal defect; VSD, ventricular septal defect; RVdis, a variety of CHDs
having right ventricular hypertrophy is common; RA, right atrium; IVS,
interventricular septum.

1. Number of cells and different cell types in the sample.

2. RNA isolation and labeling efficiency.
3. Hybridization efficiency.
4. Signal measurement sensitivity.
The most widely used data normalization method is the normalization by
global scaling (6). Here, the sum of the measurements of each array is simply
scaled to a constant sum. This scales the total signal on all arrays to a value of
one, with the advantage that each individual measurement is expressed as a
fraction of the total signal, in other words, as the fraction of total messenger
RNA (mRNA).
Because our hybridizations were performed on arrays from two different pro-
duction batches, which significantly affected the measurements, we corrected
the influence of the production as follows. We considered two virtual reference
hybridizations, defined by the spot-wise medians of 10 hybridizations from the
respective array batch. These two sets of hybridizations were performed with
samples from patients as well as with control samples sharing equal phenotype
profiles. The logarithms of ratios between the intensities of each hybridization
of interest and those of the respective batch-specific virtual reference hybrid-
ization were shifted, such that the median over the 40% of spots with highest
average log intensity became zero. Finally, the obtained log-ratio values were
averaged over duplicate spots per clone, resulting in values of “normalized”
expression levels. To limit the analysis to meaningful data that did not show
242 Sperling

consistently low intensity or low variance across the samples, all further statis-
tical analysis was performed on the normalized expression levels of 8069 se-
lected genes, whose intensities were among the 15% highest in at least four
samples, and whose natural log-ratios had a standard deviation across the
samples of at least 0.5 (see Note 6).
The statistical analysis follows normalization and array data preprocessing.
As a road map, the statistical analysis can be essed between a control (normal
tissue) and experimental situation (disease tissue) is addressed. The second level
is multiple genes, where clusters of genes are analyzed in terms of common
functionalities, interactions, coregulations, and so on. Finally, the third level
attempts to infer and understand the underlying gene and protein networks that
ultimately are responsible for the pattern observed. One approach commonly
used in the literature (at least in the first wave of publications) is a fold-change
approach, in which a gene is declared to have significantly changed if its aver-
age expression level varies by more than a constant factor, typically two, be-
tween the treatment and control conditions. Inspection of gene expression data
suggest, however, that such a simple “twofold rule” is unlikely to yield optimal
results. First, it depends on well data normalization, because a factor of two can
have quite different significance and meaning in different regions of the spec-
trum of expression levels, in particular, at the very high and very low ends.
Moreover, this approach does not account for the influence of major confound-
ing factors that can hardly be completely balanced by the sample selection in a
disease study.
Therefore, we used linear models, incorporating the factors age, gender, dis-
ease, and tissue type, as a statistical framework for identifying genes that are
affected in particular phenotypes (7). We subjected the normalized expression
levels of each clone to a linear model of the following form: yhijk = μ + Ah + Si
+ Tj + Dk + ε, where Ah is the effect of age h, Si the effect of the patient’s
gender, Tj the effect of tissue j, and Dk the effect of disease status k. Thus, we
obtained a p value quantifying the statistical significance of differential expres-
sion for each gene and each phenotype comparison of interest. Estimating the
rates of falsely significant genes with a permutation approach further assessed
the reliability of the obtained results (8). An overview of the numbers of differ-
entially expressed genes obtained for the phenotype of TOF, the feature of RVH
in response to pressure overload, and the comparison of atria and ventricle, is
given in Table 2.
Most, if not all, genes act in concert with other genes. What DNA microarrays
are really investigating are the patterns of expression across multiple genes and
phenotypes.
We hierarchically clustered all known genes that seemed significantly dif-
ferential (p < 0.01) in at least one of our overall comparisons (Fig. 2; –log10 (P)
Molecular Dissection of Tetralogy of Fallot 243

Table 2
Overview of Differentially Expressed Genes (p < 0.01)a
Data set TOF in RV RVH in RV A vs V
Clones 8069 324 198 438
Estimated false discovery rate 14% 25% 12%
Unigene cluster 6059 264 154 315
Known genes 1880 86 49 100
aTotal numbers of cDNA clones differentially expressed in different phenotype comparisons
together with the represented number of Unigene clusters and known genes. The estimated false
discovery rate is given. A, atrial; RVH, right ventricle hypertrophy; TOF, tetralogy of Fallot; V,
ventricular.

color-coded). This overview allows for a comparison between the transcrip-

tional portraits of each of these genes in the different phenotypes.
Furthermore, array data can be used to discriminate among different known
or previously unknown cell types or conditions, which is addressed by many
powerful techniques for class prediction and class discovery.
To see which class distinctions among our cardiac tissue samples are most
pronounced in terms of gene expression profiles, we applied the class discovery
method, ISIS (9). This is an unsupervised algorithm that is designed to detect
groups of samples with distinctive gene expression patterns. Within our data,
the most outstanding binary class distinction identified, irrespective of sample
annotations, was exactly the distinction between atria and ventricle samples.
Finally, one of the central challenges within the analysis of array data is to
cope with the enormity of data sets. Examining a spreadsheet of gene names
and expression ratios and significance values often provides little insight into
the interesting trends or patterns that may exist within the data.
To provide a global view of the association of functional gene categories
with particular phenotypes, we used the statistical method of correspondence
analysis after assigning our genes to the gene ontology categories (AmiGO,
http://www.godatabase.org) according to the annotation in LocusLink database
(http://www.ncbi.nlm.nih.gov/LocusLink).
In addition to these analysis methods, several software packages for the
analysis and visual display of array data are freely or commercially available
(for selection, see Subheading 2.4.).

4. Notes
1. Different developmental origins of the heart have to be taken into account when
selecting the samples. Furthermore, the comparison of biopsies obtained by car-
244 Sperling
Molecular Dissection of Tetralogy of Fallot 245

diac catheterization with samples obtained by surgical procedures should be

avoided, because the cell-types within these samples could differ significantly
regarding the proportion of endocardial and myocardial cells.
2. Having confounding factors in mind, we screened our sample population for addi-
tional clinical factors in advance. For example, we selected only patients with
normal sinus rhythm, because cardiac arrhythmia is known to dramatically
change the myocardial gene expression profiles. On the other hand, little is known
about changes of the transcriptional portrait regarding low oxygen saturation,
heart rate (newborn and young children have a higher heart rate than adults), or
tissue temperature at the time of sample collection (most cardiac surgeries take
place in a state of low body temperature vs normal body temperature during car-
diac catheterization). For example, the oxygen saturation is influenced by vari-
ous disease factors, which can never be matched completely in an observational
study. Therefore, to enable the separation of disease- and tissue-specific expres-
sion patterns, the selected patient populations for the different phenotypes repre-
sented a range of these factors, rather than having been selected stringently for
one or another factor. Finally, the statistical analysis regarding oxygen saturation
as well as body temperature independent of the underlying diseases did not show
a significant number of differentially expressed genes within our study.
3. In cases of very little sample material, the preparation of total RNA instead of
mRNA is advisable. mRNA labeling can be achieved by the use of pd(T)12–18 in
the reverse transcription reaction. If mRNA is available, it is suggested that ran-
dom hexamers, which are slightly more efficient be used (see also Note 4).
4. The pd(A)40 was added to the hybridization solution to bind polyA stretches that
could occur within spotted probes (PCR products of 600–1200 bases) and could
lead to unspecific signals, especially in the presence of targets labeled using
pd(T). The radioactivity should be within the first half-life of the isotope.
5. When using radioactively labeled probes, the hybridization and exposure time
should be kept as stable as possible during the time period of the different experi-
ments. We managed to have a variance of 15 min for both.
6. The smallest statistical analysis group consisted of four samples.

Fig. 2. (opposite page) Overview of p values and expression levels for different
phenotype comparisons. Shown are annotated genes with p < 0.01 in at least one com-
parison. Gene names are listed. Each comparison is represented by one column, and
each gene by one row. The –log10(P) of each gene in the particular comparison is
color-coded in yellow to red for upregulated and yellow to green for downregulated
genes. For example, a value of 2 stands for p = 0.01 and is color-coded in red if the gene
is upregulated. The differentially expressed genes confirmed by real-time PCR are in-
dicated with “(1)” if tested for TOF in RV and “(2)” if tested for ventricular septal
defects (VSD) in the right atrium. V, ventricular; A, atrial.
246 Sperling

Acknowledgments
This work was supported by the Max Planck Society for the Advancement of
Science. Among many colleagues that have provided me with input, help, and
support I thank Bogac Kaynak. I express my gratitude for the intellectual sup-
port of Anja von Heydebreck, who has contributed in many ways to this work.

References
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C. L. (1993) Multiplexed biochemical assays with biological chips. Nature 364,
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ing Manual. Cold Spring Harbor, New York.
5. Kerr, M. K. (2003) Experimental design to make the most of microarray studies,
in Functional Genomics: Methods and Protocols (Brownstein, M. J. and
Khodursky, A. B., eds.), Humana, Totowa, NJ, pp. 137–147.
6. Beibarth, T., Fellenberg, K., Brors, B., et al. (2000) Processing and quality con-
trol of DNA array hybridization data. Bioinformatics 16, 1014–1022.
7. Jin, W., Riley, R. M., Wolfinger, R. D., White, K. P., Passador-Gurgel, G., and
Gibson, G. (2001) The contributions of sex, genotype and age to transcriptional
variance in Drosophila melanogaster. Nat. Genet. 29, 389–395.
8. Storey, J. D. and Tibshirani, R. (2003) SAM thresholding and false discovery
rates for detecting differential gene expression in DNA microarrays, in The Analy-
sis of Gene Expression Data: Methods and Software (Parmigiani, G., Garrett, E.
S., Irizarry, R. A., and Zeger, S. L. eds.), Springer, New York.
9. von Heydebreck, A., Huber, W., Poustka, A., and Vingron, M. (2001) Identifying
splits with clear separation: a new class discovery method for gene expression
data. Bioinformatics 17, 107–114.
ZIC3 Mutation Analysis 247

15
DNA Mutation Analysis in Heterotaxy

Stephanie M. Ware

Summary
Heterotaxy refers to the abnormal arrangement of internal organs in relation to each other. It
is characterized by complex cardiac malformations that are thought to result from abnormal
left–right patterning in early embryonic development. Mutations in four genes have been iden-
tified in human heterotaxy. ZIC3, a zinc finger transcription factor, causes X-linked heterotaxy.
EGF-CFC, ACVR2B, and LEFTYA are all members of a transforming growth factor-β signal
transduction pathway that is critical for proper left–right development. Point mutations have
been identified in each of these genes using polymerase chain reaction-based mutation analysis
strategies. ZIC3 mutation screening will be used to illustrate the methods for molecular
sequence data acquisition and examination. These techniques are applicable to any gene of
interest and will be useful for further evaluation of candidate genes for heterotaxy.
Key Words: Left–right asymmetry; molecular sequence data; point mutation; candidate
gene; ZIC3; heterotaxy; nodal signal transduction pathway; ARMS assay; RFLP.

1. Introduction
Heterotaxy is a clinical phenotype that results from a partial or complete
failure of appropriate patterning of the left and right sides during early
embryogenesis (1,2). Research in a number of different model organisms has
identified genes important in initiating and maintaining left–right asymmetry
in the early embryo (3–5). Loss of these genes results in complex cardiovascu-
lar malformations. To date, point mutations in four genes have been identified
in patients with heterotaxy: ZIC3, EGF-CFC, ACVR2B, and LEFTYA (6–11).
In addition, deletions of the ZIC3 locus have been identified using fluores-
cence in situ hybridization (12). Analysis of these genes is currently available
only on a research basis, although ZIC3 mutation screening should be clini-
cally available in the near future. Using ZIC3 as an example, this chapter dis-
cusses the design of oligonucleotide primers for sequence analysis, PCR

From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

247
248 Ware

amplification and purification, analysis of sequence data, and design of con-

trols.

2. Materials
1. Sample genomic DNA.
2. 10X polymerase chain reaction (PCR) buffer: 500 mM KCl, 100 mM Tris-base,
pH 8.3, 1.5 mM MgCl2.
3. Taq DNA polymerase.
4. dNTPs (dCTP, dATP, dGTP, and dTTP).
5. Oligonucleotide primers.
6. Agarose and gel electrophoresis equipment.
7. 10X Tris-acetate-EDTA running buffer.
8. Ethidium bromide.
9. PCR purification kit.
10. PCR thermocycler equipment.
11. Restriction enzymes and buffers.

3. Methods
3.1. Preparation of Genomic DNA
There are a variety of methods and kits available for preparation of genomic
DNA. Most commercially available kits work well to generate substrates for
PCR. We currently use the Gentra Puregene DNA extraction kit for prepara-
tion of DNA from cells, blood, tissues, or Ficoll, according to the
manufacturer’s instructions.
3.2. Design of Oligonucleotide Primers
The open reading frames of ZIC3, EGF-CFC, ACVR2B, and LEFTYA have
been screened for point mutations (6–11). The design of oligonucleotide prim-
ers is critical to the success of the PCR amplification reactions and subsequent
screening.
3.2.1. Identification of the Intron–Exon Boundaries
of the Gene of Interest
Information on intron–exon boundaries can be obtained from a number of
the publicly available databases for many genes. The information in these da-
tabases is annotated on a regular basis and it is therefore worthwhile to periodi-
cally check for updates. Fig. 1 shows an example of a search for ZIC3 on the
University of California, Santa Cruz genome browser.
1. Go to http://genome.ucsc.edu/ and click on the genome browser link.
2. On the human genome browser gateway page, enter ZIC3 (or your gene of inter-
est) in the box marked “position.” A menu of search results will be displayed.
ZIC3 Mutation Analysis 249

Fig. 1. University of California, Santa Cruz Genome Browser web page. The three
exons and two introns of ZIC3 are shown in black boxes and lines, respectively. The
location on the X chromosome is given. Links to additional information can be found
in the columns at the left. A link to Ensembl (arrow) is useful for obtaining sequence
data with introns and exons demarcated.

3. Click on any human ZIC3 listing to get to the page shown in Fig. 1 (see Note 1).
4. Click on “Ensembl gene predictions” (Fig. 1, arrow) followed by “genomic se-
quence from assembly” to view the genomic sequence with intron–exon bound-
aries demarcated (13–15).

3.2.2. Selection of Primers

Figure 2 shows information from Ensembl for ZIC3 and illustrates the loca-
tion of oligonucleotide primers within the sequence.
1. For exons of fewer than 400 bp, such as exon 2 and 3 of ZIC3, oligonucleotide
primers are designed to flank the exon (see Note 2).
2. For exons larger than 400 bp, design overlapping primer sets (see Fig. 2, exon 1)
(see Note 2).
3. Design oligonucleotide primers of 18 to 22 bases with a GC base content close to 50%.
3.2.3. Oligonucleotide Primers for X-Linked Heterotaxy (see Note 3)
Oligonucleotide primers can be purchased from a variety of commercial
sources and do not require any additional purification steps for use with PCR.
Primers used for ZIC3 sequence analysis are listed in Table 1 (see Note 4).
250 Ware

F–ig. 2. Partial sequence information for ZIC3. Exons (bold) and partial sequence
from introns are shown. The oligonucleotide primers used for sequence analysis are
underlined. Note that exon 1aR and 1cF are the same primer in opposite orientations
(see Table 1).
ZIC3 Mutation Analysis 251

Table 1
Oligonucleotide Primers for ZIC3 Exon Amplification by PCRa
Annealing
temperature Product
Amplicon Primer pair (°C) size

Exon 1a 1aF 5' TCTTGCAGTGACGGAAAGTT 3'

1aR 5'TTCATGTTCATGGGGCTGTA 3' 56 839
Exon 1b 1bF 5' GCGCACGATCTATCTTCAGG 3'
5' CCGCATATAACGGAAGAAGG 3' 53 546
Exon 1c 1cF 5' TACAGCCCCATGAACATGAA 3'
1cR 5' TCTCCCTCGCGCTCTAAGT 3' 56 483
Exon 2 2F 5' GCTGCTTGCCTCTGAGAAAC 3'
2R 5' ACGTGGAAGACAGAGGGTTG 3' 56 334
Exon 3 3F 5' GCTCTTGTTTTTGCTTGCAC 3'
3R 5' CATTTCCATCTGATTGGTCTCA 3' 56 329
aF, forward; R, reverse.

3.3. PCR Amplification

For each patient genomic DNA sample, five PCR reactions are performed,
using the primers listed in Table 1. The reaction conditions are given in Table
2 (see Note 5).
Make a master mix according to Table 2, with a sufficient quantity for all
patient samples, and aliquot 48 μL per tube. Add 2 μL of sample DNA (50 ng/
μL) to each tube. The general PCR thermocycling program is given in Table 3
(see Note 5).
A 5-μL aliquot from each sample can be removed and run on a 2% agarose
gel to monitor PCR amplification. The remaining 45 μL is purified for subse-
quent sequencing.
3.4. Purification of PCR Products
PCR products are purified using Qiagen QIAquick PCR purification kit ac-
cording to the manufacturer’s instructions (see Note 6). The DNA is now ready
to be submitted for sequencing.
3.5. Sequence Analysis
There are a variety of software programs available for purchase to perform
mutation analysis on sequence traces. This section will describe the basic goals
of sequence analysis and give instructions for analysis without sequence analy-
sis software (see Note 7).
 252 Ware

Table 2
PCR Mix
10X PCR buffer (100 mM Tris-base, pH 8.3; 500 mM KCl; and 1.5 mM MgCl2) 5 μL dNTPs
(200 μM each) 4 μL
Oligonucleotide primers, 100 pmol/μL each 0.2 μL each
Taq DNA polymerase 0.2 μL (1 U)
H2O 38.4 μL

Table 3
PCR Thermocycling Program

Step Temperature (°C) Time Procedure

1 94 3 min Initial denaturation
2 94 30 s Denaturation
3 See Table 1 30 s Annealing of primers
4 72 45 s Extension
5 Repeat 34 times from step 2
6 72 10 min Final extension
7 4°C forever

1. Scan the sequence trace for each sample to determine the quality of the sequence.
2. Copy the sequence text and paste into the BLAST two-pair nucleotide alignment
page (http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html).
3. Run a two-way alignment using human ZIC3 (accession number NM_003413)
and the sequence output data (see Note 8).
4. Confirm any mismatches by visualization of the sequence trace (see Fig. 3).
5. If a nucleotide mismatch is identified, translate the sequence containing the mis-
match in all six frames. Paste sequence into the box provided at http://
us.expasy.org/tools/dna.html, and submit. The results can be compared with the
ZIC3 amino acid sequence to determine whether the mutation results in a silent,
nonsense, or missense change.
6. If a sequence software program is not used, the exon–intron boundaries must be
analyzed for each exon, to determine whether splice site mutations are present.

3.6. Design of Controls

For missense amino acid changes, control samples must be analyzed to determine
whether the change represents a polymorphism (>1% of control samples). The two
most commonly used methods are restriction fragment length polymorphism (RFLP)
analysis and amplification refractory mutation system (ARMS) assay.
ZIC3 Mutation Analysis 253

Fig. 3. Sequence data from a proband and his carrier mother. A nonsense ZIC3
mutation results from a G-A nucleotide substitution (arrow). Note that the hemizy-
gous male has only the mutant allele. The carrier mother is heterozygous. Although
her sequence trace shows both G and A alleles, the wild-type “G” assigned by the
sequence trace misses the mutation, illustrating the importance of careful visual se-
quence analysis.

3.6.1. Restriction Fragment Length Polymorphism

1. Determine whether the mutation has created or deleted a restriction site by using
a program such as Webcutter (http://www.firstmarket.com/cutter/cut2.html) to
identify restriction sites in both the wild-type and mutant sequence.
2. Perform PCR for the exon of interest and purify the fragment, as described previ-
ously (see Note 9).
3. Cut purified DNA with the restriction enzyme and analyze by agarose gel elec-
trophoresis, using standard molecular biology techniques (16).
4. Ethnically matched controls should be analyzed.
3.6.2. ARMS Assay
In the event that no restriction site has been altered by the mutation, ARMS
assay analysis can be performed on controls. This technique uses primers
incorporating either the mutation or wild-type nucleotide as the last base of the
oligonucleotide primer.
1. Generate a wild-type and mutation oligonucleotide primer that differ only at the
most 3'-base. The same reverse primer can be used with both wild-type and mu-
tation forward primers.
2. Perform PCR. Each DNA sample should have one reaction performed with wild-
type primers and one performed with mutation primers (see Note 10).
3. Purify PCR reactions and analyze by gel electrophoresis, using standard molecu-
lar biology techniques.
254 Ware

4. Notes
1. This page provides information about the structure and alignment of ZIC3. Links
to additional databases provide information about intron–exon structure, com-
parative sequence analysis between species, bacterial artificial chromosomes con-
taining the sequence of interest, protein structure, and more.
2. The primers should be a minimum of 50 bp outside of the exon, so that all coding
sequence will be visible on the sequence trace. To ensure that high-quality se-
quence can be obtained from the entire coding region, exons larger than 400 to
500 bp should be divided into segments. The length that can be screened in a
single sequence trace will depend on both the architecture of the genomic DNA
region as well as the sequencing facility.
Publicly available primer design programs include Net Primer (http://
www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html) , Primer 3
(http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi), and Prophet (the
National Institutes of Health program, now discontinued but still very useful).
There are also commercially available primer design programs, including Primer
Premier (http://www.premierbiosoft.com/products/price_list/price_list.html) and
Oligo (www.oligo.net). In addition to oligonucleotide length and GC content,
these programs will identify primers without significant secondary structure or
hairpin loop formation, and will usually eliminate annealing between primers
that can result in primer–dimer formation.
3. Primers for PCR amplification of the open-reading frames of EGF-CFC,
ACVR2B, and LEFTYA are published (9–11). These genes were all screened ini-
tially by single-stranded conformation polymorphism (SSCP) analysis, and
abnormalities were confirmed by direct sequencing. SSCP, denaturing high-per-
formance liquid chromatography (DHPLC), and direct sequence analysis all use
PCR amplification of exons as an initial step. The choice of procedure depends
on the scale of the mutation screening, the available equipment, and technical
expertise. Direct sequencing is attractive because of its widespread commercial
availability and its increasing affordability. However, the cost of DHPLC re-
mains substantially below direct sequencing (after the initial equipment costs
and training) and is a better choice for screening of very large genes or large
sample numbers. Both SSCP and DHPLC are screening tools and require direct
sequencing to confirm abnormalities.
4. Exon 1a is the most problematic to amplify. If multiple bands amplify, the frag-
ment of interest can be cut from the agarose gel and purified before sequencing.
A 20-μL reaction gave better results than a 50-μL reaction.
5. The annealing temperatures are determined empirically. Thermocycling programs
using a gradient of annealing temperatures were used to establish the temperature
that maximizes the product and minimizes nonspecific products. In general, for
difficulties with amplification, any component of the reaction mixture can be
altered. Changing the annealing temperature or altering the magnesium chloride
content will often increase specificity. If these modifications are not effective,
we have generally found that it is most efficient and cost effective to try at least
ZIC3 Mutation Analysis 255

one primer redesign before significantly attempting to further optimize reaction

conditions.
6. Higher throughput purification can be achieved using a 384- or 96-well plate
format. Purification is performed using a vacuum manifold. Multichannel
pipetters are useful for both PCR reaction set up and purification.
7. “N” is the sequence designation assigned when no nucleotide call can be made. In
genes on the autosomes, mutations result in heterozygosity at a nucleotide position,
read as “N” on the sequence trace. It is important to evaluate all “N” designations
because this may simply reflect poor sequence quality within a region. It is also
important to look at all sequence traces (or know how your sequence analysis soft-
ware functions), because heterozygous positions can fail to be designated as “N”
(see Fig. 3, carrier). In males with ZIC3 mutations, a nucleotide mismatch will be
observed. In these patients, “N” usually implies poor sequence results.
8. This method will fail to align two regions of exon 1a of the ZIC3 gene. Both the
polyhistidine and polyalanine tracts must be aligned manually because of failure
of BLAST two-pair alignment.
9. If the mutation site is very near one end of the amplicon, new primers may need
to be designed, such that restriction digestion of the product results in two readily
visible bands after gel electrophoresis.
10. The ARMS assay is predicated on failure of amplification when a mismatch be-
tween the last (most 3') base of the primer and genomic DNA exists. In reality,
the amplification may be robust and occur even with this mismatch. Therefore, it
is very important to optimize reaction conditions to ensure both proper amplifi-
cation and failure of amplification in known samples before screening additional
probands or controls.

Acknowledgments
I thank Jianlan Peng, Trang Ho, Laura Molinari, Brett Casey, Jeff Towbin,
and John Belmont for their contribution to the ZIC3 mutation analysis. This
work was supported by the National Institutes of Health grants HL67355 and
HD41648.

References
1. Aylsworth, A. S. (2001) Clinical aspects of defects in the determination of lateral-
ity. Am. J. Med. Genet. 101, 345–355.
2. Ware, S. M. and Belmont, J. W. (2004) ZIC3, CFC1, ACVR2B, and EBAF and the
visceral heterotaxies, in Inborn Errors of Development: The Molecular Basis of
Clinical Disorders of Morphogenesis (Epstein, C. J., Erickson, R. P., and
Wynshaw-Boris, A., eds.), Oxford University Press, New York, pp. 300–314.
3. Hamada, H., Meno, C., Watanabe, D., and Saijoh, Y. (2002) Establishment of
vertebrate left–right asymmetry. Nat. Rev. Genet. 3, 103–113.
4. Bisgrove, B., Morelli, S., and Yost, H. (2003) Genetics of human laterality disor-
ders: insights from vertebrate model systems. Ann. Rev. Genomics Hum. Genet. 4,
1–32.
256 Ware

5. Tabin, C. J. and Vogan, K. J. (2003) A two-cilia model for vertebrate left–right

axis specification. Genes Dev. 17, 1–6.
6. Gebbia, M., Ferrero, G. B., Pilia, G., et al. (1997) X-linked situs abnormalities
result from mutations in ZIC3. Nat. Genet. 17, 305–308.
7. Megarbane, A., Salem, N., Stephan, E., et al. (2000) X-linked transposition of the
great arteries and incomplete penetrance among males with a nonsense mutation
in ZIC3. Eur. J. Hum. Genet. 8, 704–708.
8. Ware, S. M., Peng, J., Zhu, L., et al. (2004) Identification and functional analysis
of ZIC3 mutations in heterotaxy and related congenital heart defects. Am. J. Hum.
Genet. 74, 93–105.
9. Bamford, R. N., Roessler, E., Burdine, R. D., et al. (2000) Loss-of-function muta-
tions in the EGF-CFC gene CFC1 are associated with human left–right laterality
defects. Nat. Genet. 26, 365–369.
10. Kosaki, K., Bassi, M. T., Kosaki, R., et al. (1999) Characterization and mutation
analysis of human LEFTY A and LEFTY B, homologues of murine genes impli-
cated in left–right axis development. Am. J. Hum. Genet. 64, 712–721.
11. Kosaki, R., Gebbia, M., Kosaki, K., et al. (1999) Left–right axis malformations
associated with mutations in ACVR2B, the gene for human activin receptor type
IIB. Am. J. Med. Genet. 82, 70–76.
12. Ferrero, G. B., Gebbia, M., Pilia, G., et al. (1997) A submicroscopic deletion in
Xq26 associated with familial situs ambiguus. Am. J. Hum. Genet. 61, 395–401.
13. Birney, E., Andrews, D., Bevan, P., et al. (2004) Ensembl 2004. Nucleic Acids Res.
32(Database issue), D468–470.
14. Clamp, M., Andrews, D., Barker, D., et al. (2003) Ensembl 2002: accommodating
comparative genomics. Nucleic Acids Res. 31, 38–42.
15. Hubbard, T., Barker, D., Birney, E., et al. (2002) The Ensembl genome database
project. Nucleic Acids Res. 30, 38–41.
16. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, A Labo-
ratory Manual, Cold Spring Harbor Laboratory Press, NY.
DHPLC in Pediatric Cardiomyopathies 257

16
Use of Denaturing High-Performance Liquid
Chromatography to Detect Mutations in Pediatric
Cardiomyopathies

Amy J. Sehnert

Summary
This chapter describes the use of denaturing high-performance liquid chromatography as a
high-throughput method to detect genetic mutations in pediatric cardiomyopathies. An over-
view of the classification, incidence, and etiologies of the major cardiomyopathies is provided,
with emphasis on the special circumstances of the pediatric patient. During the past 15 yr, the
genetic bases of inherited dilated, hypertrophic, and restrictive cardiomyopathy have been elu-
cidated. As the list of known and candidate cardiomyopathy genes continues to grow and our
ability to screen for genetic mutations improves, the cause of cardiomyopathy will be identified
in a larger percentage of cases. This outcome is highly relevant to children with cardiomyo-
pathy as well as those at risk for developing the disease because of their family history.
Key Words: Cardiomyopathy; DCM; HCM; RCM; genetic mutations; DHPLC.

1. Introduction
1.1. Classification of Cardiomyopathies
Cardiomyopathies are the leading cause of heart failure, arrhythmias, and
sudden cardiac death, and are the leading indication for heart transplantation
(1). Three major classes of cardiomyopathies, dilated cardiomyopathy (DCM),
hypertrophic cardiomyopathy (HCM), and restrictive cardiomyopathy (RCM),
are defined by clinical criteria established by the World Health Organization
(2). Patients with DCM show thin-walled, enlarged ventricles with systolic
dysfunction. Patients with HCM show a thick-walled, hypercontractile heart of
increased mass, which may exhibit abnormal relaxation. Patients with RCM
show normal or nearly normal ventricular size, wall thickness, and systolic
function, with restrictive ventricular filling pressures and atrial enlargement
(1,3,4). Cardiomyopathies may occur at any time from fetal life through old
From: Methods in Molecular Medicine, vol. 126: Congenital Heart Disease: Molecular Diagnostics
Edited by: M. Kearns-Jonker © Humana Press Inc., Totowa, NJ

257
258 Sehnert

age and are either primary (caused by an intrinsic heart muscle abnormality),
or secondary (caused by ischemia, valve abnormalities, congenital heart dis-
ease, systemic disorders, infections, or toxins). In this chapter, we focus on the
special case of primary cardiomyopathies in children.
1.2. Incidence and Causes of Pediatric Cardiomyopathies
The incidence of primary cardiomyopathy in children younger than 18 yr
old in the United States is 1.13 per 100,000. Almost half of all cases are ascer-
tained in infants younger than 1 yr of age, in which group, the incidence is 8.34
per 100,000. A second peak occurs during adolescence (5). DCM accounts for
51% of pediatric cardiomyopathies, and HCM accounts for 42% of cases. Less
common forms, such as RCM and arrhythmogenic right ventricular dysplasia
(ARVD) account for only a minor fraction of cases (<5%). Overall, the cause
remains unknown in two-thirds of children presenting with primary cardiomy-
opathy, and the mortality rate is 13% within 2 yr of diagnosis (5,6). When a
cause is assigned for DCM, it is most likely caused by a neuromuscular disor-
der (i.e., X-linked muscular dystrophy), myocarditis, or familial inherited dis-
ease. For HCM, the leading identified causes are familial inherited disease,
inborn error of metabolism (i.e., disorders of glycogen metabolism or oxida-
tive phosphorylation), and malformation syndrome (i.e., Noonan syndrome)
(5,6). In general, familial cardiomyopathies represent an important diagnostic
category that may go unrecognized if cardiovascular symptoms are absent or
mild in a child undergoing routine clinical examination. Specifically document-
ing whether a family history of cardiomyopathy and/or sudden cardiac death
exists is an essential component of pediatric care.
1.3. Genetic Basis of Familial Cardiomyopathies
Familial cardiomyopathies are largely caused by autosomal-dominant mu-
tations in structural proteins of the cytoskeleton (i.e., lamin A/C and
sarcoglycan), cardiac sarcomere (i.e., myosin heavy and light chains, troponins,
and tropomyosin), sarcoplasmic reticulum (i.e., ryanodine receptor and
phosholamban), and energy-regulating pathways (i.e., adenosine 5'-monophos-
phate-activated protein kinase) (1,3,4,7). HCM occurs in 1 in 500 adults, of
which, 80% of cases are caused by a genetic mutation (8). DCM occurs in 1 in
2500 adults, and it is currently estimated that approx 30 to 40% of cases are
genetic. For these reasons, annual clinical screening is currently recommended
for offspring in families with any form of primary cardiomyopathy to look for
evidence of disease (9). Both the discovery of mutations in inherited forms of
cardiomyopathy and the burden of disease screening have made genetic diag-
nosis in pediatric patients an important endeavor.
DHPLC in Pediatric Cardiomyopathies 259

1.4. Detecting Genetic Mutations in Cardiomyopathies

Hundreds of mutations in more than 20 genes have now been identified as
the cause of DCM, HCM, RCM, and ARVD, and more disease genes and
mutations remain to be discovered (1,3,4,11, and Sehnert, unpublished data).
Currently, the bulk of mutation screening in known and candidate genes is
conducted in research laboratories by investigators interested in cardiac genet-
ics. In this setting, a variety of methods are used to detect genetic variations
(polymorphisms and mutations) in human DNA samples. This chapter de-
scribes the use of denaturing high-performance liquid chromatography
(DHPLC) as a high-throughput method for screening cardiomyopathy genes
for mutations. It highlights examples from the cardiomyopathy literature and
our own experience (12–33 and Sehnert, unpublished data).

2. Materials
1. Polymerase chain reaction (PCR) machine.
2. DHPLC equipment and column.
3. Computer and vendor software.
4. Source DNA.
5. Taq polymerase.
6. Oligonucleotide primers.
7. HPLC-grade water.
8. HPLC-grade acetonitrile.
9. 2 M triethlyammonium acetate (TEAA).
10. Shrimp alkaline phosphatase.
11. Exonuclease I.
12. Gene-sequencing capability.

3. Methods
The use of DHPLC for mutation detection requires investment in a commer-
cially available system or access to a core facility that offers such capability (see
Note 1). The methods described in the chapter present the principle of DHPLC
technology, and provide a practical guide to optimize PCR conditions for DHPLC
analysis, interpret results, and process samples for gene sequencing.
3.1. DHPLC: How It Works
Originally developed to facilitate evolutionary studies of the Y-chromo-
some, DHPLC has subsequently been validated and used as a highly sensitive
method to detect variations in more than 300 genes that cause a variety of
diseases, including cancers, and neurological, hematological, metabolic, au-
toimmune, and cardiovascular disorders, and others (34–38). DHPLC offers a
nonbiased method to screen DNA for single base changes as well as small
260 Sehnert
Table 1
Cardiomyopathy Genes Analyzed by DHPLC
Gene
Disease gene(s) symbol Refs.
HCM
β-Myosin heavy chain MYH7 12–15
Myosin-binding protein C MYBPC3 16
Cardiac troponin T TNNT2 13,14,17,18
Cardiac troponin I TNNI3 17,18
α-Tropomyosin TPM1 17–19
α-Cardiac actin ACTC 17
HCM with WPW syndrome
AMP-activated protein kinase PRKAG2 18,20,21
Noonan syndrome (HCM)
Protein-tyrosine phosphatase nonreceptor-type 11 PTPN11 22–27
DCM
Sarcoglycan SGCD 28
Lamin A/C LMNA 29–31
ARVD
Cardiac ryanodine receptor 2 RYR2 32
Mitochondrial genome mtDNA 33,38
DHPLC, denaturing high-performance liquid chromatography; HCM, hypertrophic cardiomy-
opathy; WPW, Wolff–Parkinson–White; AMP, adenosine 5'-monophosphate; ARVD,
arrhythmogenic right ventricular dysplasia; mtDNA, mitochondrial DNA.

insertions or deletions (39,40). The method is ideal for detecting heterozygous

missense changes that are characteristic of the autosomal-dominant cardiomyo-
pathies (3,4,39,40). Table 1 shows a list of cardiomyopathy genes previously
subjected to DHPLC analysis, including references.
DHPLC relies on a reusable, novel matrix column, and an ion-pairing
reagent (TEAA) that bridges negatively charged DNA molecules to the sta-
tionary phase (36,37,39). Using this technique, mixed PCR products from nor-
mal (homozygous) and test subject DNA are denatured (heated) and reannealed
(cooled). In the presence of sequence variations, the heating and cooling step
allows heteroduplexes and homoduplexes to form (Fig. 1A). Heteroduplexes
and homoduplexes are then fractionated under partially denaturing conditions
on the heated column of hydrophobic beads. The altered denaturation and
migration properties of heteroduplex products provide the basis for detecting
sequence variations (Fig. 1B; see Note 2). The optimal temperature for DHPLC
analysis is determined using software computation programs (41). The high-
DHPLC in Pediatric Cardiomyopathies 261

Fig. 1. Homoduplex and heteroduplex formation. (A) shows the double-stranded

PCR products amplified from template DNA containing a single base G → A substitu-
tion in sample from a heterozygous individual. When the PCR products are denatured
and reannealed, homoduplexes and heteroduplexes are formed, as shown in the line
drawings. Altered denaturation and migration properties of the homoduplexes and het-
eroduplexes result in different elution times off of the DHPLC column, as shown in
(B). Heteroduplexes elute off first. Data shown is taken from the Transgenomic muta-
tion standard run in our lab. Absorbance, ultraviolet absorbance.

throughput nature of the method is achieved by combining multiple samples

for simultaneous analysis.
3.2. Amplify Target Sequence
Autosomal-dominant transmission is the most common mode of inheritance
of DCM, HCM, RCM, and ARVD (1,3,4). The vast majority of causative
mutations are single base substitutions within exons that result in missense
262 Sehnert

Fig. 2. Design PCR fragments for DHPLC. Genomic structure of a hypothetical

gene with nine exons (black, filled boxes) is shown. Ideal fragments for DHPLC analy-
sis are 200- to 500-bp long. (A) Shows the most typical fragment design including one
exon with flanking intron sequence (50–100 bp on either side of the exon). (B) Shows
a fragment spanning two small exons with an intervening intron. (C) Shows a large
exon scanned in two overlapping fragments that were independently amplified by PCR.
Small arrows indicate the PCR primers.

changes, or changes at exon–intron boundaries that alter gene splicing (3). It

is, therefore, typical to begin to scan a candidate gene for variations by tar-
geting gene fragments that contain an exon sequence with some flanking
intron (Fig. 2A). Selected portions of 5'-upstream and 3'-downstream
sequences can also be included, as well as the entire genomic sequence,
depending on gene structure, the size of introns, and the purpose of the
project. Many primers have been selected and are published (Table 1) and/or
are available online at: http://insertion.stanford.edu/dhplc_genes1.html (38).
3.2.1. Analyze the Sequence
Once a candidate gene or genes have been selected for analysis, the first step
is to gather as much information as possible from the literature and human
genome databases regarding the sequence and structure of the genes (see Note
3). At this time, it is also relevant to note the presence of verified single-nucle-
otide polymorphisms (SNPs) and their location within the sequence of interest.
When possible, sequences containing uninformative SNPs can be eliminated
from target fragments to minimize the variations that would be detected by
DHPLC. On the other hand, if knowledge of a particular SNP allele frequency
is important to the project, then fragments can be designed to include SNP
bases.
DHPLC in Pediatric Cardiomyopathies 263

Next, determine the number of fragments to be analyzed per gene, based on

the length of the coding and noncoding regions. Although the DHPLC method
is capable of detecting mutations in long fragments (i.e., 1000–1500 bp), the
ideal fragment size is 200 to 500 bp (36,37,39). In most cases, fragments for
DHPLC analysis contain a single exon with flanking intron (i.e., 50 to 100 bp
of intron sequence on each side, Fig. 2A). Occasionally, it is possible to screen
a fragment that contains two exons and an intervening intron (Fig. 2B). Some-
times it becomes necessary to scan large exons in two or more overlapping
fragments (Fig. 2C). Before designing PCR primers, it is important to look at
the melting profile of each given sequence (see Note 4). Ideally, temperatures
should vary slightly across the fragment to allow partial melting, but not by
more than 15°C (39,41). This process is reiterated as necessary to achieve the
best possible melt profiles for sequences that span the gene of interest.
3.2.2. Design Primers
Once the sequence fragments are approximated using the steps given in Sub-
heading 3.2.1., specific primers can be designed. Many software and on-line
resources are available to assist in primer picking using selected constraints
(i.e., http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi). In general,
primers with a melting temperatur between 55°C and 58°C and within 1°C of
each other are desirable. During the process of sequence analysis and primer
design, one can examine the affect of modifications to improve the melt pro-
file, such as adding a GC-clamp to the ends of primers. High-purity oligo-
nucleotide primers should be used (we recommend high-purity, salt-free
oligonucleotides from MWG Biotech, Highpoint, NC). Depending on the frag-
ment being amplified, it may be necessary to reiterate primer design to arrive
at an optimal pair. Technical support is also available from the DHPLC ven-
dors to troubleshoot and assist with primer design for difficult fragments.
3.2.3. Extract DNA
Extract DNA from blood or tissues using standard molecular methods to
produce a high-quality template for PCR (i.e., Qiagen genomic-tip system).
3.2.4. Optimize PCR conditions
Perform PCR on 50 to 100 ng of template DNA using a standard
thermocycler and a touch-down program (94°C for 4 min followed by cycling
at: 94°C for 30 s, annealing temperature for 1 min, and 72°C for 1 min; the
annealing temperature is reduced from 60°C to 55°C in 0.5°C increments with
each cycle, followed by 20 to 30 cycles at 55°C; and a final extension at 72°C
for 10 min). Run a test PCR for each primer pair to examine the strength and
quality of the product by gel electrophoresis, and confirm its sequence before
264 Sehnert

proceeding to DHPLC. For best results on small fragments (100 to 500 bp), we
recommend using a 9:1 ratio of AmpliTaq Gold® (Applied Biosystems) to Pfu
Turbo (Stratagene) with the AmpliTaq Gold buffer. To allow adequate sample
for gel electrophoresis (8–10 μL), DHPLC (20–30 μL), and sequencing (5–10 μL),
we amplify in 50-μL PCR volumes with primers, dNTPs, buffer, MgCl2+, and
Taq polymerase. A pure PCR product is critical to good DHPLC results. Alter
PCR conditions as needed to meet this end (see Note 5). Once the PCR condi-
tions are optimized, amplify the fragments for DHPLC analysis from template
DNA, including a control sample.
3.3. Denature and Reanneal PCR Product
After PCR, combine equal amounts of the product from each test sample
with the control product (i.e., 15–20 μL each), then denature and reanneal the
mixed sample. The mixture of samples can also be approached through sample
pooling (i.e., three or more samples combined together). In the case of cardi-
omyopathies, in which most mutations are heterozygous in nature, it is also
reasonable to screen individual samples without mixing, as long as it is under-
stood that this will not detect homozygous changes. To denature, heat samples
to 95°C for 8 min, then gradually decrease the temperature by 2°C/min down
to 21°C.
3.4. Perform DHPLC
3.4.1. Select Operating Temperatures
Select operating temperatures for DHPLC analysis based on the melt profile
for each fragment. Ideal temperatures are calculated using system software or
programs such as the one at http://insertion.stanford.edu/dhplc.html. It is highly
recommended that each fragment be run at two or three different temperatures
to ensure detection of all polymorphisms in a fragment. The operating tem-
peratures typically vary by 1 to 2°C, and sometimes more, depending on the
sequence.
3.4.2. Run Samples
DHPLC is an automated method (36,37). Running buffers can be purchased
or prepared according to manufacturer’s directions using volumetric flasks and
HPLC-grade water (see Note 6). Buffer A is a 0.1 M TEAA solution, Buffer B
contains 0.1 M TEAA with 25% acetonitrile. Wash solutions of 8% acetoni-
trile and 75% acetonitrile are used for the injection syringe and DHPLC col-
umn, respectively. A 96-well plate format and autosampler allow for long runs
once the conditions are specified and entered in a table on the computer. In
general, use a 10-μL volume for each DHPLC injection and test each fragment
DHPLC in Pediatric Cardiomyopathies 265

at a minimum of two operating temperatures. Run a mutation standard at the

beginning of each run and blank injections before and between samples. When
possible, include positive-control samples for selected fragments. Start by using
running buffer gradients selected by the system software. The buffer gradients
can be adjusted, if necessary, to improve detection for any given fragment.
Consult vendor manuals and technical support for detailed operating instruc-
tions and troubleshooting information.
3.4.3. Interpret Results
Once samples have been run, review the data using the system software.
Analyze the peaks for their quality (cleanliness and amplitude) and informa-
tive value (presence of homoduplex and heteroduplex peaks). Example traces
are shown in Fig. 3. Be aware that a variety of trace morphologies may be
encountered and that these may also vary between runs for the same fragment.
Every effort should, therefore, be taken in the process of PCR to generate con-
sistent, high-quality products for analysis. Newer instruments offer software
that can perform automated peak analysis and classification to aid high-
throughput analysis. Each application needs to be customized at the beginning
of the project and confirmed by sequencing to achieve the most reliable and
repeatable results.
3.5. Examine Suspect Fragments for Sequence Variations
Purify PCR products from fragments that show heteroduplexes for direct
sequencing using standard methods (i.e., add shrimp alkaline phosphatase
[Roche Molecular Biochemicals] and exonuclease I [New England Biolabs];
heat to 37°C for 35 min, then to 95°C for 15 min). Perform automated DNA
sequencing and analyze sequence traces for variations using appropriate soft-
ware (Fig. 3).

4. Notes
1. DHPLC instrumentation is commercially available from two major manufactur-
ers, the Transgenomic WAVE™ (Omaha, NE) and Varian Helix HPLC (Palo
Alto, CA). We found that the quality and condition of the column, technical sup-
port provided by the vendor, and routine system maintenance were critical to
successful operation of the WAVE instrument.
2. Samples are injected into a flow path with TEAA and acetonitrile. The hydro-
phobic portion of TEAA interacts with hydrophobic beads in the column, and the
negatively charged phosphate backbone of partially denatured PCR products in-
teract with the positively charged ammonium groups of TEAA. At increasing
concentrations of acetonitrile, the TEAA to DNA attraction is reduced, and prod-
ucts are eluted off of the column such that heteroduplexes with the mismatched
266 Sehnert

Fig. 3. DHPLC spectra and sequence traces. This figure shows DHPLC spectra
above the corresponding sequence traces for three PCR fragments (top to bottom).
Results from homozygous (normal) samples are on the left, and results from heterozy-
gous samples (containing a sequence variation) are on the right. Normal samples show
a single elution peak, whereas heterozygous samples show a separation of the elution
peaks. This indicates the presence of heteroduplexes in the sample. Arrows below
sequence traces point to base changes confirmed in these fragments.
DHPLC in Pediatric Cardiomyopathies 267

bases elute off first and homoduplexes elute off next (Fig. 1B). As fragments
pass through the UV detector, absorbance is measured and data are sent to the
computer for analysis (http://www.transgenomic.com/).
3. We routinely used the University of California at Santa Cruz website (http://
genome.ucsc.edu/) as a primary source for sequence information and related links.
4. The melting curve of the fragment can be examined using DHPLC system soft-
ware or melting curve calculators available on-line (i.e., http://insertion.
stanford.edu/melt.html or http://web.mit.edu/osp/www/melt.html).
5. We found that subamplification of small fragments from a long-range PCR prod-
uct (6 to 8 kb amplified with SuperMix High Fidelity Taq polymerase
[Invitrogen]) yielded specific, strong products for DHPLC. A potential limitation
is that this requires an additional round of PCR.
6. Prepare buffers using volumetric flasks provided by the vendor. To prevent bac-
terial growth in Buffer A, add 250 μL of HPLC grade acetonitrile to 1 L of buffer.
Use clean, glass wide-mouth bottles with screw caps for operation and storage of
buffers. DO NOT autoclave water or bottles used for DHPLC buffers because
small metal fragments may damage the column.

Acknowledgments
The author thanks Renee Reijo Pera, PhD, who shared her DHPLC equip-
ment for studies of pediatric cardiomyopathies, the patients who participated,
and their families. I also acknowledge the technical expertise of Matthew
Bensley, who performed the majority of our mutation detection experiments.
This work was supported by grants from the National Institutes of Health
(K08HL004068), the Greenberg Foundation Young Investigator Award in Car-
diovascular Genetics, and the University of California at San Francisco Pediat-
ric Clinical Research Center (to AS).

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25. Legius, E., Schrander-Stumpel, C., Schollen, E., Pulles-Heintzberger, C.,
Gewillig, M., and Fryns, J. P. (2002) PTPN11 mutations in LEOPARD syndrome.
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27. Musante, L., Kehl, H. G., Majewski, F., et al. (2003) Spectrum of mutations in
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28. Love, D. R. (2004) Limb girdle muscular dystrophy: use of dHPLC and direct
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29. Taylor, M. R., Fain, P. R., Sinagra, G., et al. (2003) Natural history of dilated cardi-
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30. Taylor, M. R., Robinson, M. L., and Mestroni, L. (2004) Analysis of genetic varia-
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31. Arbustini, E., Pilotto, A., Repetto, A., et al. (2002) Autosomal dominant dilated
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35. Underhill, P. A., Shen, P., Lin, A. A., et al. (2000) Y chromosome sequence varia-
tion and the history of human populations. Nat. Genet. 26(3), 358–361.
36. Premstaller, A. and Oefner, P. J. (2003) Denaturing high-performance liquid chro-
matography. Methods Mol. Biol. 212, 15–35.
37. Frueh, F. W. and Noyer-Weidner, M. (2003) The use of denaturing high-perfor-
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stanford.edu/dhplc_genes1.html. Accessed at UCSF.
39. Oefner, P. and Underhill, P. (1998) DNA mutation detection using denaturing
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Seidman, J. G., and Smith, D. R., eds), John Wiley and Sons, New York, pp.
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40. Xiao, W. and Oefner, P. J. (2001) Denaturing high-performance liquid chroma-
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41. Jones, A. C., Austin, J., Hansen, N., et al. (1999) Optimal temperature selection
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1133–1140.
Index 271

Index
A epidemiology, 19, 31
ACVR2B, mutations in heterotaxy, 247 preimplantation genetic diagnosis,
ADCL, see Autosomal-dominant cutis laxa clinical follow-up, 35, 36
Alagille syndrome, in vitro fertilization and blastomere
clinical features, 217 biopsy, 34
JAG1 mutation detection, materials, 33, 34
cardiovascular manifestations, 218 overview, 2, 3, 33
conformation-sensitive gel restriction fragment length
electrophoresis, 220, 221, 225, polymorphism analysis, 35, 36
227, 230 TBX5 mutation detection, 34, 35
fluorescence in situ hybridization, Autosomal-dominant cutis laxa (ADCL),
223–225, 230
materials, 222, 223, 228–230 clinical features, 130, 131
mutation types, 220 overview, 9, ELN gene mutation analysis,
10, 220, 221 polymerase chain denaturing high-performance liquid
reaction, 225, 230 sequencing, 230, chromatography,
231 polymerase chain reaction, 143,
Amplification refractory mutation system 145, 154, 155
(ARMS) assay, ZIC3 mutation principles, 144
screening in heterotaxy, 253, 255 running conditions, 145
Andersen syndrome, see Long QT syndrome genotyping,
ANKB, mutation in long QT syndrome, 69 fluorescent genotyping, 150
ARMS assay, see Amplification refractory microsatellite markers, 149
mutation system assay nonfluorescent genotyping, 149, 150
ASD, see Atrial septal defect
Atrial septal defect (ASD), see also specific single nucleotide
diseases, polymorphisms, 149
cardiogenesis, 20 lesion types, 132, 133
diseases, 22–24 materials, 133–136
epidemiology, 19, 20 overview, 7, 130, 131, 136, 137
GATA-4 mutations, 28, 29 partial deletion and translocation
NKX2.5 mutations, 26–28 analysis, 148
preimplantation genetic diagnosis, reverse transcriptase-polymerase
clinical follow-up, 35, 36 chain reaction of transcripts in
in vitro fertilization and blastomere cultured fibroblasts,
biopsy, 34 amplification reaction, 154
materials, 33, 34 applications, 150
overview, 2, 3, 33
first-strand cDNA synthesis, 153
restriction fragment length
polymorphism analysis, 35, 36 RNA preparation, 152, 153
TBX5 mutation detection, 34, 35 sequencing, 145, 146, 148
Atrioventricular septal defect (AVSD), see single-strand conformation
also specific diseases, polymorphism analysis,
candidate genes, 32 gel electrophoresis, 140, 142, 144
cardiogenesis, 20 polymerase chain reaction, 139–142
chromosomal aberration association, 31, 32 principles, 137–139
diseases, 22–24 silver staining of gels, 144
AVSD, see Atrioventricular septal defect
271
272 Index
B clinical features, 73, 171, 172
Brugada syndrome, genetic analysis,
clinical features, 72 denaturing high-performance liquid
clinical genetics, 72 chromatography,
genetic analysis, analysis, 179, 181, 182
denaturing high-performance liquid anticipated results, 64
chromatography, polymerase chain reaction of target
anticipated results, 64 sequences, 60, 74, 176, 182
polymerase chain reaction of principles, 59, 60
target sequences, 60, 74 running conditions, 60–62, 74, 75,
principles, 59, 60 176, 177, 182
running conditions, 60–62, 74, 75 materials, 58, 59, 73, 74, 173, 174, 181
materials, 58, 59, 73, 74 overview, 4, 8
overview, 4 sequencing,
sequencing, analysis, 77, 179, 182
anticipated results, 64 anticipated results, 64
cycle sequencing reaction, 63, 64 BigDye sequencing, 175, 181
overview, 62, 63 cycle sequencing reaction, 63, 64
primer labeling, 63 overview, 62, 63
template preparation, 63 polymerase chain reaction and
SCN5A mutations, 72 electrophoresis of products,
175, 176, 181 primer
C labeling, 63 template
CardioChip, see DNA microarray preparation, 63
Cardiomyopathy, KCNJ2 mutations, 173
clinical features, 257, 258 RyR2 mutations, 73, 172
DNA microarray analysis, see DNA Chromosome 22q11 deletion syndrome, see
microarray DiGeorge syndrome;
forms, 157, 257 Velocardiofacial syndrome
pediatric cardiomyopathy, Conformation-sensitive gel electrophoresis
incidence, 258 (CSGE), JAG1 mutation detection
etiologies, 258 in Alagille syndrome, 220, 221,
genetics, 258 225, 227, 230
denaturing high-performance liquid CPVT, see Catecholaminergic polymorphic
chromatography of gene mutations, ventricular tachycardia
amplification product denaturation CRELD1, atrioventricular septal defect
and reannealing, 264 mutations, 32
DNA extraction, 263 CSGE, see Conformation-sensitive gel
instrumentation, 259, 265 electrophoresis
interpretation, 265
materials, 259 D
overview, 11, 12 Denaturing high-performance liquid
polymerase chain reaction, 263, 264 chromatography (DHPLC),
primer design, 263 cardiac arrhythmia gene mutation screening,
principles, 259–261 anticipated results, 64
running conditions, 264, 265, 267 polymerase chain reaction of target
target sequence selection, 262, sequences, 60, 74
263, 267 principles, 59, 60
sequencing of gene mutations, 265 running conditions, 60–62, 74, 75
Catecholaminergic polymorphic ventricular
tachycardia (CPVT), catecholaminergic polymorphic ventricular
CASQ2 mutations, 172, 173 tachycardia genetic analysis,
analysis, 179, 181, 182
Index 273
anticipated results, 64 DiGeorge syndrome (DGS),
polymerase chain reaction of target chromosome 22q11 deletions,
sequences, 60, 74, 176, 182 characteristics, 45, 46, 49
principles, 59, 60 diagnostic testing, control
running conditions, 60–62, 74, 75, probe, 48–50
176, 177, 182 cytogenetic analysis, 47
ELN gene mutation analysis, fluorescence in situ hybridization,
Marfan syndrome FBN1 mutations, 47, 49
85–91 materials, 48
Noonan syndrome PTPN11 microsatellite markers, 50, 51
mutations, 101, 102 prenatal resting indications, 47
polymerase chain reaction, 143, 145, quantitative polymerase chain
154, 155 reaction, 51
principles, 144 overview, 3, 4
running conditions, 145 clinical features, 30, 43–45
Marfan syndrome FBN1 mutations, TBX1 mutations, 30, 50
genomic DNA isolation, messenger DNA microarray,
RNA isolation, and cDNA applications, 158, 160, 233, 234
production, 84, 85 CardioChip analysis of cardiomyopathy,
materials, 83, 84 data processing, 164–166
overview, 4, 5 materials, 161, 162
polymerase chain reaction, 85–91 microarray construction, 162, 163
principles, 82, 83 overview, 7, 8, 161
running conditions, 85, 87, 94 polymerase chain reaction products, 162
sample preparation, 83, 84, 87, 94 probe labeling and hybridization,
sequencing, 87 163–165
Noonan syndrome PTPN11 mutation reverse transcriptase–polymerase chain
analysis with WAVE, reaction verification, 164, 166
Analysis Page entries, 106, 110 scanning, 164, 165
DNA Page entries, 104, 105 historical perspective, 158
Injection Page entries, 105, 106 platforms, 159
principles, 159, 160, 234, 235
materials, 98, 100, 101, 106
mutation types, 99 tetralogy of Fallot analysis,
overview, 5, 6, 97, 98 array selection, 237, 238
polymerase chain reaction, 101, 102 data normalization and statistical
running conditions, 102, 103, 106, analysis, 239, 241, 242, 243, 245
108–110 experimental design, 238–241
hybridization, 239, 245
pediatric cardiomyopathy gene mutations, materials, 235, 236
amplification product denaturation overview, 10, 11, 234, 235
and reannealing, 264 RNA isolation, cDNA synthesis, and
DNA extraction, 263 labeling, 239, 245
instrumentation, 259, 265 sample selection, 237, 245
interpretation, 265
materials, 259
overview, 11, 12 E
polymerase chain reaction, 263, 264 EGF-CFC, mutations in heterotaxy, 247
primer design, 263 Elastin,
principles, 259–261 ELN gene,
running conditions, 264, 265, 267 mutations, see Autosomal-dominant
target sequence selection, 262, 263, 267 cutis laxa; Supravalvular aortic
DGS, see DiGeorge syndrome stenosis
DHPLC, see Denaturing high-performance structure, 130
liquid chromatography synthesis, 129, 130
tissue distribution, 129
274 Index
Ellis–van Crevald syndrome, molecular diagnostics,
clinical features, 29 materials, 206
EVC genes and mutations, 29, 30 overview, 9, 205, 206
ELN, see Elastin point mutation detection, 208–211
polymerase chain reaction, 207,
F 208, 210
FA, see Friedreich ataxia sequencing, 208, 210
FBN1, see Marfan syndrome Southern blot, 208, 210
FISH, see Fluorescence in situ hybridization pathogenesis, 201, 203, 204
prognosis, 200
Fluorescence in situ hybridization (FISH), treatment prospects, 205
chromosome 22q11 deletion syndrome
diagnostics, 47, 49 G–H
JAG1 mutation detection in Alagille
syndrome, 223–225, 230 GATA-4,
Williams–Beuren syndrome diagnosis, cardiogenesis role, 28, 29
congenital heart malformations and
chromosome counterstaining and mutations, 28, 29
banding, 125, 126 Heart failure, see Cardiomyopathy
deletion detection, 127 Heterotaxy,
denaturation, 124 definition, 247
hybridization, 124 gene mutations, 247
imaging, 126, 128 ZIC3 mutation screening,
immunodetection, 125, 128 amplification product purification and
inversion detection, 127 gel electrophoresis, 251, 252, 255
materials, 114, 117, 118 controls for polymorphisms,
overview, 6, 7, 113, 114 amplification refractory mutation
probe preparation, system assay, 253, 255
restriction fragment length
biotin labeling, 122, 123 polymorphism, 253, 255
clone selection, 120 genomic DNA preparation, 248
combination labeling, 123 materials, 248
common deletion probe, 120 overview, 11, 247, 248
digoxigenin labeling, 122 polymerase chain reaction, 251,
genomic clone propagation, 254, 255
amplification and DNA primer design, 248, 249, 254
isolation, 121, 122 Hey genes, cardiogenesis role, 31
inversion probes, 121, 127, 128 Holt–Oram syndrome (HOS),
larger deletion probes, 121 clinical features, 21, 25
sizing of labeled fragments, 123 epidemiology, 21
gene expression, 26
smaller deletion probes, 121 TBX5 mutations, 25
Spectrum Green labeling, 123 HOS, see Holt–Oram syndrome
target DNA preparation,
lymphoblastoid cell line culture I–K
and harvest, 119, 120
peripheral blood lymphocyte Ivemark syndrome, atrioventricular septal
culture and harvest, 119 defects, 33
JAG1, see also Alagille syndrome,
slide preparation, 120 congenital heart disease mutations, 218, 219
washing, 125 protein function, 219
Frataxin, see Friedreich ataxia vascular manifestations of mutations, 219
Friedreich ataxia (FA), animal Jervell and Lange-Nielson syndrome, see
models, 204, 405 clinical Long QT syndrome
presentation, 198–200 KCNE1, mutation in long QT syndrome, 69–71
epidemiology, 198
frataxin gene mutations, 200, 201
laboratory findings, 200
Index 275
KCNE2, mutation in long QT syndrome, 70 M
KCNH2, mutation in long QT syndrome, 67, 68 Marfan syndrome (MFS),
KCNJ2,
catecholaminergic polymorphic ventricular clinical features, 81, 82
tachycardia mutations, 173 FBN1,
long QT syndrome mutations, 71, 173 denaturing high-performance liquid
KCNQ1, mutation in long QT syndrome, 66, chromatography analysis of
70, 71 mutations,
genomic DNA isolation,
L messenger RNA isolation and
LEFTYA, mutations in heterotaxy, 247 cDNA production, 84, 85
LOH, see Loss of heterozygosity materials, 83, 84
Long QT syndrome (LQTS), overview, 4, 5
Andersen syndrome gene mutations, 71, polymerase chain reaction, 85–91
72, 173 principles, 82, 83
clinical description, 65 running conditions, 85, 87, 94
genetic analysis, sample preparation, 83, 84, 87, 94
denaturing high-performance liquid sequencing, 87
chromatography, genotype–phenotype correlations, 82
anticipated results, 64 protein function, 82
polymerase chain reaction of structure, 82
target sequences, 60, 74 MFS, see Marfan syndrome
principles, 59, 60 Microsatellite markers,
running conditions, 60–62, 74, 75
ELN gene mutation analysis, 149
materials, 58, 59, 73, 74
overview, 4 loss of heterozygosity analysis in
sequencing, tuberous sclerosis complex,
anticipated results, 64 autoradiography, 190, 191, 194
cycle sequencing reaction, 63, 64 denaturing gel electrophoresis, 189,
overview, 62, 63 primer 190, 195 interpretation,
labeling, 63 template 192 microsatellite markers,
preparation, 63 186
genetics, 65, 66
Jervell and Lange-Nielson syndrome N
gene mutations, 70, 71 NKX2.5,
Romano–Ward syndrome gene cardiogenesis role, 27, 28
identification, congenital heart malformations and
ANKB, 69 mutations, 26–28
KCNE1, 69, 70 Noonan syndrome,
KCNE2, 70 atrioventricular septal defects, 32
KCNH2, 67, 68 clinical features, 97
KCNQ1, 66 PTPN11 mutation analysis with WAVE
SCN5A, 68, 69 denaturing high-performance
treatment, 70 liquid chromatography,
Loss of heterozygosity (LOH), Analysis Page entries, 106, 110
microsatellite markers analysis in DNA Page entries, 104, 105
tuberous sclerosis complex, Injection Page entries, 105, 106
autoradiography, 190, 191, 194 materials, 98, 100, 101, 106
denaturing gel electrophoresis, 189, mutation types, 99
190, 195
overview, 5, 6, 97, 98
interpretation, 192
polymerase chain reaction, 101, 102
microsatellite markers, 186
LQTS, see Long QT syndrome running conditions, 102, 103, 106,
108–110
276 Index
P Rhabdomyoma, see Tuberous sclerosis
PCR, see Polymerase chain reaction complex
Pediatric cardiomyopathy, see Romano–Ward syndrome, see Long QT
syndrome
Cardiomyopathy
RT-PCR, see Reverse transcriptase-
Polymerase chain reaction (PCR), see also
polymerase chain reaction
Reverse transcriptase-polymerase RyR2, polymorphic ventricular tachycardia
chain reaction, mutations, 73, 172
Brugada syndrome target sequences, 60, 74
CardioChip analysis of cardiomyopathy, 162 S
catecholaminergic polymorphic
SCN5A,
ventricular tachycardia genes, 175,
Brugada syndrome mutations, 72
176, 181
long QT syndrome mutations, 68, 69
chromosome 22q11 deletions, 51 Single nucleotide polymorphisms (SNPs),
denaturing high-performance liquid genotyping in supravalvular aortic
chromatography target sequences, stenosis, 149
cardiac arrhythmia gene mutation Single-strand conformation polymorphism
screening, 60, 74 (SSCP),
catecholaminergic polymorphic ELN gene mutation analysis,
ventricular tachycardia, 60, 74, gel electrophoresis, 140, 142, 144
176, 182 polymerase chain reaction, 139–142
ELN gene, 143, 145, 154, 155 principles, 137–139
pediatric cardiomyopathy gene silver staining of gels, 144
mutations, 263, 264 tuberous sclerosis complex analysis,
ELN gene mutation analysis, 139–142 191, 194
frataxin gene mutations in Friedreich SNPs, see Single nucleotide polymorphisms
ataxia, 207, 208, 210 Southern blot, frataxin defect detection in
JAG1 mutation detection in Alagille Friedreich ataxia, 208, 210
syndrome, 225, 230 SSCP, see Single-strand conformation
TSC1/2 mutation detection, 189, 193, 194 polymorphism
Sudden cardiac death, incidence, 57
ZIC3 mutation screening in heterotaxy, Supravalvular aortic stenosis (SVAS),
251, 254, 255 clinical features, 13
Polymorphic ventricular tachycardia, see ELN gene mutation analysis,
Catecholaminergic polymorphic denaturing high-performance liquid
ventricular tachycardia chromatography,
PTPN11, see Noonan syndrome polymerase chain reaction, 143,
145, 154, 155
R principles, 144
Restriction fragment length polymorphism running conditions, 145
(RFLP), genotyping,
preimplantation genetic diagnosis, 35, 36 fluorescent genotyping, 150
ZIC3 mutation screening in heterotaxy, microsatellite markers, 149
253, 255 nonfluorescent genotyping, 149, 150
Reverse transcriptase-polymerase chain single nucleotide polymorphisms, 149
reaction (RT-PCR), lesion types, 132, 133
CardioChip verification, 164, 166 materials, 133–136
ELN transcripts in cultured fibroblasts, overview, 7, 130, 131, 136, 137
amplification reaction, 154 partial deletion and translocation
applications, 150 analysis, 148
first-strand cDNA synthesis, 153 reverse transcriptase-polymerase
RNA preparation, 152, 153 chain reaction of transcripts in
RFLP, see Restriction fragment length cultured fibroblasts,
polymorphism
Index 277
amplification reaction, 154 polymerase chain reaction, 189, 193, 194
applications, 150 sequencing, 191–194
first-strand cDNA synthesis, 153 single-strand conformational
RNA preparation, 152, 153 polymorphism analysis, 191, 194
sequencing, 145, 146, 148 tumor suppressor gene mutations, 185, 186
single-strand conformation Tumor suppressor genes, see Tuberous
polymorphism analysis, sclerosis complex
gel electrophoresis, 140, 142, 144
polymerase chain reaction, V
139–142
principles, 137–139 VCFS, see Velocardiofacial syndrome
silver staining of gels, 144 Velocardiofacial syndrome (VCFS),
SVAS, see Supravalvular aortic stenosis chromosome 22q11 deletions,
characteristics, 45, 46, 49
T diagnostic testing, control
TBX1, probe, 48–50
DiGeorge syndrome mutations, 30, 50 cytogenetic analysis, 47
sequencing, 50 fluorescence in situ hybridization,
TBX5, 47, 49
cardiogenesis role, 25, 26 materials, 48
Holt–Oram syndrome mutations, 25 microsatellite markers, 50, 51
preimplantation genetic diagnosis, 34 prenatal resting indications, 47
Tetralogy of Fallot (TOF), quantitative polymerase chain
DNA microarray analysis, reaction, 51
array selection, 237, 238 overview, 3, 4
data normalization and statistical clinical features, 30, 44, 45
analysis, 239, 241, 242, 243, 245 Ventricular septal defect (VSD), see also
experimental design, 238–241 specific diseases,
hybridization, 239, 245 cardiogenesis, 20
materials, 235, 236 diseases, 22–24
overview, 10, 11, 234, 235 epidemiology, 19
RNA isolation, cDNA synthesis, and GATA-4 mutations, 28, 29
labeling, 239, 245 preimplantation genetic diagnosis,
sample selection, 237, 245 clinical follow-up, 35, 36
molecular pathogenesis, 235 in vitro fertilization and blastomere
TOF, see Tetralogy of Fallot biopsy, 34
TSC, see Tuberous sclerosis complex
Tuberous sclerosis complex (TSC), materials, 33, 34
clinical features, 185 overview, 2, 3, 33
TSC1/2 mutation detection in archival restriction fragment length
tissue specimens, polymorphism analysis, 35, 36
DNA extraction, 187–189, 193 TBX5 mutation detection, 34, 35
gene structures, 186 Ventricular tachycardia, see Catecholaminergic
laser capture microdissection, 188, polymorphic ventricular tachycardia
189, 193 VSD, see Ventricular septal defect
loss of heterozygosity analysis,
autoradiography, 190, 191, 194 W
denaturing gel electrophoresis, WAVE, see Denaturing high-performance
189, 190, 195 liquid chromatography
interpretation, 192 WBS, see Williams–Beuren syndrome
microsatellite markers, 186 Williams–Beuren syndrome (WBS),
materials, 186, 187 clinical features, 113
overview, 8, 9, 186 epidemiology, 113
fluorescence in situ hybridization diagnosis,
278 Index
chromosome counterstaining and target DNA preparation,
banding, 125, 126 lymphoblastoid cell line culture
deletion detection, 127 and harvest, 119, 120
denaturation, 124 peripheral blood lymphocyte
hybridization, 124 imaging, culture and harvest, 119
126, 128 immunodetection, slide preparation, 120
125, 128 inversion washing, 125
detection, 127 materials, supravalvular aortic stenosis, see
114, 117, 118 overview, 6, Supravalvular aortic stenosis
7, 113, 114 probe
preparation, Z
biotin labeling, 122, 123 ZIC3, heterotaxy mutation screening,
clone selection, 120 amplification product purification and
combination labeling, 123 gel electrophoresis, 251, 252, 255
common deletion probe, 120 controls for polymorphisms,
digoxigenin labeling, 122 amplification refractory mutation
genomic clone propagation, system assay, 253, 255
amplification and DNA restriction fragment length
isolation, 121, 122 polymorphism, 253, 255
inversion probes, 121, 127, 128 genomic DNA preparation, 248
larger deletion probes, 121 materials, 248
sizing of labeled fragments, 123 overview, 11, 247, 248
smaller deletion probes, 121 polymerase chain reaction, 251, 254, 255
Spectrum Green labeling, 123 primer design, 248, 249, 254