Chapter 1 Genetics and Medical Science

Ⅰ. The concepts of Genetics in Medicine

The Concepts of Genetics and Medical Genetics
The Concept of Gene
What is an Inherited Disease or Genetic Disorder
A genetic disorder is a disease that is caused by an DNA abnormality
1.chromosome disorder 4.mitochondria genetic disorder
2.single-base disorder 5.somatic cell genetic disorder
3.complex disorder
What is a Congenital Disease
- affected at birth
- some diseases are not genetic disorder
What is a Familial Disease
-not definitely genetic disorder
-from parent to their offspring
The relationship between Genetic and Environmental factors on Human Diseases
-every disease has its genetic components
-which genetic effects can be modified by environment exposures
Ⅱ.The History of Genetics in Mbyedicine
Mendel and his contribution to Genetics
Morgan and His students’ contributions
The technique developments in Medical Genetics
Ⅲ.Ontology of inherited disease
Chromosome disorder - number of chromosomes or a structural abnormality in one or
more chromosomes.
Single-gene disorder - involve mutations in the DNA sequences of single genes
Mitochondrial genetic disorder - only in the living things that use mitochondria as DNA

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Multifactorial disorder - many genes
Somatic cell genetic disorder - cancer
Ⅳ.Types of Cell Division- mitosis and meiosis
Chromosome structure, organization and function
The chromosome number and DNA content of eukaryotic cells varies between species
and
between the cells of a single organism. In human cells, there are 23 chromosomes,
comprising a sex chromosome (chromosome which determines sex- either X or Y) and 22
different autosomes (nonsex chromosomes).
Zygote: fertilized egg cell.
Homologous chromosomes: carry almost identical DNA sequences, one homolog of each
pair being denoted by each parent.
Packaging of DNA into chromosome requires multiple hierarchies of DNA folding.
The chromosome number of normal undifferentiated somatic cells does not change
during the
mitotic cell cycle, the DNA content clearly does. The cell cycle comprises a very short stage
of cell division, the M phase (mitosis phase) and a long intervening interphase which
comprises three phases: S phase (DNA synthesis phase), G1 phase (gap between M phase
and S phase) and G2 phase.
Mitosis: prophase metaphase. anaphase telophase
Meiosis I: prophase I (a, leptotene stage. b, zygotene stage. c, pachytene stage. d,
diplotene stage.)
metaphase I anaphase I telophase I.
Meiosis II: prophase II metaphase II anaphase II telophase II
Human gametogenesis
General Revision
Ⅰ. Pick the best answer
1. The presence of genes in the same chromosome is an example of
A. Linkage B. Coordination C. Free assortment D. Segregations E. Fusion
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 2. Cross-over is a familiar term to
A. Hybridiztion

B. Interchange of sections of chromatids

C. Migration across difficult geographical barriers

D. Diffusion from one side of a membrane to the other

E. Pollination involving separate flowers, male and female
3. The hereditary characteristics are transmitted as units was discovered by
A. Fleming B. Mendel C. Morgan D. Sutton
4. Meiosis 1 is known as the
A. diploid division
B. reduction division
C. sexual division
D. equilibration division
Ⅱ. Review questions
1. Consider a human male heterozygous for the following genes:
∴ On chromosome 22, A/a and B/b
∴ On chromosome 17, G/g
This man inherited a chr. 22 from his mother with the A and B alleles, and a chr. 22
from his father with the a and b alleles. Assume that the A and B genes are so closely linked
that no crossing over occurs. The chr. 17 from his mother carried the G allele, while the chr.
17 from his father carried the g allele.
a. With respect to the A/a and B/b genes, how many different kinds of sperm will be
produced? Give the allele content of each.
Ans 2 = AB and ab (A,B genes are so closely linked that no crossing over )

b. With respect to all three genes (A/a, B/b, and G/g), how many different kinds of
sperm
will be produced? Give the allele content of each.
Ans 4 = ABG , ABg , abG , abg (not closely linked can segregate independently)
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 c. State the Mendelian law that your answer to Part b illustrates.
Ans Different factors segregate independently of each other

2. How many mature sperm cells will be produced by 100 primary spermatocytes? How
many mature egg cells will be produced by 100 oocytes?
Ans 400 mature sperm and 100 mature egg

Ⅲ. Key Terms
Crossing over: a phenomenon, also known as recombination, that sometimes occurs during the formation of
sperm and egg cells (meiosis); a pair of chromosomes (one from the mother and the other from the father) break
and trade segments with one another.
Chiasma (chiasmata): A cross-shaped structure commonly observed between nonsister chromatids in meiosis; the
site of crossing-over.
Gamete: A specialized haploid cell that fuses with a gamete from the opposite sex or mating type to form a diploid
zygote; in mammals, an egg or a sperm.
Genotype: The specific allelic composition of a cell—either of the entire cell or, more commonly, for a certain
gene or a set of genes.
Meiosis: Two successive nuclear divisions (with corresponding cell divisions) that produce gametes (in animals) or
sexual spores (in plants and fungi) having one-half of the genetic material of the original cell.
Mendel's first law: The two members of a gene pair segregate from each other in meiosis; each gamete has an
equal probability of obtaining either member of the gene pair.
Mendel's second law: The law of independent assortment; unlinked or distantly linked segregating gene pairs
assort independently at meiosis.
Homologous chromosomes: Chromosomes that pair with each other at meiosis or chromosomes in different
species that have retained most of the same genes during their evolution from a common ancestor.
Mitosis: A type of nuclear division (occurring at cell division) that produces two daughter nuclei identical with the
parent nucleus.
OMIM: On-line Mendelian Inheritance in Man, an electronic catalog of inherited human diseases. The catalog has
been available on-line since 1987. It is updated weekly and accessible through the Internet
(http://www.ncbi.nlm.nih.gov/omim/).

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 Chapter 2 Gene structure and Human Genome
Ⅰ. DNA structure and structure, function of gene, gene mutation
1. Gene
Simply speaking, a gene (or a cistron) is a stretch of DNA that functions as a unit to give
rise to an RNA or protein product
Bacterial genes and proteins are colinear, however, eukaryotic genes are often
interrupted (called split gene).
Exons and introns, and RNA splicing. The processing of the RNA transcript into mature
mRNA requires the removal of the introns and splicing together of the exons. The 5’ end of
an intron always consists of the two bases GU, following by a consensus sequence that is
similar, but not identical, in all introns. This is the splice donor. The 3’ end, the splice
acceptor, ends in AG, preceded by a consensus sequence.
The definition of gene can be expanded to include regulatory regions on both sides of the
gene that are required for initiating and (sometimes) terminating gene expression.

*intron ; start at GT / end at AG (GT-AT rules) , intron เป็ นส่วนทีถู่ กตัดออก

Genes show a wide distribution of sizes.

There are several major types of DNA, including single-copy DNA, satellite DNA (α-
satellite DNA, minisatellites, and microsatellites), and dispersed repetitive DNA (SINEs, and
LINEs). Single-copy DNA comprises about 45% of the genome and includes the protein-
coding genes. But protein-coding DNA represents only a small proportion of all single-copy
DNA, most of which is found in introns or in DNA sequences that lie between genes.
Less than 5% of human DNA actually encodes proteins. Some DNA sequences code for
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more than one protein.
How many genes are essential and how many are expressed? Housekeeping gene are
genes which express proteins common to all cells, e.g. ribosomal, chromosomal and
cytoskeletal proteins. In contrast, luxury gene are those coding for specialized functions
synthesized (usually) in large amounts in particular cell types, e.g., hemoglobin in
erythrocytes; immunoglobulins in plasma cells.
Organelles have DNA (i.e. mitochondrial DNA).
Gene family: a set of genes descended by duplication and variation from some ancestral
gene.
Gene clusters (multigene family) are formed by duplication and divergence. Examples of
multigene families include those that encodes the histones, hemoglobins, immunoglobulins,
actins, keratins, collagens, heat shock proteins.
DNA sequences that closely resemble known genes but are nonfunctional are called
pseudogenes, and there are many thousands of pseudogenes related to many different
genes and gene families.
Genes for rRNA form a repeated tandem unit.
Satellite DNAs often lie in heterochromatin.
Translation moves the ribosome.Three codons (UAA, UAG and UGA) terminate protein
synthesis.

2. DNA Mutation
 Mutations change the sequence of DNA: spontaneous and induced.
 Point mutations (nucleotide substitutions), deletions, insertions.
(1) Nucleotide Substitutions (Point Mutations)
① Missense mutations (amino acid substitutions) - change in amino acid (ACG >> AAG ;
Ser >> Asp )
② Nonsense mutations (premature stop codons) - stop translation (UAC >> UAA = stop
codon)
③ RNA processing mutations (destroy consensus splice sites, cap sites, and
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polyadenylation sites or create cryptic sites)
④ Splice-site mutations leading to frameshift mutations and premature stop codons.
⑤ Regulatory mutations affecting transcription factor binding, transcriptional control,
or other aspects of gene expression.d
** Silent mutation - not affect protein expression and function (GAA >> GAG ; Glu
เหมือนเดิม)

(2) Deletions and Insertions

① Addition or deletion of a small number of bases:
② Larger gene deletions, inversions, fusions, and duplications:
③ Insertion of a LINE or Alu element:
④ Expansion of trinucleotide repeat sequences: dynamic mutation
** จำนวน nucleotide in an exon หำร3ไม่ลงต ัว >> reading frame is disrupted >> Frame-
้
shift (การอ่านพันธุกรรมผิดไปทังหมดตั ้ เกิดการเปลียนแปลง)
งแต่ ่

Ⅱ. Organization and Expression of the Human Genome

1. Nuclear genome
Nuclear genome is distributed between 24 different types of DNA duplex which show
considerable regional variation in base composition and gene density. They can be easily be
differentiated by chromosome banding techniques.
3000mb, ~23,000 genes, 74% is intergenic region, 24% is intronic region, 1% is exon
region.
Functionally similar genes are occasionally clustered in the human genome, but are more
often dispersed over different chromosomes.
Human genes show enormous variation in size and internal organization. Several kbs to
2.4 Mb. DMD (Duchenne muscular dystrophy) gene, composed of 2,300 kb, is the largest
known gene and contains 79 exons.

2. Mitochondrial genome
Mitochondrial genome consists of a single type of DNA duplex which is densely packed
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with genetic information. Totally 16.6kb, 37 genes, including two rRNA genes, 22tRNA
genes, 13 polypeptide-encoding genes.

Ⅲ. Polymorphism in gene and genome

Different variants of the same gene are called multiple alleles.
When multiple alleles exist, an animal may be a heterozygote that carries two different
mutant alleles.
There is not necessarily a unique wild-type allele at any particular locus.
Polymorphism: there are multiple functional alleles in a population.
An allele is usually defined as polymorphic if it is present at a frequency of >1% in the
population.
Although not evident from the phenotype, the wild type may itself be polymorphic.
A population may have extensive polymorphism at the level of genotype.
Some polymorphisms in the genome can be detected by comparing the restriction maps
of different individuals: restriction fragment length polymorphism (RFLP)----A polymorphic
difference in DNA sequence between individuals that can be recognized by restriction
endonucleases.

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 The enzyme EcoR1 recognizes the base sequence GAATTC and cuts both strand of DNA at
this site (top). If a single base change occurs in the recognition site, the enzyme will not cut.
An individual can have the cutting site intact on both chromosomes and be homozygous for
having the site (bottom right), or can be heterozygous for the cutting site (bottom middle),
or can be homozygous for not having the site. This constitutes a simple mendelian system
for detecting a change of a single base of DNA.
Single nucleotide polymorphism (SNP): A polymorphism in DNA sequence consisting of
่
variation in a single base.(เปลียนซิ ้
งเกิลเบสที ่ มซาๆ
เดิ ้ ต่อไปเรือยๆ)
่

It may offer a diagnostic procedure for detecting the disease

It may lead to isolation of the gene

Short tandem repeat polymorphism (STRP): A polymorphic locus consisting of a variable

number of tandemly repeated binucleotide, trinucleotide, or tetranucleotide units such as

(TG)n, (CAA)n, or (GATA)n; different numbers of units constitute the different alleles. Also

termed a microsatellite marker.

Ⅳ. The Human Genome Project, physical mapping, genetic mapping
1. History of Human Genome Project (HGP)
2. Human Genome Project Goals and Completion Dates
Before beginning a sequencing project of the human genome it is first necessary to
produce good framework maps. This can be done by physical or genetic mapping. It is
important to have high numbers of polymorphic markers to construct genetic maps.
The construction of framework maps is completed. The major effort now is to place
genes on the map and to obtain sequence data thoroughly.
* Physical Mapping: The physical maps depend on their physical distance apart on a DNA
molecule. For example: Restriction Endonuclease physical map. DNA sequence itself is the
finest physical map.
* STS: sequence-tagged site. A short DNA sequence, readily located and amplified by PCR,
that uniquely identifies a physical genomic location. Expressed sequence tags (ESTs) are
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STSs obtained from cDNAs.
* Human genetic maps: Genetic maps are based on recombination frequencies between
markers.
* Centimorgan: The distance on a DNA molecule which have 1% recombinant frequency.
1 cM =1000kb.
* RFLP markers: The first human genetic marker map.
* Microsatellite markers: High resolution human genetic marker map.
* SNP: A new generation of human genetic marker map.

General Revision
Ⅰ. Pick the best answer
1. If the sequence of nucleotides in a gene is T-T-A-C-G-A-G, the sequence of nucleotides
in mRNA synthesized by it is
A. T-T-A-C-G-A-G B. A-A-U-G-C-U-C C. A-A-T-G-C-T-C
D. A-A-T-G-C-T-G E. T-T-U-G-C-U-G
2. A nucleotide substitution cannot cause which of the following?
A. Frameshift B. nonsense C. missense D. same sense

3. Gene is split, alternate with the exons and the introns.

A. Exons are the encoding sequences corresponding to the sequence of mRNA

and their mutations will influence the formation of proteins.

B. Introns are the non-encoding sequences and the corresponding RNA

sequence will be removed from mRNA. Their mutations do not influence the splicing of RNA

and affect the production of mRNA

C. The numbers of exons and introns in a gene are N+1 and N respectively. Exons

are variable and introns are conserved.

D. Splice site is located in the junction region of intron and exon, where intron

always starts at AT and ends at CG.

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 4. The hypothetical Southern blot show below illustrates a DNA “fingerprinting” analysis

to examine paternity, where maternal (M), child (C), and paternal (F) DNA samples have

been restricted, blotted, and hybridized simultaneously to the probe D1S220 and D7S123.

(DNA marker is the standard ladder). The distributions of restriction fragment alleles

suggest

A. The child is adopted B. False maternity (i.e. baby switched in the nursery)

C. False paternity D. Correct maternity and paternity E. None of the above

5. Which of the following statement about polymorphysim

is not correct?

A. RFLP is the 1st generation of markers used in

humans

B. Minisatellites and Microsatellites are not the

repeat DNA sequence in the human genome and both can not be used as

polymorphysim marker.

C. Single nucleotide polymorphisms (SNPs) occur about once every 500-1000 bp in the

human genome.

D. Restriction RFLP Mapping can be combined with Southern Blot Analysis to detect

the differences in DNA samples.

Ⅱ. Review questions
1. In the following list, the normal amino acid sequence is given first, followed by
sequences that are produced by different types of mutations. Identify the type of mutation
most likely to cause each altered amino acid sequence.
Normal： Phe-Asn-Pro-Thr-Arg
Mutation 1： Phe-Asn-Pro (nonsense mutation)
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 Mutation 2： Phe-Asn-Ala-His-Thr (frameshift mutation)
Mutation 3： Phe-His-Pro-Thr-Arg (missense mutation)
2. There are more proteins than there are genes. What are some of the mechanisms that
account for this discrepancy?
Genetic code is constituted of 64 codons. But, because there are only 20 amino acids,
most amino acids are specified by more than one codon. Therefore, the code is said to be
degenerate.

Ⅲ. Key Terms
Genome: The complete DNA sequence, containing the entire genetic information, of a
gamete, an individual, a population, or a species.
Genomics: The field of genetics concerned with structural and functional studies of the
genome.
Proteome: The collection of all proteins present in a cell, tissue, or organism at a
particular time. Contrast with transcriptome, the collection of all RNA transcripts, and
genome, the collection of all DNA sequences.

Proteomics: A field of biochemistry encompassing the comprehensive analysis and

cataloguing of the structure and function of all the proteins present in a given cell or tissue

(see proteome). Parallels genomics, a similarly comprehensive approach to the analysis of

DNA sequence and mRNA expression.

Microsatellite DNA: A type of repetitive DNA based on very short repeats such as
dinucleotides.
Minisatellite DNA: A type of repetitive DNA sequence based on short repeat sequences
with a unique common core; used for DNA fingerprinting.
Gene: The fundamental physical and functional unit of heredity, which carries
information from one generation to the next; a segment of DNA, composed of a transcribed
region and a regulatory sequence that makes possible transcription.
Gene family: A set of genes in one genome all descended from the same ancestral gene.
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 Gene fusion: The accidental joining of the DNA of two genes, such as can occur in a
translocation. Gene fusions can give rise to hybrid proteins or to the misregulation of the
transcription unit of one gene by the cis-regulatory elements (enhancers) of another.
Euchromatin: Slightly and evenly stained, non- or low-repetitive DNA regions.The major
component of chromatin.
Heterochromatin: Darkly and unevenly stained, highly repetitive DNA regions.
Mutation
(1) The process that produces a gene or a chromosome set differing from the wild type.
(2) The gene or chromosome set that results from such a process.
Nonsense mutation: A mutation that alters a gene so as to produce a nonsense codon.
Point mutation: A mutation that can be mapped to one specific locus.
Pseudogene: An inactive gene derived from an ancestral active gene.(non function gene)
Silent mutation: Mutation in which the function of the protein product of the gene is
unaltered.
Transition: A type of nucleotide-pair substitution in which a purine replaces another
purine or a pyrimidine replaces another pyrimidine -e.g., GC → AT.
Transversion: A type of nucleotide-pair substitution in which a purine replaces a
pyrimidine or vice versa-e.g., GC → TA.
Frame-shift mutation: The insertion or deletion of a nucleotide pair or pairs, causing a
disruption of the translational reading frame.
Missense mutation: A mutation that alters a codon so that it encodes a different amino
acid.
Exon: Any nonintron section of the coding sequence of a gene; together, the exons
constitute the mRNA and are translated into protein.
Intron: Non-encoding sequences, corresponding RNA sequence will be removed from
mRNA.

Chapter 3 Recombinant DNA and Gene Manipulations

13
 There are two major approaches to study a specific DNA sequence within a complex DNA
population: DNA cloning and molecular hybridization.

Ⅰ. Cell-based DNA cloning

DNA cloning is a technique which allows individual DNA sequences in complex mixture to
be isolated and copied permitting detailed analysis and manipulation.
Cell-based DNA cloning – an in vivo DNA cloning method.
Principle of cell-base DNA cloning--The specific DNA to be cloned is recombined with
vector DNA and introduced into host cells where it is copied. Recombinants is separated and
purified from cultures of host cells and the cloned DNA can be recovered for analysis.
Four steps for the cell-based DNA cloning:
(1) Construction of recombinant DNA molecules;
(2) Transformation;
(3) Selective propagation of cell clones;
(4) Isolation of recombinant DNA clones.
Restriction Enzymes--Recombinant DNA molecules for cloning depends on the use
bacterial restriction enzymes which cut DNA molecules at palindromic sequences and
produce sticky ends. Two DNA molecules cut with the same restriction enzyme can be
joined by complementary base-pairing between the sticky ends and covalently linked using
DNA ligase.
The enzyme EcoR1 recognizes the base sequence GAATTC and cuts both strand of DNA at
this site (top). If a single base change occurs in the recognition site, the enzyme will not cut.
An individual can have the cutting site intact on both chromosomes and be homozygous for
having the site (bottom right), or can be heterozygous for the cutting site (bottom middle),
or can be homozygous for not having the site. This constitutes a simple mendelian system
for detecting a change of a single base of DNA.
Vector systems for cloning different sizes of DNA fragment.
Plasmids: small circular DNA molecules found in bacteria that are frequently used as
cloning vectors. They are easily purified and manipulated and confer antibiotic resistance to
14
host bacteria allowing easy identification of recombinants.
Lamda Phages: another type of cloning vectors, which are used to construct libraries.
Cosmids—resemble plasmids but contain lamda phage cos sequences which allow them
to be packaged into lamda capsid.
Yeast artificial chromosome (YAC)
Bacteria artificial chromosome (BAC)
Application of cell-based DNA cloning:
(1) Identification of genes involved in disease processes;
(2) Construction of genome maps; production of recombinant proteins;
(3) Creation of genetically modified organisms.
Libraries: A library is a collection of clones, each of which carries vector molecules into
which a different fragment of DNA derived from the total DNA or RNA of a cell or tissue has
been inserted. If the collection of clones is large enough, it should theoretically contain all
of the sequences found in the original DNA source. One can then identify a clone carrying a
DNA fragment of interest in the library by using sensitive screening methods that are
capable of finding it in a collection of millions of different cloned fragments, called a
“library”.
Genomic Libraries:
cDNA Libraries:

Ⅱ. PCR-based DNA cloning and DNA analyses

– A cell-free method of DNA cloning.
1. Principle of PCR: PCR allows specific DNA sequences to be copied or amplified over a
million fold in a simple enzyme reaction.
Components of PCR: Each PCR contains four important components:
(1) Template DNA--contains the target DNA sequence to be amplified;
(2) Oligonucleotide primers--bind to the template DNA by complementary base-pairing;
(3) DNA polymerase - copies the target sequence;
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 (4) dNTPs - substrates for the polymerase.
How the PCR works: Target DNA is amplified by 20-40 cycles of DNA synthesis.
Three steps for PCR amplification:
① Denaturation--separates the strands of the double helix;
② Annealing--allows the primers to bind to the single-strand template DNA;
③ Extension--the target DNA sequence is copied or amplified.
2. Application of PCR in genetics
Detection for polymorphism, mutation screening, etc.
Quantitative PCR: a technique that measures in real time the increase in the amount of
PCR product being made during the PCR reaction. The rate of increase can be used as a
measure of the amount of template present at the start of the PCR; often referred to as
qPCR.
3. DNA sequence analysis
The most widely used approach for DNA sequence analysis is Sanger sequencing (named
after Fred Sanger, who, with Walter Gilbert, received the Nobel Prize in 1980 for developing
DNA sequencing). The sequence of virtually any purified DNA segment can now be
determined, whether it is a cloned fragment or a target sequence amplified by PCR.

Ⅲ. DNA hybridization assays

—specifically detect the individual sequence in complex mixture.
1. Principle of molecular hybridization
DNA molecules can be denatured by heat and renatured by cooling. Single-strand nucleic
acids with complementary sequences may undergo hybridization to form double-strand
hybrid.
2. Probe: Any piece of DNA (RNA) which has been labeled in some way and which is used
in a hybridization assay to identify other DNA or RNA sequences which closely related to it
in base sequence.
3. Methods and applications of Molecular hybridization
Allele-specific oligonucleotide (ASO) hybridization
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 Southern, Northern and Western blot hybridization
In situ hybridization:
(1) Fluorescence in Situ hybridization (FISH) to Chromosomes;
(2) comparative genome hybridization (CGH);
(3) RNA expression arrays.

General Revision
Ⅰ. Pick the best answer

1. Which of the following techniques was not used to detect an unknown mutations?

A. SSCP B. ASO C. DGGE D.DNA sequencing

2. The hybridization, which detects the specific RNA fragment, is called
A. Southern Blot B. Western Blot
C. Northern Blot D. Dot Blot

3. Suppose you want to clone a human DNA fragment of 500kb, which of the following

vectors do you need?

A. plasmid B. λ phage C. cosmid D. YAC

4. Which of the following elements is not an essential part element for a clone vector?

A. cos site B. restriction site (clone site)

C. select marker (a system for screen ) D. replicon

5. Which gene is most likely to be expressed under the following conditions?

A. a gene located in heterochromatin B. a gene in a DNase hypersensitive site

C. a gene which is methylated D. a pesudogene

6. Who won the Nobel Prize for His (their) contributions to PCR technique?

A. Southern E B. Sanger F C. Mullis K

17
 D. Robert R and Sharp P E. Fire AZ and Mello CC

Ⅱ. Review questions
1. Please list the disadvantages and advantages of the cell-based DNA cloning and cell-
free DNA cloning.
-How is DNA cloned?(1)Cell-based DNA cloning; (2)Cell-free DNA cloning (PCR): simple,
rapid, robust…

2. It is known that the sickle cell anemia is caused by the mutation of hemoglobin gene,
which leads to the loss of a Mst II restriction enzyme site. Please design a procedure to
screen the population for sickle cell anemia, and list the expected results from a normal
person, a carrier, and a patient.

Patient: 1band; carrier: 3bands; normal: 2bands

Cleavage of β-globin DNA by the MstII restriction enzyme. The sickle cell mutation removes

an MstII recognition site, producing a longer, 1.3-kb fragment. The normal DNA sequence

includes the restriction site (i.e., the sequence CCTGAG instead of CCTGTG), so a shorter,

1.1-kb fragment is produced. Therefore, on the autoradiogram, sickle cell homozygotes

have a single 1.3-kb band, normal homozygotes have a single 1.1-kb band, and

heterozygotes have both the 1.1-kb and the 1.3-kb bands.

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 3. The ASO technique was used to determine the genotypes of three family members

with regard to sickle cell disease, as show below. Each pair of dots represents the results of

ASO analysis for the DNA from one person. The upper row represents hybridization with the

normal oligo nucleotide, and the lower represent the results of hybridization with the

mutant oligo nucleotide. What are the genotypes of the three individuals?

Ans A = WT; a = m; 1 = AA; 2 = Aa; 3 = aa

4. Imagine you have cloned a 14.7 kb piece of DNA, which contains restriction sites as

below:

B E H B E

2 1.4 3.5 3 0.8 4 ; B= BamHⅠ, E= EcoRⅠ,

H= Hind Ⅰ

Numbers under the segment represent the sizes of the regions in kilobase (kb). You have

labeled the left end of the molecule with 32P.

What radioactive band would you expect to see following electrophoresis and southern

blot if you did a complete digestion with BamHⅠ? EcoRⅠ? Hind Ⅰ?

Ans BamHⅠ：3 picees2 kb；7.9 kb；4.8 kb

EcoRⅠ：3picees 3.4 kb；7.3 kb；4 kb

Hind Ⅲ：2 picees 6.9 kb；7.8 kb

Ⅲ. Key Terms
Probe: A piece of labeled DNA or RNA or an antibody used to detect the function of a

19
gene.
PCR: A fast, inexpensive technique for making an unlimited number of copies of any piece
of DNA. Sometimes called "molecular photocopying," PCR has had an immense impact on
biology and medicine, especially genetic research.
Electrophoresis: A technique for separating the components of a mixture of molecules
(proteins, DNAs, or RNAs) in an electric field within a gel.
Hybridization in situ: Finding the location of a gene by adding specific radioactive probes
for the gene and detecting the location of the radioactivity on the chromosome after
hybridization.
Southern blotting: A technique, devised by the British biochemist Ed Southern, for
preparation of a filter to which DNA has been transferred, following restriction enzyme
digestion and gel electrophoresis to separate the DNA molecules by size. Specific DNA
molecules can then be detected on the filter by their hybridization to labeled probes.
Northern blot: Transfer of electrophoretically separated RNA molecules from a gel onto
an absorbent sheet, which is then immersed in a labeled probe that will bind to the RNA of
interest.
Primer: A short single-stranded RNA or DNA that can act as a start site for 3′ chain growth
when bound to a single-stranded template.
Probe: Any piece of DNA (RNA) which has been labeled in some way and which is used in
a hybridization assay to identify other DNA or RNA sequences which closely related to it in
base sequence.
Western blot: Membrane carrying an imprint of proteins separated by electrophoresis;
can be probed with a labeled antibody to detect a specific protein.
Wild type: The genotype or phenotype that is found in nature or in the standard
laboratory stock for a given organism.
Allele-specific oligonucleotide (ASO): An oligonucleotide probe synthesized to match a
particular DNA sequence precisely and allow the discrimination of alleles that differ by only
a single base.

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 Chapter 4 Patterns of single-gene inheritance

Ⅰ. Proband, pedigree charts and symbols in pedigree

Allele: One of the variant forms of a gene at a particular locus, or location, on a
chromosome. Different alleles produce variation in inherited characteristics such as hair
color or blood type.
Pedigree: A simplified diagram of a family's genealogy that shows family members'
relationships to each other and how a particular trait or disease has been inherited.
Proband: The family member who first bring a family to the attention of an investigator is
proband.
Pedigree symbols

Ⅱ. Genetic disorders with classical Mendelian inheritance

1. Patterns of autosomal dominant inheritance
Criteria for autosomal dominant inheritance:
(1) The trait appears in every generation, with no skipping. Although this statement is
theoretically true, in clinical genetics there are apparent exceptions, when the
proband is a new mutant or because of failure of penetrance or variability of
expression.
(2) Any child of an affected person has a 50 percent risk of inheriting the trait. Because
statistically each child is an "independent event," in an individual family wide
variation from the expected 1:1 ratio may be present.
(3) Unaffected family members do not transmit the trait to their children: As in point one
above, failure of penetrance of the condition can lead exceptions to this rule.
(4) The occurrence and transmission of the trait are not influenced by sex; that is males
and females are equally likely to have the trait and equally likely to transmit to
children of either sex.

21
 Examples of AD diseases:
Huntington disease (HD): Severe progressive disease of the central nervous system, loss
of motor and intellectual control, onset age 25 – 60, autosomal dominant, Gene locus on
4p16.3, it spans 210kb and codes for a protein ( called “huntingtin ) of unknown function.
CAG repeat size increased.
Myotonia muscular dystrophy (MD): Mask-like face, cataract, alopecia, autosomal
dominant, Gene locus on 19p13.3, CTG repeat increased, onset age typically in 5th decade ,
variable expression.
Marfan syndrome: Autosomal dominant, variable expression, long limbs with long
extremities and arachnodactyly, genu valgum, long faces and pectus lentis. Gene locus on
15q21.1, it spans 110kb and 65 exons.
Achondroplasia: Small stature with short limbs, large head, prominent forehead, lumbar
lordosis.
Familial hypercholesterolemia (FH): A human hereditary disease characterized by an
elevation in the plasma concentration of low-density lipoproteins (LDLs). FH is inherited as
an autosomal dominant, and the gene responsible resides on 19p13.2-3. The prevalence of
heterozygotes is about 1/500 among American, European, and Japanese populations, and
this makes FH among the most common hereditary diseases.
Neurofibromatosis typeⅠ(NFl): Autosomal dominant, Frequency I in 3000. NFl gene locus
on 17q, codes for a gene product with 2485 amino acids. Between amino acids 840 and
1200, this large protein contains a domain that corresponds to a GTPase-activating protein.
Cafb-au-lait spots, Lisch nodules in the iris, Multiple neurofibromas, Skeletal anomalies,
Predisposition to tumors of the nervous system, 50% new mutations.
Osteogenesis imperfecta (OI): Blue sclerae, brittle bones, presenile deafness. Incidence is
about 1 in 10,000, Type I collagen is the major structural protein of bone and other fibrous
tissues, mutations affect the synthesis or structure of type I collagen.
Adult polycystic kidney disease (APKD): APKD is characterized by large cysts in one or
both kidneys and a gradual loss of normal kidney tissue which can lead to chronic renal
failure. The role of the kidneys in the body is to filter the blood, excreting the end products
22
of metabolism in the form of urine and regulating the concentrations of hydrogen, sodium,
potassium, phosphate and other ions in the extracellular fluid.
Family polyposis of the colon: Family polyposis of the colon (FAP) is an autosomal
dominant hereditary disease. In late childhood and early adulthood, up to 1000 and more
polyps develop in the mucous membrane of the large colon. Each polyp can develop into a
carcinoma. Early recongnition of this risk is important.
Polydactyly, syndactyly, brachydatyly: Polydactly is the presence of a sixth digit. In
modern times the extra finger has been cut off at birth and individuals do not know they
carry this trait. One of the wives of Henry VIII had an extra finger. The extra digit is rarely
functional and definitely causes problems buying gloves.
Germinal mutation: affecting the gametes can be transmitted to the next generation
(inherited). Usually, a disorder due to a new autosomal dominant mutation does not recur
within the sibship of the patient, but there are rare exceptions in which parents who are
phenotypically normal have more than one affected child sach as polydactyly. One potential
cause of such unusual pedigrees is that during the early development of the parent, a
somatic mutation has occurred in a germline cell or precursor, has persisted in all the clonal
descendants of that cell, and has reached a proportion of the gametes.

2. Patterns of autosomal recessive inheritance

Recessive allele: A gene that is expressed only when its counterpart allele on the
matching chromosome is also recessive (not dominant). Autosomal recessive disorders
develop in persons who receive two copies of the mutant gene, one from each parent who
is a carrier.
Carrier: A person who has a recessive mutated gene, together with its normal allele.
Carriers do not usually develop disease but can pass the mutated gene on to their children.
Criteria for autosomal recessive inheritance:
(1) The trait characteristically appears only in sibs, not in their parents. Offspring or other
relatives.
(2) On the average, one fourth of the sibs of the proband are affected; in other words.
23
The recurrence risk is one in four for each birth.
(3) The parents of affected child may be consanguineous.
(4) Males and females are equally likely to be affected.
(5) There are many small groups in which the frequency of certain rare recessive genes is
quite different from that in the general population.
Examples of AR diseases:
Cystic fibrosis (CF): Severe progressive disease of the bronchial system and
gastrointestinal tract, disturbed function of a chloride ion channel by mutations of one
gene, autosomal recessive, CF gene locus 7q31.3, its 24 exons code for a 6.5-kb transcript,
from which a protein with 1480 amino acids is translated. The protein is a membrane-bound
regulator of a chloride ion channel designated CFTR (Cystic fibrosis transmembrane
conduction regulator). Disease incidence approx. 1:2000.
Phenylketonuria (PKU): Autosomal recessive, Gene locus 12q22-24, Disease incidence
approx. 1:16000, cirrhosis of liver, galactosuria and mental retardation. Mutations in the
gene for phenylalanine hydroxylase.
Sickle cell anemia: an inherited, potentially lethal disease in which a defect in
hemoglobin, the oxygen-carrying pigment in the blood, causes distortion (sickling) and loss
of red blood cells, producing damage to organs throughout the body.
Albinism: A pigmentless “white” phenotype, determined by a mutation in a gene coding
for a pigment-synthesizing enzyme.
Tay-Sachs disease (TSD): A lethal hereditary disease due to a deficiency of
hexosaminidase A. This deficiency results in storage of its major substrate. Progressive
accumulation of this compound causes developmental retardation, followed by paralysis,
mental deterioration, and blindness. Most patients die by the age of three. TSD affects
about one in every 2,500 newborn Ashkenazi Jews, and it is estimated that approximately
one in every 25 Jews in the US is a carrier of the TSD gene.
Spinal muscular atrophy (SMA): SMA is a disorder characterized by degeneration of
lower motor neurons and occasionally bulbar motor neurons leading to progressive limb
and trunk paralysis as well as muscular atrophy. It is the second most common autosomal
24
recessive neuromuscular disorder after cystic fibrosis, affecting approximately one in 6,000
live births and with a carrier frequency of approximately one in 50. Three types of SMA are
recognized depending on the age of onset, the maximum muscular activity achieved and
survivorship: SMA1, SMA2 and SMA3. The survival of motor neuron (SMN) gene has been
identified as a SMA determining gene. In humans, SMN is contained in a 500-kb sequence
on chromosome 5q12.2-q13.3 which consists of nine exons.
Xeroderma pigmentosum (XP): The skin changes are limited to UV-exposed areas and
show a tendency to develop tumors. Lack one or more of the enzymes needed to repair the
dimmer and then produce defective DNA strands in the progeny cells. Thymidine dimmer
(TT) the linkage of two bases.

3. Patterns of X-linked recessive inheritance

Hemizygote: no corresponding loci on the Y chromosome, only one allele of each X
chromosome locus.
Criteria for X-Linked Recessive Inheritance:
(1) The incidence of the trait is much higher in males than in females.
(2) The trait is passed from an affected man through all his daughters to, on the average,
half their sons.
(3) The trait is never transmitted directly from father to son.
(4) The trait may be transmitted through a series of carrier females; if so, the affected
males in a kindred are related to one another through females.
(5) Carriers show variable expression of the trait.
Examples of XR diseases:
Duchenne Muscular Dystrophy (DMD): DMD occurrs in about 1 in 3500 males, onset in
early childhood, death by 3rd decade male births; X-linked recessive, lethal in males, 1/3 of
patients are new mutants; 2/3 have carrier mothers, Gene location Xp21, Extremely large
gene (more than 2000 kb), 79 exons. High mutation rate, probably due to large size of gene,
60% to 65% of the mutations are deletions, and about 6% are duplications , Allelic
mutations in the same gene cause a milder disorder, Becker muscular dystrophy.
25
 Hemophilia A: A classical example anti Hemophilia factor Ⅷdeficiency. Normally, females
have two X chromosomes, whereas males have one X and one Y chromosome. Since males
have only a single copy of any gene located on the X chromosome, they cannot offset
damage to that gene with an additional copy as can females. Consequently, X-linked
disorders such as hemophilia A are far more common in males. The HEMA gene codes for
Factor VIII, which is synthesized mainly in the liver, and is one of many factors involved in
blood coagulation; its loss alone is enough to cause Hemophilia A even if all the other
coagulation factors are still present.
Glucose-6-Phosphate dehydrogenase deficiency (G6PD): G6PD is in the hexose
monophosphate pathway, the only NADPH-generation process in mature red cells, which
lack the citric acid cycle. For this reason G6PD deficiency has adverse physiologic effects.
Deficiency of the red cell enzyme, in various forms, is the basis of favism, primaquine
sensitivity and some other drug-sensitive hemolytic anemias, anemia and jaundice in the
newborn, and chronic nonspherocytic hemolytic anemia advanced the hypothesis that the
incidence of cancer is inversely related to the frequency of G6PD deficiency in blacks. The
protomer of G6PD has a molecular weight of 58,000 and consists of 531 amino acids
determined that the human G6PD gene located in Xq28 and is 18 kb long, with 13 exons.
The protein-coding region is divided into 12 segments, ranging in size from 12 to 236 bp,
and an intron is present in the 5-prime untranslated region. African, Mediterranean and
Canton types occur most often.
Red-green color blindness: Color blindness afflicts 8% of males and 0.04 % of human
females. Color perception depends on three genes, each producing chemicals sensitive to
different parts of the visible light spectrum. Red and green detecting genes are on the X-
chromosome, while the blue detection is on an autosome.

4. Patterns of X-linked dominant inheritance

Criteria for X-linked dominant inheritance:
(1) Affected males have no normal daughters and no affected sons.
(2) Affected heterozygous females transmit the condition to half their children of either
26
sex. Transmission by females follows the same pattern as an autosomal dominant
inheritance cannot be distinguished from autosomal dominant inheritance by the progeny
of affected females, but only by the progeny of affected males.
(3) Affected females are more common than affected males, but as they are almost
always heterozygotes they usually have milder (but Variable) expression.
Examples of XD diseases:
Vitamin D-resistant rickets: There were no instances of male-to-male transmission of
either bone disease or hypophosphatemia, and all daughters of hypophosphatemic males
were themselves hypophosphatemic. Affected persons show a reduction in renal phosphate
Tm to about 50% of normal. Males and females are not significantly different in this respect.
Because of the homology and the function of the gene, the authors referred to it as PEX.

5. Patterns of Y-linked inheritance

Criteria for Y-linked inheritance:
They are always passed from father to son, and they never appear in females.
Examples of Y-linked traits:
Hairy pinna
SRY: Analysis of such individuals has revealed some of the molecules involved in sex
determination, including one called SRY, which is important for testis formation. The testis-
determining factor (TDF), formed under the influence of the SRY gene, induces the
development of the fetaltestis from an undifferentiated gonad. SRY (which stands for sex-
determining region Y gene) is found on the Y chromosome. In the cell, it binds to other DNA
and in doing so distorts it dramatically out of shape. This alters the properties of the DNA
and likely alters the expression of a number of genes, leading to testis formation.

III. Other factors affecting pedigree patterns

1. Onset age

27
 Many genetic disorders are not present at birth but become manifest later in life, some at
a characteristic age and others at variable ages throughout the life span.
2. Pleiotropy: one gene, more than one effect
Each gene has only one primary effect in that it directs the synthesis of a polypeptide
chain. From this primary effect, however, many different consequences may arise. Mulitiple
phenotypic effects produced by a single mutant gene or gene pair are examples of the
principle of pleiotropy or pleiotropism. In any sequence of events, interference with one
early step may have ramifying effects. Thus a single defect occurring early in development
can lead to various abnormalities in fully differentiated structures. In some cases a primary
of gene product might participate in a number of unrelated biosynthetic pathways, possibly
at different time.
3. Genetic heterogeneity
Locus heterogeneity: identical phenotypes from different genotype.
Allelic heterogeneity: describes the observation that, in a given gene, various mutations,
usually a great number of different mutations may result in the disease phenotype in
question.
☆ Mutations in the same gene can result in different phenotype.
☆ Based on the specific mutations of a gene, the same phenotype maybe expressed as
dominant or recessive.
4. Expressivity and penetrance
Penetrance is the probability that a gene will have any phenotypic expression at all.
Expressivity is the degree of expression of the phenotype.
5. Coefficient of relationship and consanguineous marriage
6. Sex-limited phenotypes and sex-influenced phenotypes
Sex-limited phenotype: A trait that is autosomally transmitted but expressed in only one
sex is said to be sex-limited. E.g., precocious puberty.
Sex-influenced phenotypes: Traits are said to be sex-influenceed when they are
expressed in both sexes, but with widely different frequencies. E.g., baldness,
hemochromatosis.
28
 7. Genetic imprinting
The phenomenon of a gene or region of a chromosome showing different expression
depending on the parent of origin.
8. Anticipation
The tendency for some AD diseases to manifest at an earlier age and/or to increase in
severitywith each succeeding generation. Heritable changes in the number repeated groups
of three nucleotides each (trinucleotide or triplet repeat) represent a new class of
mutations in man, for which there is no parallel in other organisms. They occur either within
the gene and are translated or outside the gene in an untranslated region, and they are
unstable during transmission through the germline. Unaffected persons may carry a
premutation, which may be converted to a full mutation when passed through the germline
to the next generation. Therefore, the effects of the mutation may be of varied severity in
affected members within the same family.
9. X inactivation
Inactivation of genes on one X chromosome in somatic cells of female mammals,
occurring early in embryonic life, at about the time of implantation.
10. Germline mosaicism
In an individual, the presence of two or more genetically different types of germline cells,
resulting from mutation during the proliferation and differentiation of the germline.

General Revision
I. Pick the best answer
1. Contrasting genes at the same locus are called
A. Homologus B. Alleles C. Allies D. Difactors E. Associates
2. One characteristic of a mutation is that it is
A. Almost an improvement B. Genetically transmitted to future generations
C. Always a dominant characteristic D. Limited to high organisms
E. Prevented by using colchicine
3. Color blindness is more likely to occur in males than females because
29
 A. Males have a tendency to deposit cholesterol in small blood vessels thereby
reducing the oxygen and food supply to the retina
B. Genes for the characteristic are located in sex chromosomes
C. The trait is dominant in males and recessive in females
D. Males require more vitamin A to achieve the same sensitivity in the rods and cones
of the retina
E. Some males have difficulty absorbing vitamin A, a necessary prerequisite to the
synthesis of visual purple (rhodopsin)
4. If there is a large percentage of crossing-over between gene A and B, the explanation is
that the genes are
A. Located on separate chromosomes B. Located close together
C. Located far apart on the same chromosome D. Separated only by the
centromere
E. Connected by weak linkage
5. Mutt and Jeff are two brothers who were born with congenital deafness. Their parents
had normal hearing. Mutt married Mabel. Mabel was also congenitally deaf and her parents
had normal hearing. Mutt and Mabel had 10 children (5 boys and 5 girls) all of whom were
born congenitally deaf. Jeff married Jane. Jane is not related to Mabel. Jane was congenitally
deaf although her parents had normal hearing. Jane’s sister, Myrna, was also congenitally
deaf. Jeff and Jane had 10 children (5 boys and 5 girls) none of whom were congenitally
deaf. The probable explanation of the above pedigree is that:
A. there is a single genetic locus with at least 2 different abnormal recessive alleles
(a and b) which will result in congenital deafness when homozygous as either
recessive aa, ab or bb.
B. there are at least 2 different genetic loci which have abnormal recessive alleles
which will result in congenital deafness when both loci are homozygous for their
abnormal alleles.
C. there are at least 2 different genetic loci which have abnormal recessive alleles
which will result in congenital deafness when either locus is homozygous for its
30
 abnormal allele.
D. Jeff’s congenital deafness resulted from a spontaneous mutation and hence
cannot be passed on.
6. Thus far, two genes have been found that can cause autosomal dominant breast cancer
(one

on chromosome 13 and one on chromosome 17). This is best described as an example of:

A. Linkage B. Allelic heterogeneity

C. Linkage disequilibrium D. Locus heterogeneity

7. Many biochemical defects, which are inherited in a single-gene Mendelian fashion,
have multiple effects upon the individual affected. This phenomenon is known as:
A. phenocopying B. pleiotropy C. incomplete penetrance D. codominance
8. A young couple both affected with classical achondroplasia come to you for genetic
counseling. There is no other family history of achondroplasia. You should inform them that
if they have a tull term liveborn, the probabi1ity that the newborn wi11 not have
achondroplas if about:
A. < 1% B.25% C. 33% D. 50%

Match the descriptions below with the appropriate term. Questions 9-12

(A)Genetic heterogeneity (B) Variable expressivity

(C) Germinal mosaicism (D) Nonrandom X iinactivation

(E) Incomplete penetrance

9. A female carrier of hemophilia (X-linked disorder) has severe bleeding after routine

cuts or abrasions

D) Nonrandom X iinactivation

10. A grandson and paternal grandfather have ectrodactyly (autosomal dominant

disorder with absent middle fingers), but the father has normal hands

(E) Incomplete penetrance

31
 11. A albino couple has a normal child (albinism is an autosomal recessive disorder)

(A)Genetic heterogeneity

12. A 90-year-old man with autosomal dominant neurofibromatosis has a son and

grandson who died in their twenties from neural tumors

(B) Variable expressivity

Phenylketonuria (PKU) is an autosomal recessive disease that causes severe mental

retardation if it is undetected. Two normal parents are told by their state neonatal screening

program that their third child has PKU. Assume the initial screening is accurate and answer

the questions below. Questions 13-15

(A) 100 %

(B) 67%

(C) 50%

(D) 25%

(E) Virtually 0

13. What is the risk for their next child to have PKU?

D.25%

14. What is the risk of their oldest child to be a carrier for PKU?

B.67%

15. What is the risk for mother to be a carrier for PKU?

A.100 %

Match the characteristics to the mode of inheritance. Questions 16-23

(A) Autosomal dominant

(B) Autosomal recessive

32
 (C) X-linked recessive

(D) Chromosomal

(E) Polygenic

16. When male-to-male transmission is observed, this mode is unlikely

C.X-linked recessive

17. Elevated material age is characteristic

D.Chromosomal

18. Parents with three affected children have a higher recurrence risk than parents with

two affected children

E.Polygenic

19. Elevated paternal age is characteristic

A.Autosomal Dominant

20. Variable expressivity is associated

A.Autosomal Dominant

21. Daughters of affected fathers are obligate carriers

C.X-linked recessive

22. Inborn errors of metabolism are associated

B. Autosomal recessive

23. Consanguinity is characteristic

B. Autosomal recessive
II. Review questions
1. For each pedigree shown in problems 1.1 through1.3, determine whether the trait is
caused by a dominant allele or a recessive allele, and determine the genotype of the
individuals marked by an asterisk (*).
1.1
33
 Ans recessive *1=Aa *2=Aa *3=Aa

1.2

Ans dominant *=Aa * =aa

1.3

Ans recessive*=Aa

2. The accompanying pedigree was obtained for a rare kidney disease.

34
 a. Deduce the inheritance of this condition, stating your reasons.

Ans Autosomal recessive: affected individuals inherited the trait from

unaffected parents and a daughter inherited the trait from an unaffected father.

b. If individuals 1 and 2 marry, what is the probability that their first child will have
the kidney disease?
Ans 1/8

3. Duchenne muscular dystrophy is sex-linked and usually affects only males. Victims of
the disease become progressively weaker, starting early in life.
a. What is the probability that a woman whose brother has the disease will have an
affected child?
Ans 1/8
b. If your mother's brother (your uncle) had Duchenne's disease, what is the
probability that you have received the allele?
Ans 1/4

c. If your father's brother had the disease, what is the probability that you have
received the allele?
Ans 0

4. The following pedigree is for blue sclera (bluish thin outer wall to the eye) and brittle
bones
35
 a. Are these two abnormalities caused by the same gene or separate genes? State your
reasons clearly.
Ans The gene causing blue sclera and brittle bones is pleiotropic with variable
expressivity. b. Is the gene (or genes) autosomal or sex linked?

Ans The allele appears to be an autosomal dominant.

c. Does the pedigree

show any evidence of
incomplete penetrance or
expressivity? If so, make the
best calculations that you can
of these measures.
Ans Both incomplete penetrance and variable expressivity are demonstrated in
the pedigree. Individuals II-4, II-14, III-2, and III-14 have descendants with the disorder,
although they do not themselves express the disorder. Therefore, 4 of 20 people that can
be inferred to carry the gene do not express the trait. That is 80 percent penetrance.
(Penetrance could be significantly less than that since many possible carriers have no
shown progeny.) The pedigree also exhibits variable expressivity. Of the 16 individuals who
have the allele expressed in their phenotypes, 9 do not have brittle bones. Usually,
expressivity is put in such terms as none, variable, and highly variable rather than expressed
as percentages.

5. The following pedigree is for a dominant phenotype governed by an autosomal gene.

What does this pedigree suggest about the phenotype, and what can you deduce about the

genotype of individual A?

36
1.AD

2.autosomal gene

3.individual A not Penetrance

III. Key Terms

Allele: One of the variant forms of a gene at a particular locus, or location, on a
chromosome. Different alleles produce variation in inherited characteristics such as hair
color or blood type.
Pedigree: A simplified diagram of a family's genealogy that shows family members'
relationships to each other and how a particular trait or disease has been inherited.
Proband: The family member who first bring a family to the attention of an investigator is
proband.
Recessive allele: a gene that is expressed only when its counterpart allele on the
matching chromosome is also recessive (not dominant). Autosomal recessive disorders
develop in persons who receive two copies of the mutant gene, one from each parent who
is a carrier.
Carrier: a person who has a recessive mutated gene, together with its normal allele.
Carriers do not usually develop disease but can pass the mutated gene on to their children.
Locus heterogeneity: identical phenotypes from different genotype.
Allelic heterogeneity: describes the observation that, in a given gene, various mutations,
usually a great number of different mutations may result in the disease phenotype in
question.
Penetrance is the probability that a gene will have any phenotypic expression at all.
Expressivity is the degree of expression of the phenotype.
Sex-influenced phenotypes: traits are said to be sex-influenceed when they are
expressed in both sexes, but with widely different frequencies.
Sex-limited phenotypes: A trait that is autosomally transmitted but expressed in only one
sex is said to be sex-limited.
37
 Imprinting: a biochemical phenomenon that determines, for certain genes, which one of
the pair of alleles, the mother's or the father's, will be active in that individual.
Anticipation: used for the apparent worsening and earlier onset age of a disease in
successive generations.
Genotype: The genetic identity of an individual that does not show as outward
characteristics.
Homozygous: Possessing two identical forms of a particular gene, one inherited from
each parent.
Phenotype: The observable traits or characteristics of an organism, for example hair
color, weight, or the presence or absence of a disease. Phenotypic traits are not necessarily
genetic.
Barr body: A densely staining mass that represents an inactivated X chromosome.
Dosage compensation: The process in organisms using a chromosomal sex determination
mechanism (such as XX versus XY) that allows standard structural genes on the sex
chromosome to be expressed at the same levels in females and males, regardless of the
number of sex chromosomes. In mammals, dosage compensation operates by maintaining
only a single active X chromosome in each cell; in Drosophila, it operates by hyperactivating
the male X chromosome
Germinal mutations: Mutations in the cells that are destined to develop into gametes.
Hemizygous gene: A gene present in only one copy in a diploid organism—for example, X-
linked genes in a male mammal.
Heterozygote: An individual having a heterozygous gene pair.
Inbreeding coefficient: The probability of homozygosity that results because the zygote
obtains copies of the same ancestral gene.
Triplet expansion:The expansion of a 3-bp repeat from a relatively low number of copies
to a high number of copies, which is responsible for a number of genetic diseases, such as
fragile X syndrome.

38
 Chapter 5 Cytogenetics and Clinical Cytogenetics

I. General principles of cytogenetics

The development of techniques: colchicines, hypotonic and fixation (methanol and
acetic acid)
1. Morphology of metaphase chromosome
Sister chromatid, arm (p and q), centromere, satellites.
Centromere: The constricted region near the center of a human chromosome. This is
the region of the chromosome where the two sister chromatids are joined to one
another.
metacentric, submetacentric, acrocentric.
2. Chromosome classification
Relative length: Single / total (haploid set)
Arm index: q: p
Centromere index：p / single
ISCN: an international system for human cytogenetic nomenclature
Karyotype: The chromosomal complement of an individual, including the number of
chromosomes and any abnormalities. The term is also used to refer to a photograph of an
individual's chromosomes.

3. Banding chromosome
G bands: In this widely used technique chromosomes are treated with trypsin, which
denatures chromosomal protein, and are then stained with Giemsa stain. The chromosomes
take up stain in a pattern of dark and light staining bands (G bands).
Q bands: Caspersson and his colleagues (1970) found that when chromosomes are
stained with quinacrine mustard or relation compounds and examined by fluorescence
microscopy, each pair stains in a specific pattern of bright and dim bands (Q bands).
R bands: If the chromosomes receive a heat pretreatment and then Giemsa staining, the
39
resulting dark and light stained bands (R bands) are the reverse of those produced by Q and
G banding.
C bands: constitutive heterochromatin in the centromeric region can be specifically
stained (C bands). The distal half of the long arm of the Y chromosome is also C-band
positive. The centromeric heterochromatin in chromosomes 1, 9 and 16 and in the long arm
of the Y chromosome in humans is polymorphic. The lengths of the heterochromatic
segments in one or more of these regions may vary between different individuals.
SCE (Sister Chromatid Exchange): Cultured cells are allowed to replicate twice in
bromodeoxyuridne (BUdR), allowing incorporation of BudR into newly anytheszed DNA in
the place of thymine. BUdR modifies the staining properties of the chromatids; The
frequency of SCE is greatly increased in a particular genetic disorder, Bloom syndrome.
High-resolution bands: This type of banding is achieved through G-banding or R-banding
techniques to stain chromosomes that have been obtained at an early stage of mitosis
(prophase or prometaphase), when they are still in a relatively uncondensed state. It is
especially useful when a subtle structural abnormality of a chromosome is suspected.
Fluorescence in situ hybridization (FISH): A molecular cytogenetic technique in which
labeled probes are hybridized with chromosomes and then visualized under a fluorescence
microscope.
Comparative genome hybridization (CGH): A fluorescence hybridization technique used to
compare two different DNA samples with respect to their relative content of a particular
DNA
segment or segments. CGH can be used with fluorescence in situ hybridization of
metaphase
chromosomes (FISH) or with hybridization to large numbers of DNA fragments fixed to a
solid
support (CGH array).

II. Chromosome abnormalities

1. Types of Chromosome abnormality
40
 Changes in chromosome number are of two basic types: changes in whole chromosome
sets (resulting in a condition of aberrant euploidy) and changes in parts of chromosome sets
(resulting in aneuploidy).
(1) Aberrations of Chromosomes Number
Euploid Organisms that have more or less than the normal number of sets are aberrant
euploids. The number of chromosomes in most cells except the gametes. In humans, the
diploid number is 46. Tthere are other conditions associated with an abnormal number of
chromosomes.
Polyploids are individual organisms in which there are more than two chromosome sets.
They can be represented by 3n (triploid), 4n (tetraploid).
Aneuploidy
Loss or gain of a single chromosome
Hypoaneuploid 2n-1 (monosomy)
Hyperaneuploid 2n+1 (trisomy)
Errors in the distribution of chromosome at division.
Nondisjunction may occur during the first or the second maturation division (meiosis I or
meiosis II). If nondisjunction occurs in meiosis I, the three chromosomes will be different (1
+ 1 + 1), whereas if nondisjunction occurs during meiosis II, two of the three chromosomes
will be identical (2 + 1). In humans, about 70% of nondisjunctions occur in meiosis I, and
30% in meiosis II. Nondisjunction as the cause of especially in trisomy 21, the frequency of
nondisjunction depends on the age of the mother at the time of conception.
Mosaicism
(2) Aberrations of Chromosomes Structure
Deletion Duplication Inversions
Isochromosomes Ring chromosomes
Inversions Pericentric Inversions
Paracentric Inversions
Translocation Reciprocal Translocation
Robertsonian Translocation
41
 (3) Nomenclature of human chromosome

2. Disorders of autosomes
Down syndrome: Include mental retardation (with an IQ in the 20-to-50 range), broad
flat face, eyes with an epicanthic fold, short stature, short hands with a crease across the
middle, and a large wrinkled tongue. Karyotype is 47, XY (XX), +21.
Trisomy 18 syndrome (Edward syndrome): severe physical and mental abnormalities,
“faunlike” ears, a small jaw, a narrow pelvis, and rocker bottom feet.
Trisomy 13 (Patau syndrome): severe physical and mental abnormalities, includes a
harelip, a small malformed head, “rocker bottom” feet, and a mean life expectancy of 130
days.
5p- syndrome: Cri Du Chat syndrome.
Microdeletion: A chromosomal deletion that is too small to be seen under the
microscope but detectable by comparing the base sequences of the normal and deleted
DNA segments.

3. The sex chromosome and their abnormalities

Klinefelter syndrome: The patients are tall and thin, with relatively longlegs. They appear
physically normal until puberty, when signs of hypogonadism become obvious. The testes
remain small, and the secondary sexual characteristics remain underdeveloped. Klinefelter
patients are almost always infertile.
Turner syndrome: Affected people have a characteristic phenotype: they are sterile
females, short in stature, and often have a web of skin extending between the neck and
shoulders
47, XYY syndrome: tall stature, absent or decreased development of male secondary sex
characteristics, and infertility due to absent spermatogenesis. Has a controversial history.
Attempts have been made to link the XYY condition with a predisposition toward violence.
This linkage is still hotly debated, although it is now clear that an XYY condition in no way
guarantees such behavior. The XYY males are usually fertile.
42
 Trisomy X syndrome: Girls with three X chromosomes (47, XXX) are also physically
unremarkable. However, learning disorders and delayed speech development have been
observed in some of these children.
Fragile X syndrome: X-linked trait and the second most common identifiable cause of
genetic mental retardation after Down syndrome. The disease is found in males carrying an
X chromosome that has a fragile site at the interface of bands q27 and q28.

4. Disorder of sexal development with normal chromosome

(1) True hermaphroditism
True hermaphroditism is very rare. A true hermaphrodite has both testicular and ovarian
tissue, either as two separate organs or as a single ovotestis, not necessarily functional but
histologically identifiable. The internal and external sexual organs are very variable and not
in any way diagnostic. The great majority of hermaphrodites are XX, some are XY and other
are not chromosomally normal but are XX/XY chimeras or mosaics.
(2) Pseudohermaphroditism
Testicular feminization syndrome (TFM): X-chromosomal inherited complete or
incomplete androgen resistance. Defects of androgen receptors.
Congenital adrenal hyperplasia: inherited as autosomal recessives and each
characterized by a block in a specific step in cortisol bioaynthesis, resulting in increased
secretion of ACTH (adrenocorticotropic hormone) and hyperplasia of the adrenal glands.
This in turn leads to masculinnization of female fetuses. Affected baby girls frequently have
major anomalies of the external gentalia, often to the point that sex assignment may be
impossible. In male the same genotype produces premature virillization, but there is not
difficulty in identifying the sex.
(3) 46, XX male:
The testis-determining factor (TDF), formed under the influence of the SRY gene on the Y
chromosome, induces the development of the fetal testis from an undifferentiated gonad.
Defects of sex determination due to mutation or structural aberration of the SRY gene.
Normally, the male-determining Y-specific DNA sequences on the Y chromosome and are
43
not transferred to the X chromosome during the homologous pairing and crossing-over of
meiosis. However, since the male-determining region SRY is located very close to the
pseudoautosomal region (PAR), crossing-over in the PAR border region may result in a
transfer of the SRY region to the X chromosome. This results in a male individual with an XX
karyotype (XX male). Conversely, if the SRY region is missing from a Y chromosome, a female
phenotype with XY chromosome. The SRY gene in humans has no introns and codes for a
transcript of 1.1 kb. In the critical region of the SRY protein, the DNA-binding region (HMG
box, high mobility group protein), the exchange of a single amino acid can lead to sex
reversal.
General Revision
I. Pick the best answer
1. Which of the following chromosomal aberrations can be of either sex:
A. XYY B. XXY C. trisomy 21 D. monosomic X

2. Which of the following techniques was mostly used to detect a trisomy?

A. RFLP B. Southern blotting C.FISH D. PCR-SSCP

3. If an eneuploid with a karyotype that is 2N +1 has 9 chromosomes, what is the normal
haploid number of this species?
A. 10 B. 9 C. 8 D. 5 E. 4

4. Each of the following chromosome abnormalities involves a 20 megabase region of

the long arm of chromosome 5 (5q). Which abnormality is most likely to cause severe

disease?

A. Deletion of the region

B. Duplication of the region

C. A balanced translocation involving the region (i.e., in the translocation

carrier)

D. Pericentric inversion

44
 5. Which of the following is not true of Fragile X syndrome?

A. It is associated with methylation B. It can be diagnosed using a

karyotype

C. It is caused by a trinucleotide repeat expansion D. It displays nearly 100%

penetrance

6. Which of the following could produce an XY female?

A. Deletion of the Sry gene B. Point mutation in the Sry gene

C. Translocation of the Sry gene to the X chromosome during meiosis in the

father

D. All of the above

7. A cytogenetic term that refers to a mitotic cell that contains twice the normal number
of chromosomes is:
A. diploid B. polyploid C. endoreduplicated D. tetraploid

II. Review questions

1. How many different kind of gametes can an XYY male form, and what are they?
Ans four (X, XY, YY, Y)
2. Why do chromosomal abnormalities involving the sex chromosomes usually have less
severe phenotypic effects than those involving the autosomes?
Ans Because the Y carries very few genes and the X is subject to dosage
compensation.

3. What is the parental origin of the extra chromosome in the Down syndrome child

below,

and was the error in meiosisⅠor meiosisⅡ?

45
 Ans Father in meiosis Ⅱ

4. A male with the green form of color blindness and a normal female have a child with
Turner syndrome who has normal color vision. In which parent did the nondisjunction
occur?
Ans Nondisjunctionhave occurred in the father; otherwise, the child would be
color blind.
5. A normal woman with 45 chromosomes has a child with Down syndrome, this child
has 46 chromosomes. How would you explain this?
Ans The mother is a balanced translocation heterozygote.

46
III. Key Terms
Centromere: The constricted region near the center of a human chromosome.
Karyotype: he chromosomal complement of an individual, including the number of
chromosomes and any abnormalities. The term is also used to refer to a photograph of an
individual's chromosomes.
Deletion: is the loss of a segment within one chromosome arm and the juxtaposition of
the two segments on either side of the deleted segment.
Duplication: is a repetition of a segment of a chromosome arm. In the simplest type of
duplication, the two segments are adjacent to one another (a tandem duplication).
Inversions: An inversion occurs when a single chromosome undergoes two breaks and is
reconstituted with the segment between the breaks inverted.
Paracentric Inversions: If the centromere is outside the inversion, then the inversion is
said to paracentric Inversions.
Pericentric Inversions: be whereas inversions spanning the centromere are pericentric
Inversions.
Reciprocal Translocation: is the exchang of blocks of chromatin between two
nonhomologous chromosomes.
Robertsonian Translocation involves two acrocentric chromosomes, which fuse at the
centromere region and lose their heterochromatic short arms.
Isochromosomes: During cell division the centromere of a chromosome sometimes
mistakenly divides so that it separates the two arms rather than the two chromatids.
Ring chromosomes: A special type of deletion chromosomes in which both ends have
been lost and the two broked ends have reunited to form a ring.
Diploid: The number of chromosomes in most cells except the gametes. In humans, the
diploid number is 46.
Haploid: The number of chromosomes in a sperm or egg cell, half the diploid number.
Fragile X syndrome: X-linked trait and the second most common identifiable cause of
genetic mental retardation after Down syndrome. The disease is found in males carrying an
47
X chromosome that has a fragile site at the interface of bands q27 and q28.
Trisomy: Possessing three copies of a particular chromosome instead of the normal two
copies.
Acrocentric chromosome: A chromosome having the centromere located slightly nearer
one end than the other.
Chromatid: One of the two side-by-side replicas produced by chromosome division.
Chromosome aberration: Any type of change in the chromosome structure or number
Down syndrome: An abnormal human phenotype, including mental retardation, due to a
trisomy of chromosome 21; more common in babies born to older mothers.
Klinefelter syndrome: An abnormal human male phenotype with an extra X chromosome
(XXY).
Metacentric chromosome: A chromosome having its centromere in the middle.
Monosomic: Refers to a cell or individual that is basically diploid but that has only one
copy of one particular chromosome type and thus has chromosome number 2n − 1.
Mosaic: A chimera; a tissue containing two or more genetically distinct cell types or an
individual composed of such tissues.
Nondisjunction: The failure of homologs (at meiosis) or sister chromatids (at mitosis) to
separate properly to opposite poles.
Polyploid: A cell having three or more chromosome sets or an organism composed of
such cells.
Sex reversal: A syndrome known in humans and mice in which chromosomally XX
individuals develop as males. In some cases, sex reversal is now known to be due to the
translocation of the testis-determining region of the Y chromosome to the tip of the X
chromosome in such individuals.
Telocentric chromosome: A chromosome having the centromere at one end.
Telomere: The tip (or end) of a chromosome.
Testicular feminization syndrome: A human condition, caused by a mutation in a gene
encoding androgen receptors, in which XY males develop into phenotypic females.
Tetraploid: A cell having four chromosome sets; an organism composed of such cells
48
 Triploid: A cell having three chromosome sets or an organism composed of such cells.
Turner syndrome: An abnormal human female phenotype produced by the presence of
only one X chromosome.
Fluorescence in situ hybridization (FISH): A molecular cytogenetic technique in which
labeled probes are hybridized with chromosomes and then visualized under a fluorescence
microscope.

Chapter 6 Prenatal diagnosis for congenital abnormalities

I. Indications for prenatal diagnosis by Invasive Testing

* Advanced maternal age
* Previous child with de novo chromosomal aneuploidy
* Presence of structural chromosome abnormality in one of the parents
* Family history of a genetic disorder that may be diagnosed or ruled out by biochemical
or DNA analysis
* Family history of an X-linked disorder for which there is no specific prenatal diagnostic
test
* Risk of a neural tube defect
* Maternal serum screening and ultrasound examination

II. Methods of prenatal diagnosis and Screening

1. Invasive testing
(1) Amniocentesis: typically at the 15th to 16th week of pregnancy.
(2) Chorionic villus sampling (CVS): at the 10th to 12th week of pregnancy.
(3) Cordocentesis: usually after the 16th week of gestation.
(4) Preimplantation genetic diagnosis (PGD):

2. Noninvasive testing
(1) Maternal serum alpha-fetoprotein (MSAFP): Maternal serum screening can help

49
identify fetuses at increased risk of open neural tube defects (NTDs), some chromosomal
abnormalities including Down syndrome, and other disorders.
(2) First- and second-trimester maternal serum screening:
First-trimester screening is ideally performed between 11 and 13 weeks of
gestation.Three of most useful measurements are free β-human chorionic gonadotropin
(FβhCG), pregnancy-associated plasma protein A (PAPP-A), and an ultrasound assessment of
nuchal translucency. PAPP-A is depressed below the normal range in all trisomies; Fβ-hCG is
elevated in trisomy 21 but depressed in the other trisomies.
Second-trimester screening is usually accomplished by measuring three substances in the
mother’s serum: MSAFP, free β-hCG, and unconjugated estriol. This battery of tests is
referred to as a triple screen. Some laboratories offer a quadruple screen consisting of the
triple screen plus measurement of a fourth substance, inhibin A. All of these substances are
depressed below the normal range in all trisomies with the exception of free β-hCG, which
is elevated in trisomy 21 but depressed in the other trisomies, and inhibin A, which is
elevated in trisomy 21 but not significantly affected in the other trisomies.
(3) Ultrasonography:
(4) Isolation of fetal cells from maternal circulation: Fetal cells that enter the maternal
circulation can be isolated and evaluated for mutations using PCR or FISH. This experimental
procedure entails no risk of fetal loss.

III. Laboratory Studies

1. Cytogenetics in prenatal diagnosis
Demonstration of various techniques such as FISH.
Mosaicism refers to the presence of two or more cell lines in an individual or tissue
sample. When mosaicism is found in cultured fetal cells, there may be problems in
interpreting whether the fetus is truly mosaic and in determining the clinical significance of
this apparent mosaicism.
2. Biochemical assays for metabolic diseases
50
 More than 100 metabolic disorders can be diagnosed prenatally in chorionic villus tissue
or cultured amniotic fluid cells.
3. DNA analysis
Polymerase chain reaction (PCR), SSCP, DHPLC, DNA hybridization, DNA sequencing, gene
microarrays

IV. Emerging technologies for prenatal diagnosis

1. PGD: PGD is the use of molecular or cytogenetic techniques during in vitro fertilization
to select embryos free of a specific genetic condition for transfer to the uterus.
2. Screening for Segmental Duplications or Deletions: array comparative genome
hybridization (aCGH). Comparative genome hybridization performed by hybridizing to a
wafer (“chip”) made of glass, plastic, or silicon onto which a large number of different
nucleic acids have been individually spotted in a matrix pattern.

General Revision
I. Pick the best answer

1. Which of the following prenatal diagnostic techniques routinely allows fetal

chromosomes to be analyzed during first trimester of pregnancy?

A. Cordocentesis B. Amniocentesis C. Chorionic villus sampling

D. Radiography E. Maternal triple testing

2. For what purpose are prenatal screening tests best used?

A. To diagnose a suspected disease in a fetus

B. To diagnose a suspected disease in a parent

C. To obtain fetal cells for chromosome karyotyping

D. To identify individuals who should undergo diagnostic testing

E. To examine the DNA of a fetus for suspected mutations in a specific gene

3. A couple decide to have prenatal diagnosis because their previous child has Tay-Sachs
51
disease. Which of the following prenatal diagnostic techniques is optimal for fetal
diagnosis?

A. Chorionic villus sampling (CVS) B. Percutaneous umbilical blood sampling

C. Amniotic fluid α-fetoprotein levels D. Maternal serum α-fetoprotein (MSAFP)

E. Fetal X-rays
4. A couple seek molecular testing for prenatal diagnosis of an autosomal recessive
condition. The haplotype in coupling with the mutation is found in both parents by analysis
of the parents and the affected child. Analysis of chorionic villus tissue from the fetus
reveals that the fetus inherited only the maternal haplotype in coupling with the mutation.
You would counsel them:

A. The fetus is most likely a carrier.

B. The fetus could be affected if recombination occurred in the father.

C. The fetus could be homozygous unaffected if recombination occurred in the

mother.

D. All of the above.

5. Availability of DNA testing for many single disease traits has allowed routine prenatal

screening of couples for disorders prevalent in their ethnic group. Which of the following

genetic disorders has a similar incidence in different ethnic groups and would not be subject

to different criteria for screening?

A. Cystic fibrosis B. Thalassemias

C. Tay-Sachs disease D. Down syndrome

II. Review questions
Compare the advantage and disadvantage of amniocentesis and chorionic villus sampling
(CVS).
Ans The primary advantages of amniocentesis are lower rate of fetal loss
(approximately 0.5% versus 1% to 1.3% for CVS) and the ability to do an AFP assay for the
52
 detection of neural tube defects. CVS offers the advantages of diagnosis earlier in the
pregnancy and a more rapid laboratory diagnosis. The CVS diagnosis may be complicated
by confined placental mosaicism, and there is limited evidence for an association
between early (before 10 weeks post-last menstrual period (LMP)) CVS and limb
reduction defects.

III. Key Terms

Prenatal diagnosis: The identification of a disease in a fetus or embryo.
Amniocentesis: A procedure used in prenatal diagnosis to obtain amniotic fluid, which
contains cells of fetal origin that can be cultured for analysis. Amniotic fluid is withdrawn
from the amniotic sac by syringe after insertion of a hollow needle into the amnion through
the abdominal wall and uterine wall.
Chorionic villus sampling (CVS): A procedure used for prenatal diagnosis at 8 to 10
weeks’ gestation. Fetal tissue for analysis is withdrawn from the villous area of the chorion
either transcervically or transabdominally, under ultrasonographic guidance.
Cordocentesis: A procedure used in prenatal diagnosis to obtain a sample of fetal blood
directly from the placenta.
Ultrasonography: A technique in which high-frequency sound waves are used to examine
internal body structures; useful in prenatal diagnosis.
Preimplantation genetic diagnosis (PGD): A type of prenatal diagnosis in which a cell is
removed from a multicell embryo generated by in vitro fertilization and tested for the
presence of a disease-causing mutation.
Array CGH (aCGH):

Chapter 7 Genetics of Disorders with Complex Inheritance

Multifactorial inheritance implies a genetic predisposition or susceptibility and an

environmental trigger. Often the genetic predisposition is polygenic or due to several genes
I. Genetic analysis of qualitative traits
53
 Trait: Any detectable phenotypic property or character.
Qualitative trait: A genetic disease trait that either present or absent. The pattern of
inheritance for a qualitative trait is typically monogenetic, which means that the trait is only
influenced by a single gene.
Quantitative trait: are measurable characteristics such as height, blood pressure, serum
cholesterol, and body mass index. A quantitative trait shows continued variation under the
influence of many different genes.
Polygenes: small-but-equal effect.
QTL (quantitative trait loci)
Genetic analysis of qualitative traits: Family Studies.
Goal: check that the susceptibility is at least partly genetic.
Assessing the relative contributions of genes and environment to complex traits:
(1) Twin studies;
(2) Adoption studies.
Genetic Differences between Identical Twins: All individuals, even monozygotic twins,
differ in:
(1) Their repertoire of antibodies and T-cell receptors (because of epigenetic
rearrangements and somatic cell mutations);
(2) Somatic mutations in general;
(3) The numbers of mitochondrial DNA molecules (epigenetic partitioning);
(4) The pattern of X inactivation, if female.

II. Genetic analysis of quantitative traits

1. Correlation is a statistical measure of the degree of association of variable phenomena
(a measure of the degree of resemblance or relationship between 2 parameters).
Coefficient of correlation (r):
Positive correlation: r>1
No correlation: r=0
Negative correlation: r<1
54
 2. Heritability (h2): The proportion of the total variation of a character attributable to
genetic as opposed to environment factors.
CMZ - CDZ
h2 = -----------------------
100 - CDZ
h2=0: genes contribute nothing to the phenotype
h2=1: genes are totally responsible for the phenotype

3. Characteristics of Inheritance of Complex Diseases

* Genes contribute to diseases with complex inheritance, but these diseases are not
single-gene disorders and do not demonstrate a simple mendelian pattern of
inheritance.
* Diseases with complex inheritance often demonstrate familial aggregation because
relatives of an affected individual are more likely to have disease-predisposing alleles
in common with the affected person than are unrelated individuals.
* Pairs of relatives who share disease-predisposing genotypes at relevant loci may still
be discordant for phenotype (show lack of penetrance) because of the crucial role of
nongenetic factors in disease causation. The most extreme examples of lack of
penetrance despite identical genotypes are discordant monozygotic twins.
* The disease is more common among the close relatives of the proband and becomes
less common in relatives who are less closely related and therefore share fewer
predisposing alleles. Greater concordance for disease is expected among
monozygotic versus dizygotic twins.

4．Genetic mapping of complex traits

(1) Linkage analysis
① Model-based (parametric) Linkage Analysis: Also standard lod score analysis.
Genome scan which analyzes the disease pedigrees using hundreds of polymorphic
55
markers (STRs, SNPs) throughout the entire genome.
The LOD score gives both:
* a best estimate of the recombination frequency, max, between a marker locus and the
disease locus; and
* an assessment of how strong the evidence is for linkage at that value of θ max. Values
of the LOD score above 3 are considered strong evidence.
Linkage at a particular θ max of a disease gene locus to a marker with known physical
location implies that the disease gene locus must be near the marker.
② Model-free (Nonparametric) Linkage Analysis:
Identity by State (IBS) and Identity by Descent (IBD):

Both sib pairs share allele A1. The first sib pair have two independent copies of A1 (IBS
but not IBD); the second sib pair share copies of the same paternal A1 allele (IBD). The
difference is only apparent if the parental genotypes are known.
(2) Association studies
The presence of a particular allele at a locus at increased or decreased frequency in
affected individuals compared with controls is known as a disease association.
In an association study, the frequency of a particular allele (such as for an HLA haplotype
or a particular SNP or SNP haplotype) is compared among affected and unaffected
individuals in the population

III. Example of quantitative disease

Digenic retinitis pigmentosa, Hirschsprung disease, diabetes mellitus, Alzheimer disease,
multifactorial congenital malformations: neural tube defect, cleft lip and cleft palate,
congenital heart defects.

56
 General Revision
I. Pick the best answer

1. Which of the following statements is incorrect regarding the recurrence risk of

multifactorial inherited disorders.

A. The risk gets higher when the number of patients in the family increase

B. The risk gets higher when the degree of relationship increases

C. The risk for their children gets higher when the patients are seriously affected

D. The risk gets higher when one or both parents are affected.
2. A multifactorial trait occurs more often in females than males. A couple have an
affected son. Which of the following is true regarding their risk of recurrence?
A. Recurrence is higher than if they had an affected daughter, and is most likely for a
future son.
B. Recurrence is higher than if they had an affected daughter, and is most likely
for a future daughter.
C. Recurrence is higher than if they had an affected daughter, and is most likely for a
future daughter.
D. Recurrence is lower than if they had an affected daughter, and is most likely for a
future daughter.
3. Linkage analysis is more difficult in multifactorial conditions than in single-gene
disorders because:
A. Variants in more than 1 gene are likely to contribute to the disorder
B. The number of affected persons within in a family is likely to be fewer than for a
single-gene disorder
C. The mode of inheritance is usually uncertain
D. Some multifactorial disorders are likely to have more than 1 etiology
E. Many multifactorial conditions have a late age of onset
F. All of above.
57
 4. Association Studies:
A. Can give false positive results due to population stratification
B. Include the transmission disequilibrium test (TDT)
C. Positive association studies should be replicated
D. Are used to map genes in multifactorial disorders
E. Require closely matched control and patient groups
5. To say that two alleles are in linkage disequilibrium implies that:
A. The alleles function together in the same pathway.
B. The alleles are so close that recombination never occurs between them.
C. One allele arose from the other by mutation.
D. The two alleles are together in the same haplotype more often that predicted
by chance.

6. Multiple studies of a given disorder among siblings have estimated the heritability of

the disorder as equal to 0.85. What does this finding reveal about the cause of this

disorder?

A. The majority of the variance in the phenotype of this disease is caused by

genetic influences

B. This disorder is likely caused by a single gene, with no environmental influences

C. Environmental factors exert a greater influence over disease likelihhood than

genetic factors
II. Review questions
1. What are a few of historical reasons why the results of disease association studies have
often failed to be reproducible by other investigators?

Ans There are several reasons why some of the published

disease-marker associateions have not been able to be reproduced.

(a) inappropriateor insufficientlyrigorous statistical test.

58
(b) a low relative risk for the susceptibility allele.

(c) allelic association due to reasons other than linkage disequilibrium: direct causation,

nature selection, or population stratification.

2. With regard to the genetic risk of Alzheimer Disease, name a gene which fits the
criteria of being a “high frequency/low penetrance” predisposition allele.
Ans Apo E
3. A pair of identical twins is found not to be concordance for s phenotypic trait. Does this
mean that the trait is not genetically determined?

Ans This means that genes are not sufficient in themselves to determine the trait.

There may be a genetic contribution, but something else, perhaps environmental factors or

chance, also play a role. There are also rare examples where identical twins will not share

the same gene mutation, if the mutation arose somatically in just one twin.
4. How will the haplotype map facilitate whole genome analysis for association of SNPs with
common disorders?

Ans The haplotype map will permit “tag SNPs”to be used as a marker for a haplotype

block, which may be in the range of 10 kb in length. This will reduce the number of SNPs

that must be genotyped byan order of magnitude

5. Consider a multifactoral trait that is twice as common in females as in males. Indicate
which type of mating is at higher risk for producing affected children (affected father and
normal mother versus normal father and affected mother). Is the recurrence risk higher for
their sons or their daughter?

Ans Since trait is more common in females than in males, we infer that the threshold

is lower in females than in males. An affected father is at greater risk for producing affected

offspring than is an affected mother.The recurrence risk is higher in daughter than in sons.

III. Key Terms

59
 Complex inheritance: The transmission pattern of discontinuous variants that can be
explained only by the interaction of several genes plus the environment.
Heritability: The proportion of the total variation of a character attributable to genetic as
opposed to environment factors.
Linkage: Describes two loci that are located close enough on the same chromosome that
their recombination frequency is less than 50%.
Linkage disequilibrium: Nonrandom association of alleles at linked loci in populations.
LOD score: Common logarithm of the ratio of the likelihood of linkage at a specific
recombination fraction to the likelihood of no linkage.

Chapter 8 Mitochondria genetic disorders

I. The physiology of mitochondria

The human mitochondrial genome is 16,569 base pairs (bp) in length, a closed, circular
molecule located within the mitochondrial matrix and present in thousands of copies per
cell. Mitochondrial DNA has two strands, a guanine-rich heavy (H) strand and a cytosine-rich
light (L) strand. Introns are absent in mtDNA, and all of the coding sequences are
contiguous. mtDNA codes for 2 ribosomal RNAs and 22 transfer RNAs used in the
mitochondrion, and contains only 13 recognizable genes that code for polypeptides.

II. Special features of mitochondrial genetics

The cytoplasmic location of mtDNA and the high copy number contribute to certain
unique features of mitochondrial genetics.
(1) Maternal inheritance:
(2) Replicative segregation: mitochondria undergo replicative segregation at cell division.
(3) Homoplasmy and heteroplasmy: many of the pathogenic mtDNA mutations are
heteroplasmic. For expression of a disease it is required that a certain threshold level of
mutant mtDNA should be exceeded.
(4) mtDNA genes have a much higher mutation rate than nuclear DNA genes.

60
 (5) Somatic mtDNA mutations accumulate in post-mitotic tissues with age, reducing the
ATP generating capacity.

III. Mutation of mtDNA (LHON, MERRF)

Mitochondria contain their own private DNA. In recent years, more than 20 hereditary
disorders have been shown to result from mutations in mitochondrial DNA.
Leber hereditary optic neuropathy (LHON)
LHON is a maternally inherited form of blindness predominantly affecting men and with
onset in the second or third decade of life. Painless loss of vision begins in the central visual
field, usually in one eye, and subsequently affects the other eye weeks or months later.
Recovery of vision has been reported in some patients and seems to depend on the
particular pathogenic mtDNA mutation present.
Myoclonus epilepsy with ragged-red fibers (MERRF)
MERRF is a maternally inherited neuromuscular disorder characterized by progressive
myoclonus, epilepsy, muscle weakness and wasting, cerebellar ataxia, deafness and
dementia. The most commonly observed mutation is an A>G transition at nt 8344 in the
tRNALys gene in mtDNA and a second mutation has been reported in the same gene, at
position 8356.

General Revision
I. Pick the best answer

1. A 19-year-old patient complains of a loss of central vision in both eyes. The onset was

less than 6 months ago and has progressed rapidly. The pedigree you construct of the

proband’s family reveals vision loss in the patient’s mother, all her five siblings, and the

proband’s maternal grandmother. You develop a differential diagnosis of likely disorders

that includes which of the following?

A. Retinoblastoma B. MELAS syndrome C. Leber hereditary

61
neuropathy

D. Kearns-Sayre syndrome E. Leigh syndrome

2. Ryan is affected with Leber hereditary optic neuropathy (LHON), characterized by
rapid nerve death, leading to bilateral blindness. Subsequent molecular studies reveal the
causative mutation is a single base substitution in NADH dehydrogenase subunit four,
coded by a mitochondrial gene. Ryan has two daughters. What is the probability that his
both daughters have inherited this mutation?
A. Virtually 0% B. Approximately 25% C. Approximately 38%
D. Approximately 50% E. Approximately 75%

3. The mitochondrial disorder of MELAS (mitochondrial encephalomyopathy with lactic

acidosis and stroke-like episodes) and MERRF (myoclonic epilepsy with ragged-red fibers)

are generally both caused by what type of mutation?

A. Single base mutations in mitochondrial tRNA genes

B. Large nonspecific deletions in the mitochondrial genome

C. Mutations in nuclear-encoding genes required for function of the OXPHOS

pathway

D. Mutations in the genes responsible for maintaining mitochondrial replication

4．Match the pedigree with the most likely mode of inheritance.

A. mitochondrial

B. autosomal recessive

C. X-linked recessive

D. X-linked dominant

E. mitochondrial autosomal dominant

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II. Review questions

1．The human pedigree below concerns a rare visual abnormality in which the person
affected loses central vision while retaining peripheral vision.

a. What inheritance pattern is shown? Can it be explained by nuclear inheritance?

Mitochondrial inheritance? Molecular geneticists studied the mitochondrial DNA of the 18
members of generations II and III. A restriction fragment 212 base pairs long of the mtDNA
from each person was digested with another restriction enzyme, SfaN1, with the following
results:

Ans On the basis of the pedigree alone, it is possible, but unlikely, that the disease is
caused by a dominant nuclear allele. But we would have to invoke lack of penetrance in
individual 10, who would have to carry the allele because it is passed on to her children. In
addition, we have to explain the ratios in generation III. The matings 9 × 10 and 11 × 12
would have to be A/a× a/a, and the phenotypic ratio of affected to normal then expected
among the children in each family is 1:1. So overall this model is not an attractive one for
63
explaining the results. The results can also be explained by maternal inheritance of the
disease. Individuals 4 and 10, however, require special explanation. Once again, we can
invoke incomplete penetrance. But, alternatively, we could invoke cytoplasmic segregation;
we have learned that cells can bemixtures of normal and abnormal

b. What inheritance pattern is shown by these restriction fragments?

Ans The restriction patterns clearly show maternal inheritance, which is expected
because we are dealing with mtDNA

c. How does the restriction-pattern inheritance relate to the inheritance of the disease?

Ans There is obviously a close correlation between the presence of the large 212-bp

fragment and the disease. If this same correlation were to be found in other similar

pedigrees, one could formulate amodel in which the mutation that causes the disease

simultaneously causes the loss of an SfaN1 restriction site.

d. How can you explain individuals 4 and 10?

Ans The possibility that 4 and 10 areheteroplasmons is now less attractive because, if
there were mixtures, we would expect to see that the restriction-enzyme patterns of
some persons in the family have all three bands—95, 117, and 212—but none were seen.
Therefore the most likely explanation is the incomplete penetrance of a mitochondrial
disease.

e. What is the likely nature of the mutation?

64
 Ans According to the model, the most likely kind of mutation would be a nucleotide-
pair substitution because, if the mutation is at the SfaN1 site, no nucleotides are lost or
gained, because 117 +95 = 212.

f. How would this analysis be useful in counseling this family?

Ans If the model is upheld by other studies, appearance of the 212-bp fragment after

SfaN1 digestion would be a diagnostic marker for the mutation. All women with this marker

could pass the disease on to their children, whereas men with the marker could not

transmit the disease. Note that, in solving this problem, we have combined concepts of

Mendelian inheritance, cytoplasmic inheritance, mutation, and DNA restriction analysis.

The problem is based on patterns shown in a true pedigree for the disease Leber hereditary

optic neuropathy (LHON), which is mitochondrially based

III. Key Terms

Maternal inheritance: A type of uniparental inheritance in which all progeny have the
genotype and phenotype of the parent acting as the female.
Homoplasmy: The presence of only one type of mitochondrial DNA in the
mitochondria of a single individual.
Heteroplasmy: The presence of more than one type of mitochondrial DNA in the
mitochondria of a single individual.

Chapter 9 Inborn errors of metabolism and molecular disease

I. The effect of mutation on protein function

(1) Loss-of-Function mutation (the great majority): are sometimes seen in dominant
diseases.
(2)Gain-of-Function mutation: is seen in (1) recessive diseases; (2)diseases involving
haploinsufficiency, in which 50% of the gene product is insufficient for normal function; and
65
(3)dominant negative mutations, in which the abnormal protein product interferes with the
normal protein product.
(3) Novel property (infrequent)
(4) Mutations associated with heterochronic or ectopic gene expression: The expression
of a gene at the wrong time (heterochronic expression), or in the wrong place (ectopic
expression), or both (uncommon, except in cancer).

II. Hemoglobins and their diseases

1. Structure and function of hemoglobin

Hemoglobin (Hb) is a large protein (66.7 kD). It is the oxygen carrying substance in the
blood. It is a complex molecule consisting of 4 globin chains (polypeptide chains or proteins)
with a heme group inserted into each globin "pocket". The heme group consists of a
porphyrin ring and an iron (Fe) atom occupying the center of the ring. It is the iron atom
that binds oxygen for transport through the blood. One hemoglobinn molecule carries 4
oxygen molecules.

2. Development expression of globin and globin switching

Hemoglobin is made of two subunits derived from genes in the alpha gene cluster on
chromosome 16 and two subunits derived from genes in the beta gene cluster on
chromosome 11. The normal human hemoglobins found at different stages of development
are encoded for by 6 different structural genes resulting in 6 globin (polypeptide) chains:
alpha , beta , gamma , delta , epsilon , and zeta .
Normal adult hemoglobin: HbA contains 2 globin chains and 2 globin chains.
HbA2 contains 2 globin chains and 2 globin chains.
Fetal hemoglobin (HbF): contains 2 and 2 globin chains.
The embryonic hemoglobins, Gower 1 ( ), Gower 2 ( ) and Portland ( ),

3. Genetic disorder of hemoglobin (Hemoglobinopathy)

66
 The hereditary disorders of hemoglobin can be divided into three broad groups,
depending on whether the mutation alters the globin protein, its synthesis, or globin
developmental switching:
(1) structural variants, which alter the globin polypeptide without affecting its rate of
synthesis;
(2) thalassemias, in which there is decreased synthesis (or, rarely, extreme instability) of
one or more of the globin chains, resulting in an imbalance in the relative amounts of the α
and β chains; nd
(3) hereditary persistence of fetal hemoglobin, a group of clinically benign conditions
that are of interest because they impair the perinatal switch from γ-globin to β-globin
synthesis.
There are over 400 structural variants of normal hemoglobin.The 4 most common
structural variants are:
• Hb S (Sickle cell anemia):β chain: Glu6Val
• Hb C: β chain: Glu6Lys
• Hb E: β chain: Glu26Lys
• Hb M (Methemoglobin): An oxidizing form of Hb containing ferric iron that is
produced by the action of oxidizing poisons. Non-functional.
Variations in the alpha chain are relatively uncommon. Two variants occasionally seen
are hemoglobin G Philadelphia, found in African-Americans, and hemoglobin JT ongariki,
found in Melanesians.
Reduced rate of production of one or more globin chains
The Thalassemias: An imbalance of globin-chain synthesis.

Clinical States Associated with α-Thalassemia Genotypes

Number of α-Globin α-Chain
Clinical Condition Functional α Gene Production
Genes Genotype

67
 Normal 4 αα/αα 100%
Silent carrier 3 αα/α- 75%
α-Thalassemia trait 2 α-/α- or 50%
(mild anemia, αα/--
microcytosis)
Hb H (β4) disease 1 α-/-- 25%
(moderately severe
hemolytic anemia)
Hydrops fetalis or 0 --/-- 0%
homozygous α-
thalassemia (Hb Bart’s:
γ4)
β-thalassemia: underproduction of the β-chain.
(1) β-thalassemia trait (β+/ β or β0 /β): asymptomatic (β+: reduced; β0: absent)
(2) β-thalassemia intermedia (β+/ β+): moderate anemia
(3) β-thalassemia major (β0 /β0 or β+ /β0 or β+/β+):
* severe anemia during the first two years of life
* hepatosplenomegaly
* growth failure
* jaundice
* thalassemic facies

III. Enzyme defects

1. Aminoacidopathies
Phenylketonuria is an inherited error of metabolism caused by a deficiency in the
enzyme phenylalanine hydroxylase. Loss of this enzyme results in mental retardation, organ
damage, unusual posture and can, in cases of maternal PKU, severely compromise
pregnancy.
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Classical PKU is an autosomal recessive disorder, caused by mutations in both alleles of the
gene for phenylalanine hydroxylase (PAH), found on chromosome 12.
Alkaptonuria is a rare inherited disorder of metabolism characterized by urine which
turns black when exposed to air. Another characteristic is the development of arthritis in
adulthood. Alkaptonuria is an autosomal recessive inherited disorder.
Albinism refers to a group of inherited conditions. People with albinism have absent or
reduced pigment in their eyes, skin or hair.
Ocular Albinism (OA) is divided into two types according to the inheritance pattern:
autosomal recessive OA occurring equally in males and females and X-linked OA with
symptoms occurring primarily in males.
Oculocutaneous Albinism (OCA) involves the lack of pigment in the hair, skin and eyes.
Each parent must carry the gene for this form which follows an autosomal recessive
inheritance pattern.

2. Defects in purine metabolism

Lesch-Nyhan syndrome is a X-linked recessive inherited disease that results from
mutation in the gene for the purine salvage enzyme HGPRT. Results in severe mental
retardation and distressing behavioral abnormalities, such as compulsive self-mutilation.

3. Lysosomal storage diseases

Tay-Sachs disease is one of a group of heterogeneous lysosomal storage diseases, the
GM2 gangliosidoses, that result from the inability to degrade a sphingolipid, GM2
ganglioside. The biochemical lesion is a marked deficiency of hexosaminidase A (hex A).
Affected infants appear normal until about 3 to 6 months of age but then gradually undergo
progressive neurological deterioration until death at 2 to 4 years.
Mucopolysaccharidoses are a heterogeneous group of more than a dozen storage
diseases in which mucopolysaccharides accumulate in lysosomes as a result of a deficiency
of one of the enzymes required for their degradation. The first two mucopolysaccharidoses
to be recognized were X-linked recessive Hunter syndrome and the more severe autosomal
69
recessive Hurler syndrome. Affected children are mentally retarded, have skeletal
abnormalities and short stature, and manifest other abnormalities.

4. Alpha1-antitrypsin deficiency
α1-Antitrypsin (α1AT) deficiency is an important autosomal recessive condition associated
with a substantial risk of chronic obstructive lung disease (emphysema) and cirrhosis of the
liver. The α1AT protein belongs to a major family of protease inhibitors, the serine protease
inhibitors or serpins.
VI. Defects in receptor proteins
Familial hypercholesterolemia belongs to a group of metabolic disorders called the
hyperlipoproteinemias, which are characterized by elevated levels of plasma lipids
(cholesterol, triglycerides, or both) and specific plasma lipoproteins. Mutations in the gene
encoding the LDL receptor are the most common cause of familial hypercholesterolemia.

General Revision
I. Pick the best answer
1. Gene frequency is especially high among Ashkenazi Jews:
A. Marfan syndrome B. Sickle cell disease C. Cystic fibrosis
D. Tay-Sachs disease E. Osteogenesis imperfecta
2. A single nucleotide change in the gene for beta globin substitutes the amino acid valine
for glutamic acid at the sixth position. This change affects the solubility of the resulting
protein under certain conditions. What is the corresponding disorder?
A. Hydrops fetalis B. hereditary persistence of fetal hemoglobin
C. Delta beta thalassemia D. Cooley anemia E. Sickle cell disease
3. Ryan is diagnosed with HbH disease. This is likely caused by the deletion of how many
of the alpha globingenes?
A.1 B.2 C.3 D.4 E.5
4. Which enzyme is most likely deficient in individuals with a mucopolysaccharidosis
disorder?
70
 A. An enzyme in the urea cycle leading to hyperammonemia
B. Lysosomal enzymes involved in macromolecule degradation
C. Liver enzymes necessary to degrade glycogen to release glucose
D. Enzymes that cleave sphingolipids
E. An enzyme necessary for the metabolism of monosacchrides such as fructose
5. A child from Nigeria is evaluated for developmental delay. His coloring seems much
lighter than that of his family background, and his physician orders a blood amino acid test
that demonstrates elevated phenylalanine. A special low phenylalanine formula is begun
(Lofenelac) as treatment for phenylketonuria, but the parents refuse to come in for follow-
up appointments. A public health evaluation reports that the child is failing to thrive despite
apparent adherence to the diet by his parents. The symptoms of decreased skin pigment
and later failure to thrive in this child are most likely related to which of the following?
A. Deficiency of alanine B. Deficiency of tyrosine and melanin
C. Deficiency of tryptophan and niacin D. Deficiency of leucine and isoleucine
E. Deficiency of phenylalanine

6. Increased resistance to malaria is seen in persons with hemoglobin AS, where A is the

normal allele and S is the allele for sickle hemoglobin. Which of the following terms applies

to this situation?

A. Founder effect B. Heterozygote advantage

C. Genetic drift D. Fitness E. Natural selection

II. Review questions

1. A man has sickle cell trait and his wife is heterozygous for hemoglobin C. What
proportion of his children will have normal hemoglobin?
Ans Increased resistance to malaria is seen in persons
2. Garrod found alkaptonuria to be more common in the offspring of consanguineous
matings. Explain this finding. In general, what is the association between the coefficient of
relationship and the prevalence of an inborn error of metabolism?
71
 Ans In consanguineous matings,a higher proportion of genes in the offspring are

identical by descent. The identical proportion is measured by the coefficient of

relationship.The carrier frequency of AR inborn error of metabolism such as alkaptonuria

decreases as the prevalence of the disorder diminishes. Thus, the carrier frequency of very

rare disorders is very low.If a child is diagnosed with alkaptonuria,it would be reasonable to

suspect that parents who might be related are more likely to share an individual’s

alkaptonuria gene than 2 individuals chosen at random from the population.

3. What are the general app roaches used in the treatment of inborn errors of
metabolism?
Ans (1) substrate reduction;(2) removal of toxic metabolites; (3) enzyme replacement;
(4) organ transplantation; (5) coenzyme supplementation; (6) augmentationof enzyme
action.

III. Key Terms

Molecular disease: A disease in which there is an abnormality in or a deficiency of a
particular molecule, such as hemoglobin in sickle cell anemia.
Inborn error of metabolism: Any of a group of congenital disorders caused by an inherited
defect in a single specific enzyme that result in a disruption or abnormality in a specific
metabolic pathway.
Loss-of-Function mutation: A mutation associated with a reduction or a complete loss of
one or more of the normal functions of a protein.
Gain-of-Function mutation: A mutation associated with an increase in one or more of the
normal functions of a protein. To be distinguished from novel property mutation.

Novel property mutation: A mutation that confers a new property on the protein.

Chapter 10 Genetic Variation in Populations

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I. Gene pool, genotypes, and gene frequency
Gene pool: the genetic constitution of a population of a given organism. (OR: All the
genes of all the individuals in population make up the gene pool.)
Genotypes: the genetic constitution of a single individual.
Gene frequency (allelic frequency): the frequencies of the members of a pair of allele
genes in a population.

II. Hardy-Weinberg equilibrium law

In a large population with random mating H-W equilibrium will occur after one
generation provided that the same gene frequencies occur in both sexes. Hardy-Weinberg
equilibrium implies that gene and genotype frequencies are constant from generation to
generation. If disequilibrium occurs, equilibrium will be reestablished after one generation
of random mating. The H-W conditions also imply that when the gene frequencies are p and
q, the genotype frequencies will be respectively p2, 2pq and q2 for the dominant, the
heterozygotes and the recessive in a two allele system.

III. Applications of Hardy-Weinberg law

1. How to judge the population balance?
-if balanced ; p^2 + 2pq + q^2 = 1
2. How to calculate the gene frequency and the genotype frequency of the population?
-Gentype frequency ; For Dominant : A = AA + Aa/2
Recessive : a = aa+ Aa/2

VI. Factors that disturb Hardy-Weinberg equilibrium

(1) Exceptions to random mating
(2) Exceptions constant allele frequency
(3) Genetic drift: Fluctuation in allele frequency due to chance in a small population.
(4) Gene flow: The exchange of genes between different populations.

73
 General Revision
I. Pick the best answer
1. Which is the balanced population in the following populations?
A. Population: (1) AA 0 (2) Aa 60% (3) aa 40%
B. Population: (1) AA 60% (2) Aa 0 (3) aa 40%
C. Population: (1) AA 64% (2) Aa 20% (3) aa 16%
D. Population: (1) AA 36% (2) Aa 48% (3) aa 16%
2. As for the hemophilia A disease (XR), the incidence of the male patient is 1/40000 in a
balanced population, how much is the incidence of the female patient?
A. 1/40000 B. (1/40000)2 C. 1/200 D. 0
3. The incidence of galactosemia (an autosomal recessive disorder) among newborns is
approximately 1 In 19,600 livebirths. The gene frequency of the mutant gene and carries
frequency are:
A. 1/19,600 and 1/10,000 B. 1/140 and 1/140
C. 1/140 and 1/70 D. 1/19,600 and 1/140
4. If an X-linked recessive disorder affects approximately 1/1,000,000 females (all
homozygotes) in a population, what is the expected frequency of affected males in the
population?
A. 1/100 B. 1/1000 C. 1/5000 D. 1/10000
5. If the incidence of classical PKU is 1/10,000, what is the carrier (heterozygote)
frequency?
A. 1/500 B. 1/200 C. 1/50 D. 1/20
6. If allele A has a frequency of 0.5, and marriages are at random, the frequency of
marriage of Aa X Aa is:
A. 1/2 B. 1/4 C. 1/8 D. 1/16 E. 1/32

II. Review questions

74
 1. About 70 percent of all white North Americans can taste the chemical
phenylthiocarbamide, and the remainder cannot. The ability to taste is determined by the
dominant allele T, and the inability to taste is determined by the recessive allele t. If the
population is assumed to be in Hardy-Weinberg equilibrium, what are the genotypic and
allelic frequencies in this population?

Ans Because 70 percent are tasters (T/T), 30 percent must be nontasters (t/t). This
homozygous recessive frequency is equal to q2; so, to obtain q, we simply take the square
root of 0.30:

2. In a survey of Native American tribes in Arizona and New Mexico, albinos were
completely absent or very rare in most groups (there is one albino per 20,000 North
American Caucasians). However, in three Native American populations, albino frequencies
are exceptionally high: 1 per 277 Native Americans in Arizona; 1 per 140 Jemez in New
Mexico; and 1 per 247 Zuni in New Mexico. All three of these populations are culturally but
not linguistically related. What possible factors might explain the high incidence of albinos
in these three tribes?

Ans Albinos may have been considered lucky and encouraged to breed at very high

levels in comparison with nonalbinos. They may also have been encouraged to mate with

each other. Alternatively, in the tribes with a very low frequency, albinos may have been

considered very unlucky and destroyed at birth or prevented from marriage.

75
III. Key Terms
Gene pool:
Allele frequency: A measure of the commonness of an allele in a population; the
proportion of all alleles of that gene in the population that are of this specific type.
Hardy-Weinberg equilibrium: The stable frequency distribution of genotypes A/A, A/a,
and a/a, in the proportions p2, 2pq, and q2, respectively (where p and q are the frequencies
of the alleles A and a), that is a consequence of random mating in the absence of mutation,
migration, natural selection, or random drift.
Genetic drift: Fluctuation in allele frequency due to chance in a small population.
Random mating: Mating between individuals where the choice of a partner is not
influenced by the genotypes (with respect to specific genes under study).
Population genetics: relates the processes of individual heredity and development to the
genetic composition of populations and to changes in that composition in time.
Heterozygote advantage: Mutant allele has a high frequency despite reduced fitness in
affected individuals.
Chapter 11 Genetic Counseling

Genetic counseling: The provision of information and assistance to affected individuals or

family members at risk of a disorder that may be genetic, concerning the consequences of
the disorder, the probability of developing or transmitting it, and the ways in which it may
be prevent or ameliorated. OR: The delivery of information about genetic diseases (risks,
natural history, and management) to patients and their families.

I. Steps in genetic counseling

1. Evaluating family history and medical records
2. Ordering genetic tests
3. Evaluating the results of this investigation (Risk assessment)
4. Helping patients understand and reach decisions about what to do next
5. Long-term contact and support
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II. Common indications for genetic counseling
1. Previous child with multiple congenital anomalies, mental retardation or an isolated
birth defect, such as neural tube defect, cleft lip and palate.
2. Family history of a hereditary condition, such as cystic fibrosis, fragile X syndrome, or
diabetes.
3. Prenatal diagnosis for advanced maternal age or other indication.
4. Consanguinity.
5. Teratogen exposure, such as to occupational chemicals, medications, alcohol.
6. Repeated pregnancy loss or infertility.
7. Newly diagnosed abnormality or genetic condition.
8. Before undertaking genetic testing and after receiving results, particularly when
testing for susceptibility to late-onset disorders, such as cancer or neurological disease.
9. As follow-up for a positive result of a newborn test, as with PKU; a heterozygote
screening test, such as Tay-Sachs; or a positive first- or second-trimester maternal serum
screen or abnormal fetal ultrasound examination.

III. Determining recurrence risks

Recurrence risk: The probability that a genetic disorder present in one or more members
of a family will recur in another member of the same or a subsequent generation.
Bayesian analysis: A mathematical method widely used in genetic counseling to calculate
recurrence risk.
Posterior probability = Joint probability /Σ Joint probability
Joint probability= Prior probability × Conditional probability

General Revision
I. Pick the best answer

77
 1. The pedigree shows your patient, Marsha, who is affected with a single gene,
autosomal dominant disorder that shows 80% penetrance, and her two children, Michael
and Marcus. Michael is also clinically affected with the disorder. The
probability that Marcus will have the clinical signs with the disorder
is closet to which of the following choices?

A.20%
B.40%
C.50%
D.80%
E. 100%

2. Chris and his brother Todd both have Duchnne muscular dystrophy. There is a maternal
history of this disorder. Jean, the boy’s maternal aunt, is interested in beginning a family.
What is the probability that she is a heterozygous carrier of the disease gene?
A. Virtually 0 B.1/8 C.1/4 D.3/8 E. 1/2

3. Many disorders are not caused by single gene inheritance, but are multifactorial. In
counseling situations involving these disorders, how are recurrence risks identified?
A. Single gene inheritance risks are multiplied by a factorial fraction, chosen to
represent the contribution from other genetic factors plus the environmental influence
B. Bayes theorem is applied, using modifications of “prior” risk calculation
utilized among single-gene defects
C. The risks are determined empirically, based on previous observations of
disease recurrence among actual families
D. Recurrence risks cannot determined for non-Mendelian disorders
4. Which of following action is acceptable in medical genetics practice?
A. Discuss the cases with your colleagues in the hallway

78
 B. Discuss the cases with your friend because she is very interested in anything
funny
C. Put all the patient genetic testing reports at the front desk and let the
patients search for their own ones because it is easy
D. None of the above
5．About genetic counselling
A. The individual who seeks genetic counselling is the proband
B. Genetic counselling is all about recurrence risk
C. Genetic disorders are accidents of nature, so guilt feelings are rare
D. Patient support groups have little value given that modern medical genetics is
so technically complex
E. Good counselling should not be measured by the patient’s/client’s ability to
remember genetic risks
Ⅰ. Review questions
1. Mary’s two brothers and her mother all had Duchenne muscular dystrophy (DMD) and
are now dead. Based on only this information, what is the probability that Mary is a
heterozygous carrier for this disorder? What is the probability that she will produce affected
offspring? Suppose Mary has a serum creatine kinase (CK) test and is told that her level is
above the 95th percentile for homozygous normal individuals. Approximately two thirds of
DMD carriers have CK levels above the 95th percentile. Given this information, use Bayes
theorem to calculate the probability that Mary is a carrier and the probability that she will
produce affected offspring.

Prior 1/2 1/2

probability
Conditional 2/3 0.05
probability
that her CK
is in the 95th
79
percentile
Joint 1/3 0.025
probability
Posterior 0.93 0.07
probability

2. The neurofibromatoses are a group of clinically and genetically different autosomal

dominant hereditary diseases (NF1, NF2, etc.) that predispose to benign and malignant
tumors of the nervous system. You are addressing a Neurofibromatosis Association parents’
meeting. A severely affected woman, 32 years old, comments that she is not at risk of
passing on the disorder because her parents are not affected and her neurofibromatosis,
therefore, is due to a new mutation. Comment.
Ans The woman is mistaken. She needs genetic counseling. She has a 1/2 risk of passing
the mutant NF1 gene to her offspring. The fact that she carries a new mutation only reduces
the recurrence risk elsewhere in the family.

Ⅰ. Key Terms
Genetic counseling: The provision of information and assistance to affected individuals or
family members at risk of a disorder that may be genetic, concerning the consequences of
the disorder, the probability of developing or transmitting it, and the ways in which it may
be prevent or ameliorated. OR: The delivery of information about genetic diseases (risks,
natural history, and management) to patients and their families.
Recurrence risk: The probability that a genetic disorder present in one or more members
of a family will recur in another member of the same or a subsequent generation.

80