# 01 - 479 Principles of Human Genetics

## 479 Principles of Human Genetics

Genes, the Environment, and Disease
PART 16
J. Larry Jameson, Peter Kopp

Principles of Human 

Genetics
IMPACT OF GENETICS AND GENOMICS 

ON MEDICAL PRACTICE
Over the past four decades, novel insights into human genetics and 
genomics have fundamentally impacted the practice of medicine, ush­
ering in a new area with a deeper understanding of the genetic basis 
of numerous health conditions, novel diagnostic technologies, disease 
prevention and management, personalized medicine, and targeted 
therapies. Human genetics refers to the study of individual genes, their 
role and function in disease, and their mode of inheritance. Genomics 
refers to an organism’s entire genetic information, the genome, and the 
function and interaction of DNA within the genome, as well as with 
environmental or nongenetic factors, such as a person’s lifestyle. With 
the characterization of the human genome, genomics not only comple­
ments traditional genetics in our efforts to elucidate the etiology and 
pathogenesis of disease, but it also plays a prominent and expand­
ing role in diagnostics, prevention, and therapy (Chap. 480). These 
transformative developments, originally emerging from the Human 
Genome Project, have been variably designated genomic medicine, 
personalized medicine, or precision medicine. Precision medicine aims 
at customizing medical decisions to an individual patient. For example, 
a patient’s genetic characteristics (genotype) can be used to optimize 
drug therapy and predict efficacy, adverse events, and drug dosing of 
selected medications (pharmacogenomics) (Chap. 72). The character­
ization of the mutational profile of a malignancy allows the identifica­
tion of driver mutations or overexpressed signaling molecules, which 
then facilitates the selection of targeted therapies. Genome-wide poly­
genic risk scores (PRS) for common complex diseases are beginning to 
emerge and may impact disease prevention in the future.
Genetics has traditionally been viewed through the window of 
relatively rare single-gene diseases. These disorders account for ~10% 
of pediatric admissions and childhood mortality. Historically, genetics 
has focused predominantly on chromosomal and metabolic disorders, 
reflecting the long-standing availability of techniques to diagnose these 
conditions. For example, conditions such as trisomy 21 (Down’s syn­
drome) or monosomy X (Turner’s syndrome) can be diagnosed using 
cytogenetics. Likewise, many metabolic disorders (e.g., phenylketon­
uria, familial hypercholesterolemia) are diagnosed using biochemical 
analyses. The advances in DNA and RNA diagnostics have extended 
the field of genetics to include virtually all medical specialties and 
have led to the elucidation of the pathogenesis of most monogenic 
disorders. In addition, virtually every medical condition has a genetic 
component. As is often evident from a patient’s family history, many 
common disorders such as hypertension, heart disease, asthma, dia­
betes mellitus, and mental illnesses are significantly influenced by 
the genetic background. These polygenic or multifactorial (complex) 
disorders involve the contributions of many different genes, as well 
as environmental factors that can modify disease risk. Genome-wide 
association studies (GWAS) have elucidated numerous disease-associated 
loci and are providing novel insights into the allelic architecture of 
complex traits. These studies have been facilitated by the availability of 
comprehensive catalogues of human single nucleotide polymorphism 
(SNP) haplotypes (HapMap, International Genome Sample Resource). 
Next-generation DNA sequencing (NGS) technologies have evolved 
rapidly, and the cost of sequencing whole exomes (the exons within 
the genome; whole exome sequencing [WES]) or genomes (whole 
genome sequencing [WGS]) has plummeted. Comprehensive unbiased 
sequence analyses are now routinely used to characterize individuals 

with complex undiagnosed conditions or to determine the mutational 
profile of advanced malignancies in order to select optimal and targeted 
therapies. The assembly of diploid genomes, i.e., the characterization of 
the complete genetic information from both sets of chromosomes in an 
individual’s genome, will further enhance the complete resolution of 
genetic variation and should provide further insights into heritability 
and disease mechanisms.
Cancer has a genetic basis because it results from acquired somatic 
mutations in genes controlling growth, apoptosis, and cellular differ­
entiation (Chap. 76). In addition, the development of many cancers 
is associated with a hereditary predisposition. Characterization of the 
genome (and epigenome) in various malignancies has led to funda­
mental new insights into cancer biology and reveals that the genomic 
profile of mutations is in many cases more important in determining 
the appropriate therapy than the organ in which the tumor originates. 
The Cancer Genome Atlas (TCGA) initiative of the National Cancer 
Institute and the National Human Genome Research Institute has 
already characterized the genomic landscape across >30 malignancies. 
TCGA consists of comprehensive analyses of genomic and proteomic 
alterations and provided fundamental new insights into the molecular 
pathogenesis of cancer. These data, together with comprehensive cata­
logues of somatic mutations identified in human cancer, have direct 
clinical ramifications that impact cancer taxonomy, as well as the devel­
opment and choice of targeted therapies.
Genetic and genomic approaches have proven invaluable for the 
detection of infectious pathogens and are used clinically to identify 
agents that are difficult to culture such as mycobacteria, viruses, and 
parasites, or to track infectious agents locally or globally. In many 
cases, molecular genetics has improved the feasibility and accuracy 
of diagnostic testing and has opened new avenues for therapy, includ­
ing gene and cellular therapies (Chap. 483). Molecular genetics has 
also provided the opportunity to characterize the microbiome, a field 
that characterizes the population dynamics of bacteria, viruses, and 
parasites that coexist with humans and other animals (Chap. 483). 
The microbiome has significant effects on normal physiology as well 
as various disease states, and the field is now focusing on defining the 
mechanisms underlying these interactions.
Molecular biology has significantly changed the treatment of human 
disease. Peptide hormones, growth factors, cytokines, and vaccines can 
be produced in large amounts using recombinant DNA and RNA tech­
nology (e.g., mRNA vaccines against SARS-CoV-2; small interfering 
RNA [siRNA] to treat hypercholesterolemia). Targeted modifications 
of recombinant peptides provide improved therapeutic tools, as illus­
trated by genetically modified insulin analogues with more favorable 
kinetics or glucagon-like peptide 1 (GLP-1) agonists for treatment of 
type 2 diabetes and for weight management.
The rate at which new genetic and genomic information is being 
generated presents many challenges for health care providers and 
systems. Although many functional aspects of the genome remain 
unknown, there are many clinical situations where genetic and genomic 
information optimize patient care. Much genetic information resides in 
databases that provide easy access to the expanding information about 
the human genome, genetic disease, and genetic testing (Table 479-1). 
For example, several thousand monogenic disorders are summarized 
in a large, continuously evolving compendium, the Online Mendelian 
Inheritance in Man (OMIM) catalogue (Table 479-1). The constant 
refinement of bioinformatics and big data analytics, together with the 
widespread adoption of electronic health records (EHRs), are simplify­
ing the access, analysis, and integration of this daunting amount of new 
information. Importantly, genomic data can be integrated readily into 
EHRs and thus impact clinical practice.
■
■THE HUMAN GENOME
Structure of the Human Genome 
The Human Genome Project 
was initiated in the mid-1980s as an ambitious effort to characterize

TABLE 479-1  Selected Databases Relevant for Genomics and Genetic Disorders
SITE
URL
COMMENT
National Center for Biotechnology 
Information (NCBI)
http://www.ncbi.nlm.nih.gov/
Broad access to biomedical and genomic information, literature (PubMed), 
sequence databases, software for analyses of nucleotides and proteins
Extensive links to other databases, genome resources, and tutorials
PART 16
Genes, the Environment, and Disease
National Human Genome Research 
Institute
http://www.genome.gov/
An institute of the National Institutes of Health focused on genomic and genetic 
research; links providing information about the human genome sequence, 
genomes of other organisms, genomic research, and legislation
Catalog of Published Genome-Wide 
Association Studies
https://www.ebi.ac.uk/gwas/
Published high-resolution genome-wide association studies (GWAS)
Ensembl Genome browser
http://www.ensembl.org
Maps and sequence information of eukaryotic genomes
Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/omim
Online compendium of Mendelian disorders and human genes causing genetic 
disorders
American College of Medical Genetics 
and Genomics
http://www.acmg.net/
Extensive links to other databases relevant for the diagnosis, treatment, and 
prevention of genetic disease
American Society of Human Genetics
http://www.ashg.org
Information about advances in genetic research, professional and public 
education, and social and scientific policies
The Cancer Genome Atlas
https://cancergenome.nih.gov/
Comprehensive, multidimensional characterization of the genomic and proteomic 
landscape of malignancies with high public health impact
COSMIC Catalogue of Somatic 
Mutations in Cancer
https://cancer.sanger.ac.uk/cosmic
Comprehensive catalogue of somatic mutations in human cancer
Genetic Testing Registry
https://www.ncbi.nlm.nih.gov/gtr/
International directory of genetic testing laboratories and prenatal diagnosis 
clinics; reviews and educational materials
Genomes Online Database (GOLD)
http://www.genomesonline.org/
Information on published and unpublished genomes
HUGO Gene Nomenclature
http://www.genenames.org/
Gene names and symbols
GENECODE
https://www.gencodegenes.org/
High-quality reference gene annotation and experimental validation for human and 
mouse genomes
MITOMAP, a human mitochondrial 
genome database
http://www.mitomap.org/
A compendium of polymorphisms and mutations of the human mitochondrial DNA
The International Genome Sample 
Resource (IGSR)
http://www.internationalgenome.org
Public catalogue of human variation and genotype data from numerous ethnic 
groups
Human Genome Variation Society
https://www.hgvs.org/
Collection and documentation of genomic variations including population 
distribution and phenotypic associations
ENCODE
http://www.genome.gov/10005107
Encyclopedia of DNA Elements; catalogue of all functional elements in the human 
genome
Dolan DNA Learning Center, Cold Spring 
Harbor Laboratories
http://www.dnalc.org/
Educational material about selected genetic disorders, DNA, eugenics, and genetic 
origin
The Online Metabolic and Molecular 
Bases of Inherited Disease (OMMBID)
http://ommbid.mhmedical.com
Online version of the comprehensive text on the metabolic and molecular bases of 
inherited disease
Online Mendelian Inheritance in Animals 
(OMIA)
https://www.omia.org/home/
Online compendium of Mendelian disorders in animals
The Jackson Laboratory
http://www.jax.org/
Information about murine models and the mouse genome
Mouse genome informatics
http://www.informatics.jax.org
Mouse genome informatics, potential mouse models of human disease, information 
on phenotypic similarity between mouse models and human patients
Note: Databases are evolving constantly. Pertinent information may be found by using links listed in the few selected databases.
the entire human genome and culminated in the completion of the 
DNA sequence for the last of the human chromosomes in 2006. The 
scope of a WGS analysis can be illustrated by the following analogy. 
Human DNA consists of ~3 billion base pairs (bp) of DNA per haploid 
genome, which is nearly 1000-fold greater than that of the Escherichia 
coli genome. If the human DNA sequence were printed out, it would 
correspond to about 120 volumes of Harrison’s Principles of Internal 
Medicine.
In addition to the human genome, the genomes of thousands of 
organisms have been sequenced completely or partially (Genomes 
Online Database [GOLD]; Table 479-1). They include, among others, 
eukaryotes such as the mouse (Mus musculus), Saccharomyces cere­
visiae, Caenorhabditis elegans, and Drosophila melanogaster; bacteria 
(e.g., E. coli); and archaea, viruses, organelles (mitochondria, chloro­
plasts), and plants (e.g., Arabidopsis thaliana). Genomic information 
of infectious agents has significant impact for the characterization 
of infectious outbreaks and epidemics. Other ramifications arising 
from the availability of genomic data include, among others, (1) the 
comparison of entire genomes (comparative genomics); (2) the study 
of large-scale expression of RNAs (functional genomics), proteins 
(proteomics), or protein families (e.g., the kinome, the complete set of 

protein kinases) to detect differences between various tissues in health 
and disease; (3) the characterization of the variation among individu­
als by establishing catalogues of sequence variations and SNPs; and (4) 
the identification of genes that play critical roles in the development of 
polygenic and multifactorial disorders.
CHROMOSOMES  The human genome is divided into 23 different 
chromosomes, including 22 autosomes (numbered 1–22) and the X 
and Y sex chromosomes (Fig. 479-1). Adult cells are diploid, meaning 
they contain two homologous sets of 22 autosomes and a pair of sex 
chromosomes. Females have two X chromosomes (XX), whereas males 
have one X and one Y chromosome (XY). As a consequence of meiosis, 
germ cells (sperm or oocytes) are haploid and contain one set of 22 
autosomes and one of the sex chromosomes. At the time of fertiliza­
tion, the diploid genome is reconstituted by pairing of the homologous 
chromosomes from the mother and father. With each cell division 
(mitosis), chromosomes are replicated, paired, segregated, and divided 
into two daughter cells.
STRUCTURE OF DNA  DNA is a double-stranded helix composed of 
four different bases: adenine (A), thymidine (T), guanine (G), and 
cytosine (C). Adenine is paired to thymidine, and guanine is paired

Guanine
Cytosine
H
O
O
H
N
N
H
H
C
C
C
O
O
P
C
C
N
N
N
O–
C
C
H
H
C
N
N
C
N
H
O
H
H
Thymine
Adenine
O
N
H
H3C
C
N
H
C
O
O
P
C
C
C
C
N
O–
C
N
H
H
N
C
C
C
N
N
H
O
T
Double-strand DNA
without histones
G
A
C
A
T
C
G
Nucleosome core
Histone H2A, H2B, H4
Metaphase
chromosome
Nucleosome
fiber
p, short arm
Centromere
Solenoid
q, long arm
Telomere
Supercoiled
chromatin
FIGURE 479-1  Structure of chromatin and chromosomes. Chromatin is composed of 
double-strand DNA that is wrapped around histone and nonhistone proteins forming 
nucleosomes. The nucleosomes are further organized into solenoid structures. 
Chromosomes assume their characteristic structure, with short (p) and long (q) 
arms at the metaphase stage of the cell cycle.
to cytosine, by hydrogen bond interactions that span the double helix 
(Fig. 479-1). DNA has several remarkable features that make it ideal 
for the transmission of genetic information. It is relatively stable, and 
the double-stranded nature of DNA and its feature of strict base-pair 
complementarity permit faithful replication during cell division. 
Complementarity also allows the transmission of genetic information 
from DNA → RNA → protein (Fig. 479-2). mRNA is encoded by the 
so-called sense or coding strand of the DNA double helix and is trans­
lated into proteins by ribosomes.
The presence of four different bases provides surprising genetic 
diversity. In the protein-coding regions of genes, the DNA bases are 
arranged into codons, a triplet of bases that specifies a particular 
amino acid. It is possible to arrange the four bases into 64 different 
triplet codons (43). Each codon specifies 1 of the 20 different amino 
acids, or a regulatory signal such as initiation and stop of translation. 
Because there are more codons than amino acids, the genetic code is 
degenerate; that is, most amino acids can be specified by several dif­
ferent codons. By arranging the codons in different combinations and 
in various lengths, it is possible to generate the tremendous diversity of 
primary protein structure.
DNA length is normally measured in units of 1000 bp (kilobases, kb) 
or 1,000,000 bp (megabases, Mb). In the human genome, only ~1% of 
DNA accounts for protein-coding sequences. The noncoding DNA has 
multiple functional and structural roles including (1) sequences that 
form introns; (2) regulatory elements (promoters, enhancers, silencers, 
insulators); (3) sequences that generate RNAs that do not code for pro­
teins; (4) centromeres and telomeres; (5) regions defining chromatin 

structure and histone modifications; (6) various forms of repetitive 
sequences of variable length; and (7) pseudogenes and regions without 
currently discernible functional or structural roles (Fig. 479-1).

GENES  A gene is a functional unit that is regulated by transcription 
(see below) and encodes an RNA product, which is most commonly, 
but not always, translated into a protein that exerts activity within 
or outside the cell (Fig. 479-3). Historically, genes were identified 
because they conferred specific traits that are transmitted from one 
generation to the next. Now, they are frequently characterized based 
on expression in various tissues (transcriptome). The size of genes is 
quite broad; some genes are only a few hundred base pairs, whereas 
others are extraordinarily large (2.3 Mb). The number of genes greatly 
underestimates the complexity of genetic expression, because single 
genes can generate multiple spliced messenger RNA (mRNA) products 
(isoforms), which are translated into proteins that are subject to com­
plex posttranslational modification such as phosphorylation. Exons 
refer to the portion of genes that are eventually spliced together to form 
mRNA. Introns refer to the spacing regions between the exons that are 
spliced out of precursor RNAs during RNA processing. The gene locus 
also includes regions that are necessary to control its expression (Fig. 
479-2). Current estimates predict roughly 20,000 protein-coding genes 
in the human genome with an average of about four different coding 
transcripts per gene. Remarkably, the exome only constitutes 1.14% of 
the genome. Of note, the number of transcripts is close to 200,000 and 
includes thousands of noncoding transcripts (RNAs of various length 
such as microRNAs [miRNA] and long noncoding RNAs [lncRNA]). 
These noncoding RNAs are involved in numerous cellular processes 
such as transcriptional and posttranscriptional regulation of gene 
expression, chromatin remodeling, and protein trafficking, among 
others. Not surprisingly, aberrant expression and/or mutations in these 
RNAs play a pathogenic role in numerous diseases.
CHAPTER 479
Principles of Human Genetics 
Histone
H1
SINGLE-NUCLEOTIDE POLYMORPHISMS  On average, a typical genome 
differs from the reference human genome at 4 to 5 million sites. Some 
of these variants have no impact on health, whereas others may 
increase or lower the risk for developing a specific disease. Remarkably, 
however, the primary DNA sequence of humans has ~99.9% similarity 
compared to that of any other human. An SNP is a variation of a single 
base pair in the DNA. Across human populations from distinct ethnic 
backgrounds, there are more than 1 billion validated SNPs (Fig. 479-3). 
SNPs are the most common type of sequence variation and account for 
>90% of all sequence variation. They occur on average every 100–300 
bases and are the major source of genetic heterogeneity. SNPs that 
are in proximity are inherited together (e.g., they are linked) and are 
referred to as haplotypes (Fig. 479-4). Haplotype maps describe the 
nature and location of these SNP haplotypes and how they are distrib­
uted among individuals within and among populations, information 
that has been facilitating GWAS designed to elucidate the complex 
interactions among multiple genes and lifestyle factors in multifactorial 
disorders (see below). Moreover, haplotype analyses are useful to assess 
variations in responses to medications (pharmacogenomics) and envi­
ronmental factors, as well as the prediction of disease predisposition.
COPY NUMBER VARIATIONS  Copy number variations (CNVs) are 
relatively large genomic regions (1 kb to several Mb) that have been 
duplicated or deleted on certain chromosomes and hence alter the dip­
loid status of the DNA (Fig. 479-5). It has been estimated that 5–10% 
of the genome can display CNVs. When comparing the genomes of 
two individuals, ~0.4–0.8% of their genomes differ in terms of CNVs 
scattered throughout the genome. Some CNVs can increase or decrease 
gene dosage, potentially leading to detrimental effects if essential genes 
are impacted. Of note, de novo CNVs have been observed between 
monozygotic twins, who otherwise have identical genomes.
Replication of DNA and Mitosis 
Genetic information in DNA 
is transmitted to daughter cells under two different circumstances: (1) 
somatic cells divide by mitosis, allowing the diploid (2n) genome to repli­
cate itself completely in conjunction with cell division; and (2) germ cells 
(sperm and ova) undergo meiosis, a process that enables the reduction of 
the diploid (2n) set of chromosomes to the haploid state (1n).

Steroids
Ca2+
Cytokines
Growth
factors
Hormones
Light
UV-light
Mechanical stress
PART 16
Genes, the Environment, and Disease
Regulation of Gene Expression
Enhancer
Silencer
Nuclear
receptor
Nuclear
receptor
HAT
CoA
CBP
TAF
GTF
CREB CREB
TBP
Transcription
factor
CRE
RE
CAAT TATA

mRNA Processing
Posttranslational Processing
FIGURE 479-2  Flow of genetic information. Multiple extracellular signals activate intracellular signal cascades that result in altered regulation of gene expression through 
the interaction of transcription factors with regulatory regions of genes. RNA polymerase transcribes DNA into RNA that is processed to mRNA by excision of intronic 
sequences. The mRNA is translated into a polypeptide chain to form the mature protein after undergoing posttranslational processing. CBP, CREB-binding protein; CoA, 
co-activator; COOH, carboxyterminus; CRE, cyclic AMP responsive element; CREB, cyclic AMP response element–binding protein; GTF, general transcription factors; HAT, 
histone acetyl transferase; NH2, aminoterminus; RE, response element; TAF, TBP-associated factors; TATA, TATA box; TBP, TATA-binding protein.
Prior to mitosis, cells exit the resting, or G0 state, and enter the cell 
cycle. After traversing a critical checkpoint in G1, cells undergo DNA 
synthesis (S phase), during which the DNA in each chromosome is rep­
licated, yielding two pairs of sister chromatids (2n → 4n). The process 
of DNA synthesis requires stringent fidelity in order to avoid transmit­
ting errors to subsequent generations of cells. Genetic abnormalities 
of DNA mismatch/repair include xeroderma pigmentosum, Bloom’s 
syndrome, ataxia telangiectasia, and hereditary nonpolyposis colon 
cancer (HNPCC), among others. Many of these disorders strongly 
predispose to neoplasia because of the rapid acquisition of additional 
mutations (Chap. 76). After completion of DNA synthesis, cells enter 
G2 and progress through a second checkpoint before entering mitosis. 
At this stage, the chromosomes condense and are aligned along the 
equatorial plate at metaphase. The two identical sister chromatids, held 
together at the centromere, divide and migrate to opposite poles of the 
cell. After formation of a nuclear membrane around the two separated 
sets of chromatids, the cell divides and two daughter cells are formed, 
thus restoring the diploid (2n) state.
Assortment and Segregation of Genes During Meiosis 
Meiosis 
occurs only in germ cells of the gonads. It shares certain features with 
mitosis but involves two distinct steps of cell division that reduce the 
chromosome number to the haploid state. In addition, there is active 
recombination that generates genetic diversity. During the first cell 
division, two sister chromatids (2n → 4n) are formed for each chro­
mosome pair and there is an exchange of DNA between homologous 
paternal and maternal chromosomes. This process involves the forma­
tion of chiasmata, structures that correspond to the DNA segments that 
cross over between the maternal and paternal homologues (Fig. 479-6). 
Usually there is at least one crossover on each chromosomal arm; 
recombination occurs more frequently in female meiosis than in male 
meiosis. Subsequently, the chromosomes segregate randomly. Because 
there are 23 chromosomes, there exist 223 (>8 million) possible com­
binations of chromosomes. Together with the genetic exchanges that 

Cytoplasm
Nucleus
RNA
polymerase II
DNA
Transcription

hRNA

–Poly-A Tail
5′ -Cap
mRNA
Translation
Protein
NH2–
–COOH
occur during recombination, chromosomal segregation generates tre­
mendous diversity, and each gamete is genetically unique. The process 
of recombination and the independent segregation of chromosomes 
provide the foundation for performing linkage analyses, whereby one 
attempts to correlate the inheritance of certain chromosomal regions 
(or linked genes) with the presence of a disease or genetic trait (see 
below).
After the first meiotic division, which results in two daughter cells 
(2n), the two chromatids of each chromosome separate during a sec­
ond meiotic division to yield four gametes with a haploid state (1n). 
When the egg is fertilized by sperm, the two haploid sets are combined, 
thereby restoring the diploid state (2n) in the zygote.
■
■REGULATION OF GENE EXPRESSION
Regulation by Transcription Factors 
The expression of genes 
is regulated by DNA-binding proteins that activate or repress tran­
scription. The number of DNA sequences and transcription factors 
that regulate transcription is much greater than originally anticipated. 
Most genes contain at least 15–20 discrete regulatory elements within 
300 bp of the transcription start site. This densely packed promoter 
region often contains binding sites for ubiquitous transcription fac­
tors. However, factors involved in cell-specific expression may also 
bind to these sequences. Key regulatory elements may also reside 
at a large distance from the proximal promoter. The globin and the 
immunoglobulin genes, for example, contain locus control regions that 
are several kilobases away from the structural sequences of the gene. 
Specific groups of transcription factors that bind to these promoter 
and enhancer sequences provide a combinatorial code for regulating 
transcription. In this manner, relatively ubiquitous factors interact 
with more restricted factors to allow each gene to be expressed and 
regulated in a unique manner that is dependent on developmental 
state, cell type, and numerous extracellular stimuli. Regulatory factors 
also bind within the gene itself, particularly in the intronic regions. The

SNPs
(612,977)
Known Genes
(1260)
p22.3
p22.1
p21.3
p15.3
p15.1
p14.3
p13
p12.3
p14.1
p21.1
Chromosome 7
116.90 Mb
116.94 Mb
116.98 Mb
117.02 Mb
117.06 Mb
CFTR Gene
SNPs
Intronic
Splice site
Coding region, synonymous
Coding region, nonsynonymous
FIGURE 479-3  Chromosome 7 is shown with the density of single nucleotide polymorphisms (SNPs) and genes above. A 200-kb region in 7q31.2 containing the CFTR gene 
is shown below. The CFTR gene contains 27 exons. Close to 2000 mutations in this gene have been found in patients with cystic fibrosis. A 20-kb region encompassing exons 
4–9 is shown further amplified to illustrate the SNPs in this region.
FIGURE 479-4  The origin of haplotypes is due to repeated recombination events 
occurring in multiple generations. Over time, this leads to distinct haplotypes. These 
haplotype blocks can often be characterized by genotyping selected Tag single 
nucleotide polymorphisms (SNPs), an approach that facilitates performing genomewide association studies (GWAS).

CHAPTER 479
Principles of Human Genetics 
q31.2
q31.31
q31.33
q32.1
p21.13
q11.21
q11.22
q11.23
q21.11
q22.1
q22.3
q35
q36.1
q36.3
p12.1
p11.2
q21.3
q31.1
q33
q34
200 Kb
20 Kb
Coding region, frameshift
transcription factors that bind to DNA represent only the first level of 
regulatory control. Other proteins—co-activators and co-repressors—
interact with the DNA-binding transcription factors to generate large 
regulatory complexes. These complexes are subject to control by 
numerous cell-signaling pathways and enzymes, leading to phosphory­
lation, acetylation, sumoylation, and ubiquitination. Ultimately, the 
recruited transcription factors interact with, and stabilize, components 
of the basal transcription complex that assembles at the site of the 
TATA box and initiator region. This basal transcription factor complex 
consists of >30 different proteins. Gene transcription occurs when 
RNA polymerase begins to synthesize RNA from the DNA template. A 
large number of identified genetic diseases involve transcription factors 
(Table 479-2).
The field of functional genomics is based on the concept that under­
standing alterations of gene expression under various physiologic and 
pathologic conditions provides insight into the underlying functional 
role of the gene. The ENCODE (Encyclopedia of DNA Elements) 
project aims at identifying and annotating all functional sequences 
in the human genome. By revealing specific gene expression profiles, 
this knowledge can be of diagnostic and therapeutic relevance. The 
large-scale study of expression profiles is referred to as transcriptomics 
because the complement of mRNAs transcribed by the cellular genome 
is called the transcriptome.
Most studies of gene expression have focused on the regulatory 
DNA elements of genes that control transcription. However, it must be

Normal
Duplicated
Area
PART 16
Genes, the Environment, and Disease
Deleted
Area

log2 (ratio)

–1
–2
Chromosome 8
FIGURE 479-5  Copy number variations (CNV) encompass relatively large regions of the genome that 
have been duplicated or deleted. Chromosome 8 is shown with a CNV detected by genomic hybridization. 
An increase in the signal strength indicates a duplication, whereas a decrease reflects a deletion of the 
covered chromosomal regions.
emphasized that gene expression requires a series of steps, including 
mRNA processing, protein translation, and posttranslational modifica­
tions, all of which are actively regulated (Fig. 479-2).
Epigenetic Regulation of Gene Expression (see Chap. 497) 

Epigenetics describes mechanisms and phenotypic changes that are not 
a result of variation in the primary DNA nucleotide sequence but are 
caused by secondary modifications of DNA or histones. These modifi­
cations include heritable changes such as X-inactivation and imprint­
ing, but they can also result from dynamic posttranslational protein 
modifications in response to environmental influences such as diet, 
age, or drugs. The epigenetic modifications result in altered expression 
of individual genes or chromosomal loci encompassing multiple genes. 
The term epigenome describes the constellation of covalent modifica­
tions of DNA and histones that impact chromatin structure, as well 
as noncoding transcripts that modulate the transcriptional activity of 
DNA. Although the primary DNA sequence is usually identical in all 
cells of an organism, sex- and tissue-specific changes in the epigenome 
contribute to determining the transcriptional signature of a cell (tran­
scriptome) and hence the protein expression profile (proteome).
Mechanistically, DNA and histone modifications can result in the 
activation or silencing of gene expression (Fig. 479-7). DNA methyla­
tion involves the addition of a methyl group to cytosine residues. This 
is usually restricted to cytosines of CpG dinucleotides, which are abun­
dant throughout the genome. Methylation of these dinucleotides is 
thought to represent a defense mechanism that minimizes the expres­
sion of sequences that have been incorporated into the genome such 
as retroviral sequences. CpG dinucleotides also exist in so-called CpG 
islands, stretches of DNA characterized by a high CG content, which 
are found in the majority of human gene promoters. CpG islands in 
promoter regions are typically unmethylated, and the lack of methyla­
tion facilitates transcription.
Histone methylation involves the addition of a methyl group to lysine 
residues in histone proteins (Fig. 479-7). Depending on the specific 
lysine residue being methylated, this alters chromatin configuration, 
making it either more open or tightly packed. Acetylation of histone 
proteins is another well-characterized mechanism that results in an 

open chromatin configuration, which favors active 
transcription. Acetylation is generally more dynamic 
than methylation, and many transcriptional activation 
complexes have histone acetylase activity, whereas 
repressor complexes often contain deacetylases and 
remove acetyl groups from histones. Other histone 
modifications include, among others, phosphorylation 
and sumoylation.
Furthermore, noncoding RNAs and RNA regula­
tory networks that bind to DNA have a significant 
impact on transcriptional activity.
Physiologically, epigenetic mechanisms play an 
important role in several instances. For example, 
X-inactivation refers to the relative silencing of one of 
the two X chromosome copies present in females. The 
inactivation process is a form of dosage compensation 
such that females (XX) do not generally express twice 
as many X-chromosomal gene products as males 
(XY). In a given cell, the choice of which chromo­
some is inactivated occurs randomly in humans. 
But once the maternal or paternal X chromosome 
is inactivated, it will remain inactive, and this infor­
mation is transmitted with each cell division. The 
X-inactive specific transcript (Xist) gene encodes a 
long non-coding RNA (lncRNA) that mediates gene 
silencing on one of the X chromosomes. The inac­
tive X chromosome is highly methylated and has low 
levels of histone acetylation. While the majority of 
X-chromosomal genes are silenced by X-inactivation, 
~15% escape inactivation and are expressed.
Epigenetic gene inactivation also occurs on selected 
chromosomal regions of autosomes, a phenomenon 
referred to as genomic imprinting. Through this mechanism, a small 
subset of genes is only expressed in a monoallelic fashion. Imprinting is 
A
a
A
a
a
A
B
b
B
b
b
B
C
c
C
c
c
C
D
d
D
d
d
D
Chromatids
Homologous
chromosomes
A
a
a
A
A
a
a
A
A
a
a
A
B
b
b
B
B
b
b
B
B
b
b
B
c
c
C
C
c
c
C
C
C
c
c
C
d
d
D
D
D
d
d
D
D
d
d
D
Crossover
Double crossover
No crossover
A
a
a
A
A
a
A
a
A
a
a
A
B
b
b
B
B
b
B
b
B
b
b
B
c
c
C
C
c
c
C
C
C
c
c
C
D
d
D
d
d
d
D
D
D
d
d
D
Recombination
in gametes
Recombination
in gametes
No recombination
in gametes
FIGURE 479-6  Crossing-over and genetic recombination. During chiasma 
formation, either of the two sister chromatids on one chromosome pairs with 
one of the chromatids of the homologous chromosome. Genetic recombination 
occurs through crossing-over and results in recombinant and nonrecombinant 
chromosome segments in the gametes. Together with the random segregation of 
the maternal and paternal chromosomes, recombination contributes to genetic 
diversity and forms the basis of the concept of linkage.

TABLE 479-2  Selected Examples of Diseases Caused by Mutations and 
Rearrangements in Transcription Factors
TRANSCRIPTION 
FACTOR CLASS
EXAMPLE
ASSOCIATED DISORDER
Nuclear receptors
Androgen receptor
Complete or partial androgen 
insensitivity (recessive missense 
mutations)
Spinobulbar muscular atrophy 
(CAG repeat expansion)
Zinc finger proteins
WT1
WAGR syndrome: Wilms’ 
tumor, aniridia, genitourinary 
malformations, mental retardation
Basic helix-loop-helix
MITF
Waardenburg’s syndrome type 2A
Homeobox
IPF1
Maturity onset of diabetes mellitus 
type 4 (monoallelic mutation/
haploinsufficiency)
Pancreatic agenesis (biallelic 
mutations)
Leucine zipper
Retina leucine 
zipper (NRL)
Autosomal dominant retinitis 
pigmentosa
High mobility group 
(HMG) proteins
SRY
Sex reversal
Forkhead
HNF4α, HNF1α, 
HNF1β
Maturity onset of diabetes mellitus 
types 1, 3, 5
Paired box
PAX3
Waardenburg’s syndrome types 
1 and 3
T-box
TBX5
Holt-Oram syndrome (thumb 
anomalies, atrial or ventricular 
septum defects, phocomelia)
Cell cycle control 
proteins
P53
Li-Fraumeni syndrome, other 
cancers
Co-activators
CREB binding 
protein (CREBBP)
Rubinstein-Taybi syndrome
General transcription 
factors
TATA-binding 
protein (TBP)
Spinocerebellar ataxia 17 (CAG 
expansion)
Transcription 
elongation factor
VHL
von Hippel–Lindau syndrome 
(renal cell carcinoma, 
pheochromocytoma, pancreatic 
tumors, hemangioblastomas)
Autosomal dominant inheritance, 
somatic inactivation of second 
allele (Knudson two-hit model)
Runt
RUNX1
Familial thrombocytopenia with 
propensity to acute myelogenous 
leukemia
Chimeric proteins 
due to translocations
PML-RAR
Acute promyelocytic leukemia 
t(15;17)(q22;q11.2-q12) 
translocation
Abbreviations: CREB, cAMP responsive element–binding protein; HNF, hepatocyte 
nuclear factor; PML, promyelocytic leukemia; RAR, retinoic acid receptor; SRY, sexdetermining region Y; VHL, von Hippel–Lindau.
heritable and leads to the preferential expression of one of the parental 
alleles, which deviates from the usual biallelic expression seen for the 
majority of genes. Remarkably, imprinting can be limited to a subset 
of tissues. Imprinting is mediated through DNA methylation of one of 
the alleles. The epigenetic marks on imprinted genes are maintained 
throughout life, but during zygote formation, they are activated or 
inactivated in a sex-specific manner (imprint reset) (Fig. 479-8), which 
allows a differential expression pattern in the fertilized egg and the sub­
sequent mitotic divisions. Appropriate expression of imprinted genes is 
important for normal development and cellular functions. Imprinting 
defects and uniparental disomy, which is the inheritance of two chro­
mosomes or chromosomal regions from the same parent, are the cause 
of several developmental disorders such as Beckwith-Wiedemann syn­
drome, Silver-Russell syndrome, Angelman’s syndrome, and PraderWilli syndrome (see below). Monoallelic loss-of-function mutations in 
the GNAS1 gene lead to Albright’s hereditary osteodystrophy (AHO). 
Paternal transmission of GNAS1 mutations leads to an isolated AHO 

phenotype (pseudopseudohypoparathyroidism), whereas maternal 
transmission leads to AHO in combination with hormone resistance 
to parathyroid hormone, thyrotropin, and gonadotropins (pseudohy­
poparathyroidism type IA). These phenotypic differences are explained 
by tissue-specific imprinting of the GNAS1 gene, which is expressed 
primarily from the maternal allele in the thyroid, gonadotropes, and 
the proximal renal tubule. In most other tissues, the GNAS1 gene is 
expressed biallelically. In patients with isolated renal resistance to 
parathyroid hormone (pseudohypoparathyroidism type IB), defective 
imprinting of the GNAS1 gene results in decreased Gsα expression in 
the proximal renal tubules. Rett syndrome is an X-linked dominant 
disorder resulting in developmental regression and stereotypic hand 
movements in affected girls. It is caused by mutations in the MECP2 
gene, which encodes a methyl-binding protein. The ensuing aberrant 
methylation results in abnormal gene expression in neurons, which are 
otherwise normally developed.

CHAPTER 479
Principles of Human Genetics 
Remarkably, epigenetic differences also occur among monozygotic 
twins. Although twins are epigenetically indistinguishable during the 
early years of life, older monozygotic twins exhibit differences in the 
overall content and genomic distribution of DNA methylation and 
histone acetylation, which would be expected to alter gene expression 
in various tissues.
In cancer, the epigenome is characterized by simultaneous losses 
and gains of DNA methylation in different genomic regions, as well 
as repressive histone modifications. Hyper- and hypomethylation are 
associated with mutations in genes that control DNA methylation. 
Hypomethylation is thought to remove normal control mechanisms 
that prevent expression of repressed DNA regions. It is also associated 
with genomic instability. Hypermethylation, in contrast, results in 
the silencing of CpG islands in promoter regions of genes, including 
tumor-suppressor genes. Epigenetic alterations are more easily revers­
ible compared to genetic changes; modification of the epigenome with 
demethylating agents and histone deacetylases is being used in the 
treatment of various malignancies.
■
■TRANSMISSION OF GENETIC DISEASE
Origins and Types of Mutations 
The term mutation or variant is 
used to designate the process of generating genetic variations as well as 
the effect of these alterations. A mutation can be defined as any change 
in the primary nucleotide sequence of DNA regardless of its functional 
consequences, although it often has a negative connotation. There has 
been a shift towards using the more neutral term variant to describe 
sequence changes, and it is now recommended by several professional 
organizations and guidelines instead of mutation. Some variants may 
be lethal, others are less deleterious, and some may confer an evolu­
tionary advantage. Variations can occur in the germline (sperm or 
oocytes); these can be transmitted to progeny. Alternatively, variants 
can occur during embryogenesis or in somatic tissues. Variations that 
occur during development lead to mosaicism, a situation in which tis­
sues are composed of cells with different genetic constitutions. If the 
germline is mosaic, a mutation can be transmitted to some progeny but 
not others, which sometimes leads to confusion in assessing the pat­
tern of inheritance. Somatic mutations that do not affect cell survival 
can sometimes be detected because of variable phenotypic effects in 
tissues (e.g., pigmented lesions in McCune-Albright syndrome). Other 
somatic mutations are associated with neoplasia because they confer a 
growth advantage to cells. Epigenetic events may also influence gene 
expression or facilitate genetic damage. With the exception of triplet 
nucleotide repeats, which can expand (see below), variations are usu­
ally stable.
Sequence variants are structurally diverse—they can involve the 
entire genome, as in triploidy (one extra set of chromosomes), or gross 
numerical or structural alterations in chromosomes or individual 
genes. Large deletions may affect a portion of a gene or an entire gene, 
or, if several genes are involved, they may lead to a contiguous gene 
syndrome. Unequal crossing-over between homologous genes can 
result in fusion gene mutations, as illustrated by color blindness. Varia­
tions involving single nucleotides are referred to as point mutations.

Methylated DNA
Cytosine Methylation
NH2
NH2
N
CH3
N
PART 16
Genes, the Environment, and Disease
O
N
O
N
Histone Acetylation
Unmethylated DNA
Histone Modifications
Acetylation
Phosphorylation
Methylation 
Transcription
NH2
FIGURE 479-7  Epigenetic modifications of DNA and histones. Methylation of cytosine residues is associated with 
gene silencing. Methylation of certain genomic regions is inherited (imprinting), and it is involved in the silencing of 
one of the two X chromosomes in females (X-inactivation). Alterations in methylation can also be acquired, e.g., in 
cancer cells. Covalent posttranslational modifications of histones play an important role in altering DNA accessibility 
and chromatin structure and hence in regulating transcription. Histones can be reversibly modified in their aminoterminal tails, which protrude from the nucleosome core particle, by acetylation of lysine, phosphorylation of serine, 
methylation of lysine and arginine residues, and sumoylation. Acetylation of histones by histone acetylases (HATs), 
e.g., leads to unwinding of chromatin and accessibility to transcription factors. Conversely, deacetylation by histone 
deacetylases (HDACs) results in a compact chromatin structure and silencing of transcription.
Substitutions are called transitions if a purine is replaced by another 
purine base (A ↔ G) or if a pyrimidine is replaced by another pyrimi­
dine (C ↔ T). Changes from a purine to a pyrimidine, or vice versa, 
are referred to as transversions. If the DNA sequence change occurs in 
a coding region and alters an amino acid, it is called a missense muta­
tion. Depending on the functional consequences of such a missense 
mutation, amino acid substitutions in different regions of the protein 
can lead to distinct phenotypes.
Variants can occur in all domains of a gene (Fig. 479-9). A point 
mutation occurring within the coding region leads to an amino acid 
substitution if the codon is altered (Fig. 479-10). Point mutations that 
introduce a premature stop codon result in a truncated or missing pro­
tein. Large deletions may affect a portion of a gene or an entire gene, 
whereas small deletions and insertions alter the reading frame if they 
do not represent a multiple of three bases. These “frameshift” muta­
tions, also designated as amphigoric amino acid changes, lead to an 
entirely altered carboxy terminus. Mutations in intronic sequences or 
in exon junctions may destroy or create splice donor or splice acceptor 
sites. Variants may also be found in the regulatory sequences of genes, 
resulting in reduced or enhanced gene transcription.
Certain DNA sequences are particularly susceptible to mutagenesis. 
Successive pyrimidine residues (e.g., T-T or C-C) are subject to the 
formation of ultraviolet light–induced photoadducts. If these pyrimi­
dine dimers are not repaired by the nucleotide excision repair pathway, 
mutations will be introduced after DNA synthesis. The dinucleotide 
C-G, or CpG, is also a hot spot for a specific type of alteration. In this 
case, methylation of the cytosine is associated with an enhanced rate 
of deamination to uracil, which is then replaced with thymine. This 
C → T transition (or G → A on the opposite strand) accounts for at 
least one-third of point mutations associated with polymorphisms and 
mutations. In addition to the fact that certain types of mutations (C → 
T or G → A) are relatively common, the nature of the genetic code also 
results in overrepresentation of certain amino acid substitutions.
Polymorphisms are sequence variations that have a frequency of at 
least 1%. Usually, they do not result in a perceptible phenotype; the 
term variant is now preferred for the description of these sequence 
changes because allele frequency and functional consequences are 
often not known. Often, they consist of single base-pair substitutions 
that do not alter the protein coding sequence because of the degenerate 

nature of the genetic code (synonymous 
polymorphism), although it is possible that 
some might alter mRNA stability, transla­
tion, or the amino acid sequence (non­
synonymous polymorphism) (Fig. 479-10). 
The detection of sequence variants poses a 
practical problem because it is often unclear 
whether it creates a change with functional 
consequences or a benign variation. In this 
situation, the sequence alteration is also 
described as variant of unknown significance 
(VUS).
Methylation
MUTATION RATES  Mutations represent an 
important cause of genetic diversity as well 
as disease. Mutation rates are difficult to 
determine in humans because many muta­
tions are silent and because testing is often 
not adequate to detect the phenotypic con­
sequences. Mutation rates vary in different 
genes but are estimated to occur at a rate of 
~10−10/bp per cell division. Germline muta­
tion rates (as opposed to somatic muta­
tions) are relevant in the transmission of 
genetic disease. Because the population of 
oocytes is established very early in develop­
ment, only ~20 cell divisions are required 
for completed oogenesis, whereas sper­
matogenesis involves ~30 divisions by the 
time of puberty and 20 cell divisions each 
year thereafter. Consequently, the probability of acquiring new point 
mutations is much greater in the male germline than the female germ­
line, in which rates of aneuploidy are increased. Thus, the incidence 
of new point mutations in spermatogonia increases with paternal age 
(e.g., achondrodysplasia, Marfan’s syndrome, neurofibromatosis). It is 
estimated that about 1 in 10 sperm carries a new deleterious mutation. 
The rates for new mutations are calculated most readily for autosomal 
dominant and X-linked disorders and are ~10−5−10−6/locus per genera­
tion. Because most monogenic diseases are relatively rare, new muta­
tions account for a significant fraction of cases. This is important in the 
context of genetic counseling because a new mutation can be transmit­
ted to the affected individual, but this does not necessarily imply that 
the parents are at risk to transmit the disease to other children. An 
exception to this is when the new mutation occurs early in germline 
development, leading to gonadal mosaicism.
UNEQUAL CROSSING-OVER  Normally, DNA recombination in germ 
cells occurs with remarkable fidelity to maintain the precise junction 
sites for the exchanged DNA sequences (Fig. 479-6). However, mispair­
ing of homologous sequences leads to unequal crossover, with gene 
duplication on one of the chromosomes and gene deletion on the other 
chromosome. A significant fraction of growth hormone (GH) gene 
deletions, for example, involve unequal crossing-over (Chap. 391). The 
GH gene is a member of a large gene cluster that includes a GH vari­
ant gene as well as several structurally related chorionic somatomam­
motropin genes and pseudogenes (highly homologous but functionally 
inactive relatives of a normal gene). Because such gene clusters con­
tain multiple homologous DNA sequences arranged in tandem, they 
are particularly prone to undergo recombination and, consequently, 
gene duplication or deletion. Duplication of the PMP22 gene because 
of unequal crossing-over results in increased gene dosage and type 
IA Charcot-Marie-Tooth disease. In contrast, unequal crossing-over 
resulting in deletion of PMP22 causes a distinct neuropathy called 
hereditary neuropathy with liability to pressure palsies (HNPP) 
(Chap. 457).
Glucocorticoid-remediable aldosteronism (GRA) is caused by a 
gene fusion or rearrangement involving the genes that encode aldo­
sterone synthase (CYP11B2) and steroid 11β-hydroxylase (CYP11B1), 
normally arranged in tandem on chromosome 8q. These two genes 
are 95% identical, predisposing to gene duplication and deletion by

Maternal somatic cell
mat pat
Active
unmethylated
Inactive
methylated
Inactive
methylated
Germline development:
Imprint reset
Maternal germline
Paternal germline
mat pat
Active
unmethylated
Active
unmethylated
Inactive
methylated
Zygote
pat mat
Inactive
methylated
Active
unmethylated
FIGURE 479-8  A few genomic regions are imprinted in a parent-specific fashion. The unmethylated chromosomal 
regions are actively expressed, whereas the methylated regions are silenced. In the germline, the imprint is reset 
in a parent-specific fashion: both chromosomes are unmethylated in the maternal (mat) germline and methylated 
in the paternal (pat) germline. In the zygote, the resulting imprinting pattern is identical with the pattern in the 
somatic cells of the parents.
unequal crossing-over. The rearranged gene product contains the 
regulatory regions of 11β-hydroxylase fused to the coding sequence of 
aldosterone synthetase. Consequently, the latter enzyme is expressed in 
the adrenocorticotropic hormone (ACTH)–dependent zona fasciculata 
of the adrenal gland, resulting in overproduction of mineralocorticoids 
and hypertension (Chap. 398).
Gene conversion refers to a nonreciprocal exchange of homologous 
genetic information. It has been used to explain how an internal 
portion of a gene is replaced by a homologous segment copied from 
another allele or locus; these genetic alterations may range from a few 
nucleotides to a few thousand nucleotides. As a result of gene conver­
sion, it is possible for short DNA segments of two chromosomes to be 
identical, even though these sequences are distinct in the parents. A 
practical consequence of this phenomenon is that nucleotide substitu­
tions can occur during gene conversion between related genes, often 
altering the function of the gene. In disease states, gene conversion 
often involves intergenic exchange of DNA between a gene and a 
related pseudogene. For example, the 21-hydroxylase gene (CYP21A2) 
is adjacent to a nonfunctional pseudogene (CYP21A1P). Many of the 

nucleotide substitutions that are found in the 
CYP21A2 gene in patients with congenital 
adrenal hyperplasia correspond to sequences 
that are present in the CYP21A1P pseu­
dogene, suggesting gene conversion as one 
cause of mutagenesis. In addition, mitotic 
gene conversion has been suggested as a 
mechanism to explain revertant mosaicism 
in which an inherited mutation is “corrected” 
in certain cells. For example, patients with 
autosomal recessive generalized atrophic 
benign epidermolysis bullosa have acquired 
reverse mutations in one of the two mutated 
COL17A1 alleles, leading to clinically unaf­
fected patches of skin.

Paternal somatic cell
pat mat
CHAPTER 479
Active
unmethylated
Principles of Human Genetics 
INSERTIONS AND DELETIONS  Although 
many instances of insertions and deletions 
occur as a consequence of unequal cross­
ing-over, there is also evidence for internal 
duplication, inversion, or deletion of DNA 
sequences. The fact that certain deletions 
or insertions appear to occur repeatedly as 
independent events indicates that specific 
regions within the DNA sequence predispose 
to these errors. For example, certain regions 
of the DMD gene, which encodes dystrophin, 
appear to be hot spots for deletions and result 
in muscular dystrophy (Chap. 460). Some 
regions within the human genome are rear­
rangement hot spots and lead to CNVs.
pat mat
Inactive
methylated
ERRORS IN DNA REPAIR  Because mutations 
caused by defects in DNA repair accumulate 
as somatic cells divide, these types of muta­
tions are particularly important in the con­
text of neoplastic disorders. Several genetic 
disorders involving DNA repair enzymes 
underscore their importance. Patients with 
xeroderma pigmentosum have defects in 
DNA damage recognition or in the nucleo­
tide excision and repair pathway (Chap. 81). 
Exposed skin is dry and pigmented and is 
extraordinarily sensitive to the mutagenic 
effects of ultraviolet irradiation. Variants 
in more than 10 different genes have been 
shown to cause the different forms of xero­
derma pigmentosum.
Ataxia-telangiectasia is a multisystem 
disorder that includes progressive neuro­
degenerative cerebellar ataxia, immunologic 
defects, telangiectatic lesions, lymphomas and leukemias, and hyper­
sensitivity to ionizing radiation (Chap. 450). The discovery of the 
ataxia-telangiectasia mutated (ATM) gene revealed that it is homolo­
gous to genes involved in DNA repair and control of cell cycle check­
points. Mutations in the ATM gene give rise to defects in meiosis as 
well as increasing susceptibility to damage from ionizing radiation. 
Fanconi’s anemia is also associated with an increased risk of multiple 
acquired genetic abnormalities. It is characterized by diverse congeni­
tal anomalies and a strong predisposition to develop aplastic anemia 
and acute myelogenous leukemia (Chap. 109). Cells from these patients 
are susceptible to chromosomal breaks caused by a defect in genetic 
recombination. It can be caused by mutations in the multiple genes 
forming the Fanconi’s anemia pathway, which is involved in DNA 
repair and replication. HNPCC (Lynch syndrome) is characterized 
by autosomal dominant transmission of colon cancer, young age 
(<50 years) of presentation, predisposition to lesions in the proximal 
large bowel, and associated malignancies such as uterine cancer and 
ovarian cancer. HNPCC is predominantly caused by mutations in one 
of several different mismatch repair (MMR) genes including MutS

A
*

PART 16
Genes, the Environment, and Disease
intron 2
intron 1
Poly A
Promoter 5'UTR
ε
Gγ
Aγ ψβ
β
δ
–10 kb
0 kb
10 kb
20 kb
30 kb
40 kb
50 kb
60 kb
β-Globin Gene Cluster
FIGURE 479-9  Point mutations causing a thalassemia as example of allelic heterogeneity. The b-globin gene is 
located in the globin gene cluster. Point mutations occur in the promoter, the CAP site, the 5′-untranslated region, the 
initiation codon, each of the three exons, the introns, or the polyadenylation signal. Many mutations introduce missense 
or nonsense mutations, whereas others cause defective RNA splicing. Not shown here are deletion mutations of the 
β-globin gene or larger deletions of the globin locus that can also result in thalassemia. , promoter mutations; *, CAP 
site; , 5’UTR; 1 , initiation codon; , defective RNA processing; 
, missense and nonsense mutations; A, Poly A signal.
homologue 2 (MSH2), MutL homologue 1 and 6 (MLH1, MLH6), 
MSH6, PMS1, and PMS2 (Chap. 86). These proteins are involved in the 
detection of nucleotide mismatches and in the recognition of slippedstrand trinucleotide repeats. Germline mutations in these genes lead 
to microsatellite instability and a high mutation rate in colon cancer. 
Genetic screening tests for this disorder are now being used for families 
considered to be at risk. Recognition of HNPCC allows early screen­
ing with colonoscopy and the implementation of prevention strategies 
using nonsteroidal anti-inflammatory drugs.
UNSTABLE DNA SEQUENCES  Trinucleotide repeats may be unstable 
and expand beyond a critical number. Mechanistically, the expansion 
is thought to be caused by unequal recombination and slipped mispair­
ing. A premutation represents a small increase in trinucleotide copy 
number. In subsequent generations, the expanded repeat may increase 
further in length and result in an increasingly severe phenotype, a 
process called dynamic mutation (see below for discussion of anticipa­
tion). Trinucleotide expansion was first recognized as a cause of the 
fragile X syndrome, one of the most common causes of intellectual 
disability. Other disorders arising from a similar mechanism include 
Wild-type
AA
DNA
A
GCA
CTC
L
CTA
S
TCG
H
CAC
A
GCT
R
CGG
E
GAG
G
GGC
E
L
Silent mutation
AA
DNA
A
CGT
GCA
L
CTC
L
CTA
S
TCG
H
CAC
A
GCT
R
GAG
G
GGC
E
E
Missense mutation
AA
DNA
A
CCG
E
GCA
L
CTC
L
CTA
S
TCG
H
CAC
A
GCT
GAG
G
GGC
E
P
Nonsense mutation
AA
DNA
A
GCA
L
CTC
L
CTA
S
TCG
H
CAC
A
GCT
R
CGG
E
GAG
G
GGC
1 bp Deletion with frameshift
AA
DNA
A
GCA
L
CTC
L
CTA
CGC
ACG
CTC
GGG
AGG
GCG
R
T
L
G
R
A
A
B
FIGURE 479-10  A. Examples of mutations (now commonly referred to as variations). The coding strand is shown with the encoded amino acid sequence. B. Chromatograms 
of sequence analyses after amplification of genomic DNA by polymerase chain reaction.

Huntington’s disease, X-linked spino­
bulbar muscular atrophy, and myotonic 
dystrophy. Malignant cells are also char­
acterized by genetic instability, indicat­
ing a breakdown in mechanisms that 
regulate DNA repair and the cell cycle.
Functional Consequences of 
Mutations 
Functionally, 
muta­
tions can be broadly classified as 
gain-of-function and loss-of-function 
mutations. Gain-of-function mutations 
are typically dominant (e.g., they result 
in phenotypic alterations when a single 
allele is affected). Inactivating mutations 
are usually recessive, and an affected 
individual is homozygous or compound 
heterozygous (e.g., carrying two differ­
ent mutant alleles of the same gene) for 
the disease-causing mutations. Alter­
natively, mutation in a single allele can 
result in haploinsufficiency, a situation in 
which one normal allele is not sufficient 
to maintain a normal phenotype. Hap­
loinsufficiency is a commonly observed mechanism in diseases 
associated with mutations in transcription factors (Table 479-2). 
Remarkably, the clinical features among patients with an identical 
mutation often vary significantly. One mechanism underlying this 
variability consists in the influence of modifying genes. Haploinsuf­
ficiency can also affect the expression of rate-limiting enzymes. For 
example, haploinsufficiency in enzymes involved in heme synthesis can 
cause porphyrias (Chap. 428).
An increase in dosage of a gene product may also result in disease, 
as illustrated by the duplication of the DAX1 (NR0B1) gene in dosagesensitive sex reversal (Chap. 402). Mutation in a single allele can also 
result in loss of function due to a dominant-negative effect. In this case, 
the mutated allele interferes with the function of the normal (wild type) 
gene product by one of several different mechanisms: (1) a mutant 
protein may interfere with the function of a multimeric protein com­
plex, as illustrated by mutations in type 1 collagen (COL1A1, COL1A2) 
genes in osteogenesis imperfecta (Chap. 425); (2) a mutant protein 
may occupy binding sites on proteins or promoter response elements, 
as illustrated by thyroid hormone resistance β, a disorder in which 
Wild-type
GAA
N
AAT
E
GAG
S
AGC
F
T T C
T
A C C
D
G A C
F
T T C
I
A T A
C
T G C
GAA
N
AAT
E
GAG
S
AGC
Heterozygous point mutation
F
T T C
I
A T A
C
T G C
F
T T C
T
A C C
D
G A C
GAA
N
AAT
E
GAG
S
AGC
T A C
Y
TAA AAT GAG AGC
Homozygous point mutation
X
F
T T C
T
A C C
Y
T A C
F
T T C
I
A T A
C
T G C
AAA
ATG
AGA GC
K
M
R

inactivated thyroid hormone receptor β binds to target genes and func­
tions as an antagonist of normal receptors (Chap. 394); or (3) a mutant 
protein can be cytotoxic as in α1 antitrypsin deficiency (Chap. 303) or 
autosomal dominant neurohypophyseal diabetes insipidus (Chap. 393), 
in which the abnormally folded proteins are trapped within the endo­
plasmic reticulum and ultimately cause cellular damage.
Genotype and Phenotype 
• 
ALLELES, GENOTYPES, AND HAPLO­
TYPES  An observed trait is referred to as a phenotype; the genetic 
information defining the phenotype is called the genotype. Alternative 
forms of a gene or a genetic marker are referred to as alleles. Alleles 
may be polymorphic variants of nucleic acids that have no apparent 
effect on gene expression or function. In other instances, these variants 
may have subtle effects on gene expression, thereby conferring adap­
tive advantages associated with genetic diversity. On the other hand, 
allelic variants may reflect mutations that clearly alter the function of 
a gene product. The common Glu6Val (E6V) sickle cell mutation in 
the β-globin gene and the ΔF508 deletion of phenylalanine (F) in the 
CFTR gene are examples of allelic variants of these genes that result in 
disease. Because each individual has two copies of each chromosome 
(one inherited from the mother and one inherited from the father), an 
individual can have only two alleles at a given locus. However, there 
can be many different alleles in the population. The normal or com­
mon allele is usually referred to as wild type. When alleles at a given 
locus are identical, the individual is homozygous. Inheriting identical 
copies of a mutant allele occurs in many autosomal recessive disorders, 
particularly in circumstances of consanguinity or isolated populations. 
If the alleles are different on the maternal and the paternal copy of the 
gene, the individual is heterozygous at this locus (Fig. 479-10). If two 
different mutant alleles are inherited at a given locus, the individual 
is said to be a compound heterozygote. Hemizygous is used to describe 
males with a mutation in an X chromosomal gene or a female with a 
loss of one X chromosomal locus.
Genotypes describe the specific alleles at a particular locus. For 
example, there are three common alleles (E2, E3, E4) of the apolipo­
protein E (APOE) gene. The genotype of an individual can therefore 
be described as APOE3/4 or APOE4/4 or any other variant. These des­
ignations indicate which alleles are present on the two chromosomes 
in the APOE gene at locus 19q13.2. In other cases, the genotype might 
be assigned arbitrary numbers (e.g., 1/2) or letters (e.g., B/b) to distin­
guish different alleles.
A haplotype refers to a group of alleles that are closely linked together 
at a genomic locus (Fig. 479-4). Haplotypes are useful for tracking the 
transmission of genomic segments within families and for detect­
ing evidence of genetic recombination if the crossover event occurs 
between the alleles (Fig. 479-6). As an example, various alleles of the 
histocompatibility locus antigens (HLA) at the major histocompatibil­
ity complex (MHC) on chromosome 6 are used to establish haplotypes 
associated with certain disease states. For example, 21-hydroxylase 
deficiency, complement deficiency, and hemochromatosis are each 
associated with specific HLA haplotypes. It is now recognized that 
these genes lie in close proximity to the HLA locus, which explains why 
HLA associations were identified even before the disease genes were 
cloned and localized. In other cases, specific HLA associations with 
diseases such as ankylosing spondylitis (HLA-B27) or type 1 diabetes 
mellitus (HLA-DR4) reflect the role of specific HLA allelic variants 
in susceptibility to these autoimmune diseases. The characterization 
of common SNP haplotypes in numerous populations from different 
parts of the world has provided the necessary tools for association stud­
ies designed to detect genes involved in the pathogenesis of complex 
disorders (Table 479-1). The presence or absence of certain haplotypes 
can also be relevant for the customized choice of medical therapies 
(pharmacogenomics) or may have value for preventive strategies.
Genotype-phenotype correlation describes the association of a spe­
cific mutation and the resulting phenotype. The phenotype may differ 
depending on the location or type of the mutation in some genes. For 
example, in von Hippel–Lindau disease, an autosomal dominant mul­
tisystem disease that can include renal cell carcinoma, hemangioblas­
tomas, and pheochromocytomas, among others, the phenotype varies 

greatly, and the identification of the specific mutation can be clinically 
useful in order to predict the spectrum of disease manifestations.

ALLELIC HETEROGENEITY  Allelic heterogeneity refers to the fact that 
different mutations in the same genetic locus can cause an identical 
or similar phenotype. For example, many different mutations of the 
β-globin locus can cause β thalassemia (Table 479-3) (Fig. 479-9). In 
essence, allelic heterogeneity reflects the fact that many different muta­
tions can alter protein structure and function. For this reason, maps of 
inactivating mutations in genes usually show a near-random distribu­
tion. Exceptions include (1) a founder effect, in which a particular 
mutation that does not affect reproductive capacity can be traced to a 
single individual; (2) “hot spots” for mutations, in which the nature of 
the DNA sequence predisposes to a recurring mutation; and (3) local­
ization of mutations to certain domains that are particularly critical for 
protein function. Allelic heterogeneity creates a practical problem for 
genetic testing because one must often examine the entire genetic locus 
for mutations, because these can differ in each patient. For example, 
~2000 variants have been identified in the CFTR gene to date, although 
some of them are very rare and some may not be disease-causing (Fig. 
479-3). Mutational analysis may initially focus on a panel of mutations 
that are particularly frequent (often taking the ethnic background of 
the patient into account), but a negative result does not exclude the 
presence of a mutation elsewhere in the gene. Until recently, muta­
tional analyses tended to focus on the coding region of a gene without 
considering regulatory and intronic regions. However, disease-causing 
mutations may be located outside the coding regions, so negative 
results need to be interpreted with caution. The increasingly wide­
spread access to comprehensive sequencing technologies, WES and 
WGS, greatly facilitates unbiased mutational analyses. However, com­
prehensive sequencing can result in significant diagnostic challenges 
because the detection of a sequence alteration is not always sufficient 
to establish that it has a causal role (VUS).
CHAPTER 479
Principles of Human Genetics 
PHENOTYPIC HETEROGENEITY  Phenotypic heterogeneity occurs 
when more than one phenotype is caused by allelic mutations (e.g., 
by different mutations in the same gene) (Table 479-3). For example, 
laminopathies are monogenic multisystem disorders that result from 
mutations in the LMNA gene, which encodes the nuclear lamins A and 
C. Multiple autosomal dominant and recessive disorders are caused by 
mutations in the LMNA gene. They include several forms of lipodys­
trophies, Emery-Dreifuss muscular dystrophy, progeria syndromes, a 
form of neuronal Charcot-Marie-Tooth disease (type 2B1), and a group 
of overlapping syndromes. Remarkably, hierarchical cluster analysis 
has revealed that the phenotypes vary depending on the position of 
the mutation (genotype-phenotype correlation). Similarly, identical 
mutations in the FGFR2 gene can result in very distinct phenotypes: 
Crouzon’s syndrome (craniofacial synostosis) or Pfeiffer’s syndrome 
(acrocephalopolysyndactyly).
LOCUS OR NONALLELIC HETEROGENEITY AND PHENOCOPIES  Nonal­
lelic or locus heterogeneity refers to the situation in which a similar dis­
ease phenotype results from mutations at different genetic loci (Table 
479-3). This often occurs when more than one gene product produces 
different subunits of an interacting complex or when different genes 
are involved in the same genetic cascade or physiologic pathway. For 
example, osteogenesis imperfecta can arise from mutations in two dif­
ferent procollagen genes (COL1A1 or COL1A2) that are located on dif­
ferent chromosomes and can involve multiple other genes (Chap. 425). 
The effects of inactivating mutations in these two genes are similar 
because the protein products comprise different subunits of the helical 
collagen fiber. Similarly, muscular dystrophy syndromes can be caused 
by mutations in various genes, consistent with the fact that it can be 
transmitted in an X-linked (Duchenne or Becker), autosomal domi­
nant (limb-girdle muscular dystrophy type 1), or autosomal recessive 
(limb-girdle muscular dystrophy type 2) manner (Chap. 460). Muta­
tions in the X-linked DMD gene, which encodes dystrophin, are the 
most common cause of muscular dystrophy. This feature reflects 
the large size of the gene (2.3 MB, 79 exons), as well as the fact that the 
phenotype is expressed in hemizygous males because they have only

TABLE 479-3  Selected Examples of Phenotypic Heterogeneity and Locus Heterogeneity
Phenotypic Heterogeneity
GENE, PROTEIN
PHENOTYPE
INHERITANCE
OMIM
LMNA, Lamin A/C
Emery-Dreifuss muscular dystrophy 
(AD)
PART 16
Genes, the Environment, and Disease
Familial partial lipodystrophy Dunnigan
AD

Hutchinson-Gilford progeria
AD

Atypical Werner’s syndrome
AD

Dilated cardiomyopathy 1A
AD

Familial atrial fibrillation 3
AD

Charcot-Marie-Tooth type 2B1
AR

KRAS
Noonan’s syndrome
AD

Cardio-facio-cutaneous syndrome 1
AD

Locus Heterogeneity
PHENOTYPE
GENE
CHROMOSOMAL LOCATION
PROTEIN
Familial hypertrophic cardiomyopathy
MYH7
14q11.2
Myosin heavy chain beta
  Genes encoding sarcomeric proteins
TNNT2
1q32.1
Troponin-T2
TPM1
15q22.2
Tropomyosin alpha
MYBPC3
11p11q
Myosin-binding protein C
TNNC1
19q13.4
Troponin 1
MYL2
12q24.11
Myosin light chain 2
MYL3
3p21.31
Myosin light chain 3
TTN
2q31.2
Cardiac titin
ACTC
15q14
Cardiac alpha actin
MYH6
14q11.2
Myosin heavy chain alpha
MYLK2
20q11.21
Myosin light-peptide kinase
CAV3
3p25
Caveolin 3
  Genes encoding nonsarcomeric proteins
MT-T1
Mitochondrial
tRNA isoleucine
MT-TG
Mitochondrial
tRNA glycine
PRKAG2
7q36.1
AMP-activated protein kinase γ2 subunit
DMPK
19q13.32
Myotonin protein kinase (myotonic 
dystrophy)
FRDA
9q21.11
Frataxin (Friedreich’s ataxia)
Polycystic kidney disease
PKD1
16p13.3
Polycystin 1 (AD)
PKD2
4q22.1
Polycystin 2 (AD)
PKHD1
6p21.1-p12.2
Fibrocystin/polyductin (AR)
Noonan’s syndrome
PTPN11
12q24.13
Protein-tyrosine phosphatase 2c
KRAS
12p12.1
KRAS
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; OMIM, Online Mendelian Inheritance in Man.
a single copy of the X chromosome. Dystrophin is associated with a 
large protein complex linked to the membrane-associated cytoskeleton 
in muscle. Mutations in several different components of this protein 
complex can also cause muscular dystrophy syndromes. Although 
the phenotypic features of some of these disorders are distinct, the 
phenotypic spectrum caused by mutations in different genes overlaps, 
thereby leading to nonallelic heterogeneity. It should be noted that 
mutations in dystrophin are also associated with allelic heterogeneity. 
For example, mutations in the DMD gene can cause either Duchenne’s 
or the less severe Becker’s muscular dystrophy, depending on the sever­
ity of the protein defect.
Recognition of nonallelic heterogeneity is important for several rea­
sons: (1) the ability to identify disease loci in linkage studies is reduced 
by including patients with similar phenotypes but different genetic 
disorders; (2) genetic testing is more complex because several differ­
ent genes need to be considered along with the possibility of different 
mutations in each of the candidate genes; and (3) novel information is 
gained about how genes or proteins interact, providing unique insights 
into molecular physiology.
Phenocopies refer to circumstances in which nongenetic conditions 
mimic a genetic disorder. For example, features of toxin- or druginduced neurologic syndromes can resemble those seen in Huntington’s 

AD

disease, and vascular causes of dementia share phenotypic features with 
familial forms of Alzheimer’s dementia (Chap. 442). As in nonallelic 
heterogeneity, the presence of phenocopies has the potential to con­
found linkage studies and genetic testing. Patient history and subtle 
differences in phenotype can often provide clues that distinguish these 
disorders from related genetic conditions.
VARIABLE EXPRESSIVITY AND INCOMPLETE PENETRANCE  The same 
genetic mutation may be associated with a phenotypic spectrum in 
different affected individuals, thereby illustrating the phenomenon of 
variable expressivity. This may include different manifestations of a 
disorder variably involving different organs (e.g., multiple endocrine 
neoplasia [MEN]), the severity of the disorder (e.g., cystic fibrosis), or 
the age of disease onset (e.g., Alzheimer’s dementia). MEN 1 illustrates 
several of these features. In this autosomal dominant tumor syndrome, 
affected individuals carry an inactivating germline mutation that is 
inherited in an autosomal dominant fashion. After somatic inactiva­
tion of the alternate allele (loss of heterozygosity; Knudson two-hit 
model), patients can develop tumors of the parathyroid gland, endo­
crine pancreas, the pituitary gland, and dermatologic lesions (Chap. 400). 
However, the pattern of tumors in the different glands, the age at which 
tumors develop, and the types of hormones produced vary among

affected individuals, even within a given family. In this example, the 
phenotypic variability arises, in part, because of the requirement for 
a second somatic mutation in the normal copy of the MEN1 gene, as 
well as the large array of different cell types that are susceptible to the 
effects of MEN1 gene mutations. In part, variable expression reflects 
the influence of modifier genes, or genetic background, on the effects 
of a particular mutation. Even in identical twins, in whom the genetic 
constitution is essentially the same, one can occasionally see variable 
expression of a genetic disease.
Interactions with the environment can also influence the course of 
a disease. For example, the manifestations and severity of hemochro­
matosis can be influenced by iron intake (Chap. 426), and the course 
of phenylketonuria is affected by exposure to phenylalanine in the diet 
(Chap. 431). Other metabolic disorders, such as hyperlipidemias and 
porphyria, also fall into this category. Many mechanisms, including 
genetic effects and environmental influences, can therefore lead to 
variable expressivity. In genetic counseling, it is particularly important 
to recognize this variability, because one cannot always predict the 
course of disease, even when the mutation is known.
Penetrance refers to the proportion of individuals with a mutant 
genotype that express the phenotype. If all carriers of a mutant 
express the phenotype, penetrance is complete, whereas it is said to 
be incomplete or reduced if some individuals do not exhibit features 
of the phenotype. Dominant conditions with incomplete penetrance 
are characterized by skipping of generations with unaffected carriers 
transmitting the mutant gene. For example, hypertrophic obstructive 
cardiomyopathy (HCM) caused by mutations in the myosin-binding 
protein C gene is a dominant disorder with clinical features in only a 
subset of patients who carry the mutation (Chap. 267). Patients who 
have the mutation, but no evidence of the disease, can still transmit the 
disorder to subsequent generations. In many conditions with postnatal 
onset, the proportion of gene carriers who are affected varies with age. 
Thus, when describing penetrance, one must specify age. For example, 
for disorders such as Huntington’s disease or familial amyotrophic 
lateral sclerosis, which present later in life, the rate of penetrance is 
influenced by the age at which the clinical assessment is performed. 
Imprinting can also modify the penetrance of a disease. For example, 
in patients with AHO, mutations in the Gsα subunit (GNAS1 gene) are 
expressed clinically only in individuals who inherit the mutation from 
their mother (Chap. 422).
SEX-INFLUENCED PHENOTYPES  Certain mutations affect males and 
females quite differently. In some instances, this is because the gene 
resides on the X or Y sex chromosomes (X-linked disorders and 
Y-linked disorders). As a result, the phenotype of mutated X-linked 
genes will be expressed fully in males but variably in heterozygous 
females, depending on the degree of X-inactivation and the function 
of the gene. For example, most heterozygous female carriers of factor 
VIII deficiency (hemophilia A) are asymptomatic because sufficient 
factor VIII is produced to prevent a defect in coagulation (Chap. 121). 
On the other hand, some females heterozygous for the X-linked lipid 
storage defect caused by α-galactosidase A deficiency (Fabry’s disease) 
experience mild manifestations of painful neuropathy, as well as other 
features of the disease (Chap. 429). Because only males have a Y chro­
mosome, mutations in genes such as SRY, which causes male-to-female 
sex reversal, or DAZ (deleted in azoospermia), which causes abnor­
malities of spermatogenesis, are unique to males (Chap. 402).
Other diseases are expressed in a sex-limited manner because of 
the differential function of the gene product in males and females. 
Activating mutations in the luteinizing hormone receptor cause 
dominant male-limited precocious puberty in boys (Chap. 403). 
The phenotype is unique to males because activation of the receptor 
induces testosterone production in the testis, whereas it is function­
ally silent in the immature ovary. Biallelic inactivating mutations 
of the follicle-stimulating hormone (FSH) receptor cause primary 
ovarian failure in females because the follicles do not develop in the 
absence of FSH action. In contrast, affected males have a more subtle 
phenotype, because testosterone production is preserved (allowing 
sexual maturation) and spermatogenesis is only partially impaired 

(Chap. 403). In congenital adrenal hyperplasia, most commonly 
caused by 21-hydroxylase deficiency, cortisol production is impaired 
and ACTH stimulation of the adrenal gland leads to increased 
production of androgenic precursors (Chap. 398). In females, the 
increased androgen level causes ambiguous genitalia, which can be 
recognized at the time of birth. In males, the diagnosis may be made 
on the basis of adrenal insufficiency at birth, because the increased 
adrenal androgen level does not alter sexual differentiation, or later 
in childhood, because of the development of precocious puberty. 
Hemochromatosis is more common in males than in females, pre­
sumably because of differences in dietary iron intake and losses 
associated with menstruation and pregnancy in females (Chap. 426).

CHAPTER 479
Principles of Human Genetics 
Chromosomal Disorders 
Chromosomal disorders and the tech­
niques used for their characterization have been discussed in detail 
in previous editions of this textbook. Chromosomal or cytogenetic 
disorders are caused by numerical (aneuploidy) or structural aberra­
tions (deletions, duplications, translocations, inversions, dicentric and 
ring chromosomes, Robertsonian translocations) in chromosomes. 
They occur in ~1% of the general population, in 8% of stillbirths, 
and in close to 50% of spontaneously aborted fetuses. Indications for 
cytogenetic and cytogenomic chromosome analyses are summarized 
in Table 479-4. Contiguous gene syndromes (e.g., large deletions affect­
ing several genes) have been useful for identifying the location of new 
disease-causing genes. Because of the variable size of gene deletions in 
different patients, a systematic comparison of phenotypes and loca­
tions of deletion breakpoints allows positions of particular genes to be 
mapped within the critical genomic region.
Monogenic Mendelian Disorders 
Monogenic human diseases 
are frequently referred to as Mendelian disorders because they obey 
the principles of genetic transmission originally set forth in Gregor 
Mendel’s classic work. The continuously updated OMIM catalogue lists 
several thousand of these disorders and provides information about 
the clinical phenotype, molecular basis, allelic variants, and pertinent 
animal models (Table 479-1). The mode of inheritance for a given phe­
notypic trait or disease is determined by pedigree analysis. All affected 
and unaffected individuals in the family are recorded in a pedigree 
using standard symbols (Fig. 479-11). The principles of allelic seg­
regation, and the transmission of alleles from parents to children, are 
illustrated in Fig. 479-12. One dominant (A) allele and one recessive 
(a) allele can display three Mendelian modes of inheritance: autosomal 
dominant, autosomal recessive, and X-linked. About 65% of human 
monogenic disorders are autosomal dominant, 25% are autosomal 
recessive, and 5% are X-linked. Genetic testing is now readily available 
for the characterization of monogenic disorders and plays an important 
role in clinical medicine (Chap. 480).
TABLE 479-4  Indications for Cytogenetic and Cytogenomic Analysis 
across the Life Span
TIMING OF TESTING
INDICATIONS FOR TESTING
Prenatal
Advanced maternal age
Abnormalities on ultrasound
Increased risk for genetic disorder on maternal 
serum screen
Neonatal and childhood
Multiple congenital anomalies
Intellectual disability
Autism spectrum disorders
Developmental delay
Failure to thrive
Short stature
Disorders of sexual development
History of familial chromosomal alteration
Cancer
Adult
Infertility
Recurrent miscarriage
Familial cancer

Female
Male
Unknown
sex

PART 16
Genes, the Environment, and Disease
Multiple
siblings
Spontaneous
abortion
Deceased
male
Affected
male
Proband
Affected
female
Heterozygous
male
Heterozygous
female
Female
carrier of
X-linked trait
I

Mating
Consanguineous
union
II

Monozygotic twins
Dizygotic twins
FIGURE 479-11  Standard pedigree symbols.
AUTOSOMAL DOMINANT DISORDERS  In autosomal dominant disor­
ders, mutations in a single allele are sufficient to cause the disease. In 
contrast to recessive disorders, in which disease pathogenesis is rela­
tively straightforward because there is a biallelic loss of gene function, 
dominant disorders can be caused by various disease mechanisms, 
many of which are unique to the function of the genetic pathway 
involved. Mechanistically, the mutation may confer constitutive activa­
tion (gain of function), exert a dominant negative effect, or result in 
loss of function and haploinsufficiency.
In autosomal dominant disorders, individuals are affected in suc­
cessive generations; the disease does not occur in the offspring of 
unaffected individuals. Males and females are affected with equal 
frequency because the defective gene resides on one of the 22 auto­
somes (Fig. 479-13A). Autosomal dominant mutations alter one of the 
two alleles at a given locus. Because the alleles segregate randomly at 
meiosis, the probability that an offspring will be affected is 50%. Unless 
there is a new germline mutation, an affected individual has an affected 
parent. Children with a normal genotype do not transmit the disorder. 
Due to differences in penetrance or expressivity (see above), the clini­
cal manifestations of autosomal dominant disorders may be variable. 
Because of these variations, it is sometimes challenging to determine 
the pattern of inheritance.
It should be recognized, however, that some individuals acquire a 
mutated gene from an unaffected parent due to de novo germline muta­
tions. They occur more frequently during later cell divisions in gameto­
genesis, which explains why siblings are rarely affected. As noted, new 
germline mutations occur more frequently in fathers of advanced age. 
For example, the average age of fathers with new germline mutations that 
Aa
aa
AA
Aa
Aa
Aa
aa
Aa
Aa
AA
Aa
Aa
aa
50:50

25:50:25
FIGURE 479-12  Segregation of alleles. Segregation of genotypes in the offspring 
of parents with one dominant (A) and one recessive (a) allele. The distribution of 
the parental alleles to their offspring depends on the combination present in the 
parents. Filled symbols = affected individuals.

Autosomal dominant
A
B
Autosomal recessive
Autosomal recessive
with pseudodominance
X-linked
C
Mitochondrial
D
FIGURE 479-13  A. Dominant, B. recessive, C. X-linked, and D. mitochondrial 
(matrilinear) inheritance.
cause Marfan’s syndrome is ~37 years, whereas fathers who transmit the 
disease by inheritance have an average age of ~30 years.
AUTOSOMAL RECESSIVE DISORDERS  In recessive disorders, the 
mutated alleles result in a complete or partial loss of function. They fre­
quently involve enzymes in metabolic pathways, receptors, or proteins 
in signaling cascades. In an autosomal recessive disease, the affected 
individual, who can be of either sex, is a homozygote or compound 
heterozygote for a single-gene defect. With a few important excep­
tions, autosomal recessive diseases are rare and occur more often in the 
context of parental consanguinity. The relatively high frequency of cer­
tain recessive disorders such as sickle cell anemia, cystic fibrosis, and 
thalassemia, is partially explained by a selective biologic advantage for 
the heterozygous state (see below). Although heterozygous carriers of 
a defective allele are usually clinically normal, they may display subtle 
differences in phenotype that only become apparent with more precise 
testing or in the context of certain environmental influences. In sickle 
cell anemia, for example, heterozygotes are normally asymptomatic. 
However, in situations of dehydration or diminished oxygen pressure, 
sickle cell crises can also occur in heterozygotes (Chap. 103).
aa
In most instances, an affected individual is the offspring of heterozy­
gous parents. In this situation, there is a 25% chance that the offspring 
will have a normal genotype, a 50% probability of a heterozygous state, 
and a 25% risk of homozygosity for the recessive alleles (Figs. 479-12 and 
479-13B). In the case of one unaffected heterozygous and one affected 
homozygous parent, the probability of disease increases to 50% for

each child. In this instance, the pedigree analysis mimics an autosomal 
dominant mode of inheritance (pseudodominance). In contrast to auto­
somal dominant disorders, new mutations in recessive alleles are rarely 
manifest because they usually result in an asymptomatic carrier state.
X-LINKED DISORDERS  Males have only one X chromosome; conse­
quently, a daughter always inherits her father’s X chromosome in addi­
tion to one of her mother’s two X chromosomes. A son inherits the Y 
chromosome from his father and one maternal X chromosome. Thus, 
the characteristic features of X-linked inheritance are (1) the absence 
of father-to-son transmission and (2) the fact that all daughters of an 
affected male are obligate carriers of the mutant allele (Fig. 479-13C). 
The risk of developing disease due to a mutant X-chromosomal gene 
differs in the two sexes. Because males have only one X chromosome, 
they are hemizygous for the mutant allele; thus, they are more likely 
to develop the mutant phenotype, regardless of whether the muta­
tion is dominant or recessive. A female may be either heterozygous or 
homozygous for the mutant allele, which may be dominant or reces­
sive. The terms X-linked dominant and X-linked recessive are therefore 
only applicable to expression of the mutant phenotype in women. In 
addition, the expression of X-chromosomal genes is influenced by X 
chromosome inactivation.
Y-LINKED DISORDERS  The Y chromosome has a relatively small 
number of genes. One such gene, the sex-region determining Y factor 
(SRY), which encodes the testis-determining factor (TDF), is crucial 
for normal male development. Normally, there is infrequent exchange 
of sequences on the Y chromosome with the X chromosome. The SRY 
region is adjacent to the pseudoautosomal region, a chromosomal seg­
ment on the X and Y chromosomes with a high degree of homology. 
A crossing-over event occasionally involves the SRY region with the 
distal tip of the X chromosome during meiosis in the male. Trans­
locations can result in XY females with the Y chromosome lacking 
the SRY gene or XX males harboring the SRY gene on one of the X 
chromosomes (Chap. 402). Point mutations in the SRY gene may also 
result in individuals with an XY genotype and an incomplete female 
phenotype. Most of these mutations occur de novo. Men with oligo­
spermia/azoospermia frequently have microdeletions on the long arm 
of the Y chromosome that involve one or more of the azoospermia 
factor (AZF) genes.
Exceptions to Simple Mendelian Inheritance Patterns 
• 

MITOCHONDRIAL DISORDERS  Mendelian inheritance refers to the 
transmission of genes encoded by DNA contained in the nuclear chro­
mosomes. In addition, each mitochondrion contains several copies of 
a small circular chromosome (Chap. 481). The mitochondrial DNA 
(mtDNA) is ~16.5 kb and encodes transfer and ribosomal RNAs and 
13 core proteins that are components of the respiratory chain involved 
in oxidative phosphorylation and ATP generation. The mitochondrial 
genome does not recombine and is inherited through the maternal line 
because sperm does not contribute significant cytoplasmic components 
to the zygote. A noncoding region of the mitochondrial chromosome, 
referred to as D-loop, is highly polymorphic. This property, together 
with the absence of mtDNA recombination, makes it a valuable tool for 
studies tracing human migration and evolution, and it is also used for 
specific forensic applications.
Inherited mitochondrial disorders are transmitted in a matrilineal 
fashion; all children from an affected mother will inherit the disease, 
but it will not be transmitted from an affected father to his children 
(Fig. 479-13D). Alterations in the mtDNA that involves enzymes 
required for oxidative phosphorylation lead to reduction of ATP sup­
ply, generation of free radicals, and induction of apoptosis. Several 
syndromic disorders arising from mutations in the mitochondrial 
genome are known in humans, and they affect both protein-coding 
and tRNA genes. The broad clinical spectrum often involves (cardio)
myopathies and encephalopathies because of the high dependence of 
these tissues on oxidative phosphorylation. The age of onset and the 
clinical course are highly variable because of the unusual mechanisms 
of mtDNA transmission, which replicates independently from nuclear 
DNA. During cell replication, the proportion of wild-type and mutant 

mitochondria can drift among different cells and tissues. The resulting 
heterogeneity in the proportion of mitochondria with and without a 
mutation is referred to as heteroplasmia and underlies the phenotypic 
variability that is characteristic of mitochondrial diseases.

Acquired somatic mutations in mitochondria are thought to be 
involved in several age-dependent degenerative disorders affecting 
predominantly muscle and the peripheral and central nervous sys­
tem (e.g., Alzheimer’s and Parkinson’s diseases). Establishing that an 
mtDNA alteration is causal for a clinical phenotype is challenging 
because of the high degree of polymorphism in mtDNA and the phe­
notypic variability characteristic of these disorders. Certain pharma­
cologic treatments may have an impact on mitochondria and/or their 
function. For example, treatment with the antiretroviral compound 
azidothymidine (AZT) causes an acquired mitochondrial myopathy 
through depletion of muscular mtDNA.
CHAPTER 479
Principles of Human Genetics 
MOSAICISM  Mosaicism refers to the presence of two or more geneti­
cally distinct cell lines in the tissues of an individual. It results from a 
mutation that occurs during embryonic, fetal, or extrauterine devel­
opment. The developmental stage at which the mutation arises will 
determine whether germ cells and/or somatic cells are involved. Chro­
mosomal mosaicism results from nondisjunction at an early embryonic 
mitotic division, leading to the persistence of more than one cell line, 
as exemplified by some patients with Turner’s syndrome (Chap. 402). 

Somatic mosaicism is characterized by a patchy distribution of 
genetically altered somatic cells. The McCune-Albright syndrome, for 
example, is caused by activating mutations in the stimulatory G protein 
α (Gsα) that occur postzygotically in early development (Chap. 422). 
The clinical phenotype varies depending on the tissue distribution 
of the mutation; manifestations include ovarian cysts that secrete sex 
steroids and cause precocious puberty, polyostotic fibrous dysplasia, 
café-au-lait skin pigmentation, GH-secreting pituitary adenomas, and 
hypersecreting autonomous thyroid nodules.
X-INACTIVATION, IMPRINTING, AND UNIPARENTAL DISOMY  Accord­
ing to traditional Mendelian principles, the parental origin of a mutant 
gene is irrelevant for the expression of the phenotype. There are, 
however, important exceptions to this rule. X-inactivation prevents 
the expression of most genes on one of the two X chromosomes in 
every cell of a female. Gene inactivation through genomic imprinting 
occurs on selected chromosomal regions of autosomes and leads to 
inheritable preferential expression of one of the parental alleles. It is of 
pathophysiologic importance in disorders where the transmission of 
disease is dependent on the sex of the transmitting parent and, thus, 
plays an important role in the expression of certain genetic disorders. 
Two classic examples are the Prader-Willi syndrome and Angelman’s 
syndrome. Prader-Willi syndrome is characterized by diminished fetal 
activity, obesity, hypotonia, intellectual disability, short stature, and 
hypogonadotropic hypogonadism. Deletions of the paternal copy of 
the Prader-Willi locus located on the short arm of chromosome 15 
result in a contiguous gene syndrome involving missing paternal cop­
ies of the necdin and SNRPN genes, among others. In contrast, patients 
with Angelman’s syndrome, characterized by intellectual disability, 
seizures, ataxia, and hypotonia, have deletions involving the maternal 
copy of this region on chromosome 15. These two syndromes may 
also result from uniparental disomy. In this case, the syndromes are 
not caused by deletions on chromosome 15 but by the inheritance of 
either two maternal chromosomes (Prader-Willi syndrome) or two 
paternal chromosomes (Angelman’s syndrome). Lastly, the two distinct 
phenotypes can also be caused by an imprinting defect that impairs 
the resetting of the imprint during zygote development (defect in the 
father leads to Prader-Willi syndrome; defect in the mother leads to 
Angelman’s syndrome).
Imprinting and the related phenomenon of allelic exclusion may 
be more common than currently documented because it is difficult to 
examine levels of mRNA expression from the maternal and paternal 
alleles in specific tissues or in individual cells. Genomic imprinting, 
or uniparental disomy, is involved in the pathogenesis of several other 
disorders and malignancies. For example, hydatidiform moles contain 
a normal number of diploid chromosomes, but they are exclusively of

paternal origin. The opposite situation occurs in ovarian teratomata, 
with 46 chromosomes of maternal origin. Expression of the imprinted 
gene for insulin-like growth factor 2 (IGF-2) is involved in the patho­
genesis of the cancer-predisposing Beckwith-Wiedemann syndrome 
(BWS). These children show somatic overgrowth with organomegalies 
and hemihypertrophy, and they have an increased risk of embryonal 
malignancies such as Wilms’ tumor. Normally, only the paternally 
derived copy of the IGF2 gene is active, and the maternal copy is 
inactive. BWS can be caused by several genetic defects that result in 
overactivity of IGF-2, or a missing active copy of CDKN1C, that result 
in inhibition of cell proliferation. They include paternal uniparental 
disomy (UPD) of chromosome 11, aberrant methylation of this region, 
maternal chromosomal rearrangements, or deletions within the locus.

PART 16
Genes, the Environment, and Disease
Alterations of the epigenome through gain and loss of DNA meth­
ylation and altered histone modifications play an important role in the 
pathogenesis of malignancies.
SOMATIC MUTATIONS  Cancer can be considered a genetic disease at 
the cellular level (Chap. 76). Cancers are monoclonal in origin, indicat­
ing that they have arisen from a single precursor cell with one or sev­
eral mutations in genes controlling growth (proliferation or apoptosis) 
and/or differentiation. These acquired somatic mutations are restricted 
to the tumor and its metastases and are not found in the surrounding 
normal tissue. The molecular alterations include dominant gain-offunction mutations in oncogenes, recessive loss-of-function mutations 
in tumor-suppressor genes and DNA repair genes, gene amplification, 
and chromosome rearrangements. Chromothripsis refers to a muta­
tional process including multiple clustered chromosomal rearrange­
ments in close vicinity, for example, after injury by ionizing radiation. 
Rarely, a single mutation in certain genes may be sufficient to trans­
form a normal cell into a malignant cell. In most cancers, however, the 
development of a malignant phenotype requires several genetic altera­
tions for the gradual progression from a normal cell to a cancerous cell, 
a phenomenon termed multistep carcinogenesis. Genome-wide analyses 
of cancers using deep sequencing often reveal somatic rearrangements 
resulting in fusion genes and mutations in multiple genes (Table 479-1 
and Fig. 479-14). Comprehensive sequence analyses, now also pos­
sible through single-cell sequencing (SCS), provide insight into the 
evolution and genetic heterogeneity within malignancies; these include 
intratumoral heterogeneity among the cells of the primary tumor, 
intermetastatic and intrametastatic heterogeneity, and interpatient 

Mutations
per Mb

A

Histology
HPV clade
HPV integration
APOBEC mutagenesis
UCEC-like
EMT score
Purity
iCluster
PIK3CA (26%)
EP300 (11%)
FBXW7 (11%)
PTEN (8%)
HLA-A (8%)
ARID1A (7%)
NFE2L2 (7%)
HLA-B (6%)
KRAS (6%)
ERBB3 (6%)
MAPK1 (5%)
B
CASP8 (4%)
TGFBR2 (3%)
SHKBP1 (2%)
C
Synonymous
In-frame indel
Other non-synonymous
Missense
Splice site
Frameshift
Nonsense
3q (66%)
CD274 (8%)
PTEN (8%)
YAP1 (16%)
BCAR4 (16%)
D
0.1 ≤ log2[CN] < 0.4
log2[CN] ≤ –0.4
–0.4 < log2[CN] ≤ –0.1
log2[CN] ≥ 0.4
Gene-level SCNAs

FIGURE 479-14  Somatic alterations in cervical cancer. A. Cervical carcinoma samples ordered by histology and mutation frequency; B. clinical and molecular platform 
features; C. significantly mutated genes (SMGs); and D. select somatic copy number alterations. SMGs are ordered by the overall mutation frequency and color-coded 
by mutation type. Adeno, adenocarcinomas; Adenosq, adenosquamous cancers; CN, copy number; SCNAs, somatic copy number alterations; Squamous, squamous cell 
carcinomas. (Reproduced from The Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature 543:378–384, 
2017.)

differences. These analyses further support the notion of cancer as 
an ongoing process of clonal evolution, in which successive rounds 
of clonal selection within the primary tumor and metastatic lesions 
result in diverse genetic and epigenetic alterations that require targeted 
(personalized) therapies (precision medicine). The heterogeneity of 
mutations within a tumor can also lead to resistance to targeted thera­
pies because cells with mutations that are resistant to the therapy, even 
if they are a minor part of the tumor population, will be selected as the 
more sensitive cells are eliminated.
Telomeres, repeats of conserved sequences, protect the ends the 
chromosomes from DNA damage or fusion with neighboring chromo­
somes. Telomere length shortens with age. Most human tumors express 
telomerase, an enzyme formed of a protein and an RNA component, 
which adds telomere repeats at the ends of chromosomes during rep­
lication. This mechanism impedes shortening of the telomeres and is 
associated with enhanced replicative capacity in cancer cells. Telomer­
ase inhibitors provide a strategy for treating advanced human cancers.
In many cancer syndromes, there is frequently an inherited predis­
position to tumor formation. In these instances, a germline mutation is 
inherited in an autosomal dominant fashion inactivating one allele of 
an autosomal tumor-suppressor gene. If the second allele is inactivated 
by a somatic mutation or by epigenetic silencing in a given cell, this will 
lead to neoplastic growth (Knudson two-hit model). Thus, the defec­
tive allele in the germline is transmitted in a dominant mode, although 
tumorigenesis results from a biallelic loss of the tumor-suppressor gene 
in an affected tissue. The classic example to illustrate this phenomenon 
is retinoblastoma, which can occur as a sporadic or hereditary tumor. 
In sporadic retinoblastoma, both copies of the retinoblastoma (RB) 
gene are inactivated through two somatic events. In hereditary retino­
blastoma, one mutated or deleted RB allele is inherited in an autosomal 
dominant manner and the second allele is inactivated by a subsequent 
somatic mutation. This two-hit model applies to other inherited cancer 
syndromes such as MEN 1 (Chap. 400) and neurofibromatosis types 
1 and 2 (Chap. 95). In contrast, in the autosomal dominant MEN 2 
syndrome, the predisposition for tumor formation in various organs 
is caused by a gain-of-function mutation in a single allele of the RET 
gene (Chap. 400).
NUCLEOTIDE REPEAT EXPANSION DISORDERS  Several diseases are 
associated with an increase in the number of nucleotide repeats above 
a certain threshold (Table 479-5). The repeats are sometimes located 
Synonymous
Non-synonymous
Other
Squamous
Adenosq.
Adeno.
Negative
A9
A7
Yes
Low
High
No
No
Yes
No
0.96
–3.76
0.22
1.15
Adeno.
Keratin-high
Keratin-low
APOBEC
Non-APOBEC

Mutations
Gain
Loss

TABLE 479-5  Selected Trinucleotide Repeat Disorders
DISEASE
LOCUS
REPEAT
X-chromosomal spinobulbar muscular atrophy 
(SBMA)
Xq12
CAG
11–34/40–62
XR
Androgen receptor
Fragile X syndrome (FRAXA)
Xq27.3
CGG
6–50/200–300
XR
FMR-1 protein
Fragile X syndrome (FRAXE)
Xq28
GCC
6–25/>200
XR
FMR-2 protein
Dystrophia myotonica (DM)
19q13.32
CTG
5–30/200–1000
AD, variable penetrance
Myotonin protein kinase
Huntington’s disease (HD)
4p16.3
CAG
6–34/37–180
AD
Huntingtin
Spinocerebellar ataxia type 1 (SCA1)
6p22.3
CAG
6–39/40–88
AD
Ataxin 1
Spinocerebellar ataxia type 2 (SCA2)
12q24.12
CAG
15–31/34–400
AD
Ataxin 2
Spinocerebellar ataxia type 3 (SCA3); 

Machado-Joseph disease (MD)
14q32.12
CAG
13–36/55–86
AD
Ataxin 3
Spinocerebellar ataxia type 6 (SCA6, CACNAIA)
19p13
CAG
4–16/20–33
AD
Alpha 1A voltage-dependent 
L-type calcium channel
Spinocerebellar ataxia type 7 (SCA7)
3p14.1
CAG
4–19/37 to >300
AD
Ataxin 7
Spinocerebellar ataxia type 12 (SCA12)
5q32
CAG
6–26/66–78
AD
Protein phosphatase 2A
Dentatorubral pallidoluysian atrophy (DRPLA)
12p13.31
CAG
7–23/49–75
AD
Atrophin 1
Friedreich’s ataxia (FRDA1)
9q21.11
GAA
7–22/200–900
AR
Frataxin
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; XR, X-linked recessive.
within the coding region of the genes, as in Huntington’s disease or 
the X-linked form of spinal and bulbar muscular atrophy (SBMA; 
Kennedy’s syndrome). In other instances, the repeats probably alter 
gene regulatory sequences. If an expansion is present, the DNA frag­
ment is unstable and tends to expand further during cell division. The 
length of the nucleotide repeat often correlates with the severity of the 
disease. When repeat length increases from one generation to the next, 
disease manifestations may worsen or be observed at an earlier age; 
this phenomenon is referred to as anticipation. In Huntington’s disease, 
for example, there is a correlation between age of onset and length of 
the triplet codon expansion (Chap. 435). Anticipation has also been 
documented in other diseases caused by dynamic mutations in tri­
nucleotide repeats (Table 479-5). The repeat number may also vary in 
a tissue-specific manner. In myotonic dystrophy, the CTG repeat may 
be 10-fold greater in muscle tissue than in lymphocytes (Chap. 460).
Complex Genetic Disorders 
The expression of many common 
diseases such as cardiovascular disease, hypertension, diabetes, asthma, 
psychiatric disorders, and certain cancers is determined by a combina­
tion of genetic background, environmental factors, and lifestyle. A trait 
is called polygenic if multiple genes contribute to the phenotype or mul­
tifactorial if multiple genes are assumed to interact with environmental 
factors. Genetic models for these complex traits need to account for 
genetic heterogeneity and interactions with other genes and the envi­
ronment. Complex genetic traits may be influenced by modifier genes 
that are not linked to the main gene involved in the pathogenesis of the 
trait. This type of gene-gene interaction, or epistasis, where the expres­
sion of a gene is altered by the expression of one or several indepen­
dently inherited genes, plays an important role in polygenic traits. In 
aggregate, variants in multiple genes need to be present simultaneously 
to result in a pathologic phenotype.
Type 2 diabetes mellitus provides a paradigmatic example of a 
multifactorial disorder, because genetic, nutritional, and lifestyle fac­
tors are intimately interrelated in disease pathogenesis (Table 479-6) 

(Chap. 415). The identification of genetic variations and environmen­
tal factors that either predispose to or protect against disease is essen­
tial for predicting disease risk, designing preventive strategies, and 
developing novel therapeutic approaches. The study of rare monogenic 
diseases may provide insight into some of the genetic and molecular 
mechanisms important in the pathogenesis of complex diseases. For 
example, the identification of the genes causing monogenic forms 
of permanent neonatal diabetes mellitus or maturity-onset diabetes 
defined them as candidate genes in the pathogenesis of diabetes mel­
litus type 2 (Tables 479-2 and 479-6) (Fig. 479-15). Genome scans 
have identified numerous genes and loci that may be associated with 

TRIPLET LENGTH 
(NORMAL/DISEASE)
INHERITANCE
GENE PRODUCT
CHAPTER 479
Principles of Human Genetics 
susceptibility to development of diabetes mellitus in certain popula­
tions (Fig. 479-16). Efforts to identify susceptibility genes require very 
large sample sizes, and positive results may depend on ethnicity, ascer­
tainment criteria, and statistical analysis. Association studies analyzing 
the potential influence of (biologically functional) SNPs and SNP hap­
lotypes on a particular phenotype have revealed new insights into the 
genes involved in the pathogenesis of these common disorders. Large 
variants ([micro]deletions, duplications, and inversions) present in the 
human population also contribute to the pathogenesis of complex dis­
orders, but their contributions remain poorly understood.
Linkage and Association Studies 
There are two primary strate­
gies for mapping genes that cause or increase susceptibility to human 
disease: (1) classic linkage can be performed based on a known genetic 
model or, when the model is unknown, by studying pairs of affected 
relatives; or (2) disease genes can be mapped using allelic association 
studies (Table 479-7).
GENETIC LINKAGE  Genetic linkage refers to the fact that genes are 
physically connected, or linked, to one another along the chromosomes. 
Two fundamental principles are essential for understanding the concept 
of linkage: (1) when two genes are close together on a chromosome, 
they are usually transmitted together, unless a recombination event 
separates them (Figs. 479-6); and (2) the odds of a crossover, or recom­
bination event, between two linked genes is proportional to the distance 
that separates them. Thus, genes that are farther apart are more likely to 
undergo a recombination event than genes that are very close together. 
The detection of chromosomal loci that segregate with a disease by 
linkage can be used to identify the gene responsible for the disease and 
to predict the odds of disease gene transmission in genetic counseling.
Polymorphic variants are essential for linkage studies because they 
provide a means to distinguish the maternal and paternal chromo­
somes in an individual. On average, 1 out of every 1000 bp varies from 
one person to the next. Although this degree of variation seems low 
(99.9% identical), it means that >3 million sequence differences exist 
between any two unrelated individuals and the probability that the 
sequence at such loci will differ on the two homologous chromosomes 
is high (often >70–90%). These sequence variations include variable 
number of tandem repeats (VNTRs), short tandem repeats (STRs), 
and SNPs. Most STRs, also called polymorphic microsatellite markers, 
consist of di-, tri-, or tetranucleotide repeats that can be characterized 
readily using the polymerase chain reaction (PCR). Characterization 
of SNPs, using DNA chips or beads, permits comprehensive analyses 
of genetic variation, linkage, and association studies. Although these 
sequence variations often have no apparent functional consequences, 
they provide much of the basis for variation in genetic traits.

TABLE 479-6  Examples of Genes and Loci Involved in Mono- and Polygenic Forms of Diabetes
DISORDER
GENES OR SUSCEPTIBILITY LOCUS
Monogenic permanent neonatal 
diabetes mellitus
KCNJ11 (inwardly rectifying potassium channel Kir6.2)
11p15.1
AD
GCK (glucokinase)
7p13
AR
PART 16
Genes, the Environment, and Disease
INS (insulin)
11p15.5
AR, hyperproinsulinemia
ABCC8 (ATP-binding cassette, subfamily c, member 8; sulfonylurea receptor)
11p15.1
AD or AR
GLIS3 (GLIS family zinc finger protein 3)
9p24.2
AR, diabetes, congenital 
hypothyroidism
Maturity-onset diabetes of the 
young (MODY): monogenic forms of 
diabetes mellitus
 
 
 
MODY 1
HNF4α (hepatocyte nuclear factor 4α)
20q13.12
AD inheritance
MODY 2
GCK (glucokinase)
7p13
MODY 3
HNF1α (hepatocyte nuclear factor 1α)
12q24.31
MODY 4
IPF1 (insulin receptor substrate)
13q12.2
MODY 5 (renal cysts, diabetes)
HNF1β (hepatocyte nuclear factor 1β)
17q12
MODY 6
NeuroD1 (neurogenic differentiation factor 1)
2q31.3
MODY 7
KLF1 (Kruppel-like factor 1)
19p13.13
MODY 8
CEL (carboxyl ester lipase)
9q34.13
MODY 9
PAX4 (paired box transcription factor 4)
7q32.1
MODY 10
INS (insulin)
11p15.5
MODY 11
BLK (B-lymphocyte-specific tyrosine kinase)
8p23.1
MODY 12
ABCC8 (ATP-binding cassette, subfamily c, member 8; sulfonylurea receptor)
11p15.1
 
MODY 13
KCNJ11 (inwardly rectifying potassium channelKir6.2)
11p15.1
 
Diabetes mellitus type 2; loci and 
genes linked and/or associated with 
susceptibility for diabetes mellitus 
type 2
Genes and loci identified by linkage/association studies
 
Heavily influenced by 
diet, energy expenditure, 
obesity
PPARG, KCNJ11/ABCC8, TCF7L2, HNF1B, WFS1, SLC30A8, FTO, HHEX, 
IGF2BP2, CDKN2A/B, CDKAL1, TSPAN8, ADAMTs9, CDC123/CAMK1D, JAZF1, 
NOTCH2, THADA, KCNQ1, DUSP8, MTNR1B, IRS1, SPRY2, SRR, ZFAND6, GCK, 
KLF14, TP53INP1, PROX1, PRC1, BCL11A, ZBED3, RBMS1, HNF1A, DGKB/
TMEM195, CCND2, C2CD4A/C2CD4B, PTPRD, ARAP1/CENTD2, HMGA2, TLE4/
CHCHD9, ADCY5, UBE2E2, DUSP9, GCKR, COBLL1/GRB14, HMG20A, VPS26A, 
ST6GAL1, AP3S2, HNF4A, BCL2, LAMA1, GIPR, MC4R, TLE1, KCNK16, ANK1, 
KLHDC5, ZMIZ1, PSMD6, FITM2/R3HDML/HNF4A, CILP2, ANKRD55, GLIS3, 
PEPD, GCC1/PAX4, ZFAND3, MAEA, BCAR1, RBM43/RND3, MACF1, RASGRP1, 
GRK5, TMEM163, SGCG, LPP, FAF1, TMEM154, MPHOSPH9, ARL15, POU5F1/
TCF19, SSR1/RREB1, HLA-B, INS-IGF2, GPSM1, LEP, SLC16A13, PAM/PPIP5K2, 
SLC16A11, CCDC63, C12orf51, CCND2, HNF1A, TBC1D4, CCDC85A, INAFM2, 
ASB3, FAM60A, ATP8B2, MIR4686, MTMR3, DMRTA1, SLC35D3, GLP2R, GIP, 
MAP3K11, PLEKHA1, HSD17B12, NRXN3, CMIP, ZZEF1, MNX1, ABO, ACSL1, 
HLA-DQA1
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; MODY, maturity-onset diabetes of the young.
In order to identify a chromosomal locus that segregates with a 
disease, it is necessary to characterize polymorphic DNA markers 
from affected and unaffected individuals of one or several pedigrees. 
One can then assess whether certain marker alleles cosegregate with 
the disease. Markers that are closest to the disease gene are less likely 
to undergo recombination events and therefore receive a higher link­
age score. Linkage is expressed as a lod (logarithm of odds) score—the 
ratio of the probability that the disease and marker loci are linked 
rather than unlinked. Lod scores of +3 (1000:1) are generally accepted 
as supporting linkage, whereas a score of –2 is consistent with the 
absence of linkage.
ALLELIC ASSOCIATION, LINKAGE DISEQUILIBRIUM, AND HAPLO­
TYPES  Allelic association refers to a situation in which the frequency 
of an allele is significantly increased or decreased in individuals 
affected by a particular disease in comparison to controls. Linkage and 
association differ in several aspects. Genetic linkage is demonstrable in 
families or sibships. Association studies, on the other hand, compare 
a population of affected individuals with a control population. Asso­
ciation studies can be performed as case-control studies that include 
unrelated affected individuals and matched controls or as family-based 

CHROMOSOMAL 
LOCATION
OTHER FACTORS
studies that compare the frequencies of alleles transmitted or not trans­
mitted to affected children.
Allelic association studies are particularly useful for identifying 
susceptibility genes in complex diseases. When alleles at two loci occur 
more frequently in combination than would be predicted (based on 
known allele frequencies and recombination fractions), they are said 
to be in linkage disequilibrium. Evidence for linkage disequilibrium can 
be helpful in mapping disease genes because it suggests that the two 
loci are tightly linked.
Detecting the genetic factors contributing to the pathogenesis of 
common complex disorders is challenging. In many instances, these 
are low-penetrance alleles (e.g., variations that individually have a 
subtle effect on disease development, and they can only be identified 
by unbiased GWAS) (Catalog of Published Genome-Wide Association 
Studies; Table 479-1) (Fig. 479-16). Most variants occur in noncoding 
or regulatory sequences but do not alter protein structure. The analysis 
of complex disorders is further complicated by ethnic differences in 
disease prevalence, differences in allele frequencies in known suscepti­
bility genes among different populations, locus and allelic heterogene­
ity, gene-gene and gene-environment interactions, and the possibility 
of phenocopies. Catalogues of human variation and genotype data

Rare alleles
Mendelian disease
High
Effect size
3.0
Intermediate
1.5
Modest
Rare variants
with small effect:
difficult to identify
1.1
Low
0.001
0.005
0.05
Common
Very rare
FIGURE 479-15  Relationship between allele frequency and effect size in monogenic and polygenic disorders. In classic Mendelian disorders, the allele frequency is 
typically low but has a high impact (single-gene disorder). This contrasts with polygenic disorders that require the combination of multiple low-impact alleles that are 
frequently quite common in the general population.
(HapMap, International Genome Sample Resource) have greatly facili­
tated GWAS for the characterization of complex disorders. Adjacent 
SNPs are inherited together as blocks, and these blocks can be identi­
fied by genotyping selected marker SNPs, so-called Tag SNPs, thereby 
reducing cost and workload (Fig. 479-4). The availability of this infor­
mation permits the characterization of a limited number of SNPs to 
identify the set of haplotypes present in an individual (e.g., in cases 
and controls). This, in turn, permits performing GWAS by searching 
for associations of certain haplotypes with a disease phenotype of inter­
est, an essential step for unraveling the genetic factors contributing to 
complex disorders.
POPULATION GENETICS  In population genetics, the focus changes 
from alterations in an individual’s genome to the distribution pattern 
of different genotypes in the population. In a case where there are only 
two alleles, A and a, the frequency of the genotypes will be p2 + 2pq + 
q2 = 1, with p2 corresponding to the frequency of AA, 2pq to the fre­
quency of Aa, and q2 to aa. When the frequency of an allele is known, 
the frequency of the genotype can be calculated. Alternatively, one 
can determine an allele frequency if the genotype frequency has been 
determined.
Allele frequencies vary among ethnic groups and geographic 
regions. For example, heterozygous mutations in the CFTR gene are 
relatively common in populations of European origin but are rare in 
the African population. Allele frequencies may vary because certain 
allelic variants confer a selective advantage. For example, heterozygotes 
for the sickle cell mutation, which is particularly common in West 
Africa, are more resistant to malaria infection because the erythrocytes 
of heterozygotes provide a less favorable environment for Plasmodium 
parasites. Although homozygosity for the sickle cell mutation is associ­
ated with severe anemia and sickle ‘crises, heterozygotes have a higher 
probability of survival because of the reduced morbidity and mortality 
from malaria; this phenomenon has led to an increased frequency of 
the mutant allele. Recessive conditions are more prevalent in geograph­
ically isolated populations because of the more restricted gene pool.
APPROACH TO THE PATIENT
Inherited Disorders
For the practicing clinician, the family history remains an essential 
step in recognizing the possibility of a hereditary predisposition 
to disease. When taking the history, it is useful to draw a detailed 

Rare:
Common variants
with high effect on
complex disease
CHAPTER 479
Low-frequency
variants with
intermediate effect
Principles of Human Genetics 
Typical:
Common variants
with low effect on
complex disease
Rare
Low frequency
Allele frequency
pedigree of the first-degree relatives (e.g., parents, siblings, and 
children), because they share 50% of genes with the patient. Stan­
dard symbols for pedigrees are depicted in Fig. 479-11. The family 
history should include information about ethnic background, age, 
health status, and deaths, including infants. Next, the physician 
should explore whether there is a family history of the same or 
related illnesses to the current problem. An inquiry focused on 
commonly occurring disorders such as cancers, heart disease, and 
diabetes mellitus should follow. Because of the possibility of agedependent expressivity and penetrance, the family history will need 
intermittent updating. If the findings suggest a genetic disorder, 
the clinician should assess whether some of the patient’s relatives 
may be at risk of carrying or transmitting the disease. In this cir­
cumstance, it is useful to confirm and extend the pedigree based on 
input from several family members. Emerging artificial intelligence 
tools analyzing facial features can aid the clinician in diagnosing 
patients with genetic conditions. In aggregate, this information 
may form the basis for genetic counseling, carrier detection, early 
intervention, and disease prevention in relatives of the index patient 
(Chap. 480).
In instances where a diagnosis at the molecular level may be rel­
evant, it is important to identify an appropriate laboratory that can 
perform the appropriate test. Genetic testing is available for a large 
number of monogenic disorders through commercial laboratories. 
For uncommon disorders, the test may only be performed in a spe­
cialized research laboratory. Approved laboratories offering testing 
for inherited disorders can be identified in continuously updated 
online resources (e.g., Genetic Testing Registry; Table 479-1). 
If genetic testing is considered, the patient and the family should 
be counseled about the potential implications of positive results, 
including psychological distress and the possibility of discrimina­
tion. The patient or caretakers should be informed about the mean­
ing of a negative result, technical limitations, and the possibility of 
false-negative and inconclusive results. For these reasons, genetic 
testing should only be performed after obtaining informed consent. 
Published ethical guidelines address the specific aspects that should 
be considered when testing children and adolescents. 
IDENTIFYING THE DISEASE-CAUSING GENE
Precision medicine aims to enhance the quality of medical care 
through the use of genotypic analysis (DNA testing) to iden­
tify genetic predisposition to disease, to select more specific

# Significant Loci:

PART 16
Genes, the Environment, and Disease
African and African-American
East Asian
European
Hispanic/Native American
South Asian

Initial sample size
Replication sample size

Linkage or candidate gene
GWAS or Metabochip
Exome array
Genome or exome sequencing

Total sample size (1000s)

PPARG
KCNJ11
TCF7L2
SLC30A8
MC4R
SLC16A11

PubMed ID

2003 2006

Year

FIGURE 479-16  Genome-wide association studies (GWAS) across ancestries and discovery of loci over time. The pie charts represent type 2 diabetes GWAS, as well as 
candidate gene or sequencing studies. The x axis shows the year of publication, and the y axis shows discovery sample size. The inner circles are scaled in proportion to 
discovery sample size, and the outer circles are scaled in proportion to total (discovery + replication) sample size. Significant loci are defined as a p value of 5 × 10−8. At the 
end of 2022, 534 type 2 diabetes distinct intervals (520 autosomal, 14 X chromosomal) were defined. (Reproduced with permission from BF Voight.)
pharmacotherapy, and to design individualized medical care based 
on genotype. Genotype can be deduced by analysis of protein (e.g., 
hemoglobin, apoprotein E), mRNA, or DNA. Many (pathogenic) 
variants can be readily identified by DNA analyses; technical 
advances in RNA sequencing now add increasing depth to genetic 
and genomic investigations (e.g., for the detection of gene fusions 
or aberrant gene expression patterns).
DNA testing is performed by mutational analysis or linkage 
studies in individuals at risk for a genetic disorder known to be 
present in a family. Mass screening programs require tests of high 
sensitivity and specificity to be cost-effective. The benefits and risks 
of screening newborns with genomic sequencing, and the potential 
impact on surveillance, preventative health care, and personalized 
treatment options are topics of current research (BabySeq Project). 
Prerequisites for the success of genetic screening programs include 
the following: that the disorder is potentially serious; that it can 
be influenced at a presymptomatic stage by changes in behavior, 
diet, and/or pharmaceutical manipulations; and that the screen­
ing does not result in any harm or discrimination. Screening in 
Jewish populations for the autosomal recessive neurodegenerative 
storage disease Tay-Sachs has reduced the number of affected indi­
viduals. In contrast, screening for sickle cell trait/disease in African 
Americans has led to unanticipated problems of discrimination by 
health insurers and employers. Mass screening programs harbor 
additional potential problems. For example, screening for the most 
common genetic alteration in cystic fibrosis, the ΔF508 mutation 

PNPLA3
LPL
POC5
ANKH
TBC1D4
PAM

with a frequency of ~70% in northern Europe, is feasible and seems 
to be effective. One has to keep in mind, however, that there is 
pronounced allelic heterogeneity and that the CFTR gene can be 
affected by >2000 other mutations. While the search for less com­
mon mutations has been challenging in the past, next-generation 
genome sequencing now permits comprehensive and cost-effective 
mutational analyses. However, the bioinformatic analysis and the 
classification of the detected variants as pathogenic or benign 
alterations is still challenging. Occupational screening programs 
aim to detect individuals with increased risk for certain professional 
activities (e.g., α1 antitrypsin deficiency and smoke or dust expo­
sure). Integrating genomic data into electronic medical records is 
evolving and can provide significant decision support at the point of 
care, for example, by providing the clinician with genomic data and 
decision algorithms for the prescription of drugs that are subject to 
pharmacogenetic influences. 
Mutational Analyses  DNA sequence analysis is widely used as a 
diagnostic tool and has significantly enhanced diagnostic accuracy. 
It is used for determining carrier status and for prenatal testing in 
monogenic disorders. Numerous techniques, discussed in previous 
versions of this chapter, are available for the detection of mutations. 
Analyses of large alterations in the genome are possible using clas­
sic methods such as karyotype analysis, cytogenetics, fluorescent in 
situ hybridization (FISH), and array- or bead-based techniques that 
search for multiple single exon deletions or duplications.

TABLE 479-7  Genetic Approaches for Identifying Disease Genes
INDICATIONS AND 
ADVANTAGES
LIMITATIONS
METHOD
Linkage Studies
Classical linkage analysis 
(parametric methods)
Analysis of monogenic 
traits
Difficult to collect large 
informative pedigrees
Suitable for genome scan Difficult to obtain 
sufficient statistical 
power for complex traits
Control population not 
required
 
Useful for multifactorial 
disorders in isolated 
populations
 
Allele-sharing methods 
(nonparametric methods)
Suitable for identification 
of susceptibility genes 
in polygenic and 
multifactorial disorders
Difficult to collect 
sufficient number of 
subjects
Affected sib and relative 
pair analyses
Suitable for genome scan Difficult to obtain 
sufficient statistical 
power for complex traits
Sib pair analysis
Control population 
not required if allele 
frequencies are known
Reduced power 
compared to classical 
linkage, but not sensitive 
to specification of 
genetic mode
 
Statistical power can be 
increased by including 
parents and relatives
 
Association Studies
Case-control studies
Suitable for identification 
of susceptibility genes 
in polygenic and 
multifactorial disorders
Requires large sample 
size and matched control 
population
Linkage disequilibrium
Suitable for testing 
specific allelic variants of 
known candidate loci
False-positive results in 
the absence of suitable 
control population
Transmission 
disequilibrium test (TDT)
Facilitated by 
comprehensive catalogs 
of genotypes and 
variants
Candidate gene 
approach does not permit 
detection of novel genes 
and pathways
Whole-genome 
association studies
Does not necessarily 
need relatives
Susceptibility genes can 
vary among different 
populations
Next-Generations Sequencing Technologies
Whole exome or genome 
sequencing
Unbiased approach, 
analysis can be 
performed without 
reference sequences 
from parents or siblings
Requires appropriate 
bioinformatics, may have 
low sensitivity if CNV 
analysis is not included, 
detects numerous VUS, 
can lead to the detection 
of unrelated deleterious 
alleles
Targeted sequencing of 
gene panels
Captures multiple 
candidate genes and 
loci with hybridization 
techniques followed by 
deep sequencing
Permits analyses of 
multiple candidate 
genes in parallel; 
facilitates molecular 
characterization of 
disorders with locus 
heterogeneity
Abbreviations: CNV, copy number variation; VUS, variants of unknown significance.
The analysis of more discrete sequence alterations often rely on 
the use of PCR, which allows rapid gene amplification and analysis. 
Moreover, PCR makes it possible to perform genetic testing and 
mutational analysis with small amounts of DNA extracted from 
leukocytes or even from single cells, buccal cells, or hair roots. DNA 
sequencing can be performed directly on PCR products. The advent 
of comprehensive sequencing technologies analyzing the whole 

exome or genome, of selected chromosomes, or of numerous candi­
date genes in a single run with NGS platforms is now fundamentally 
transforming the characterization of patients with rare disorders 
and advanced malignancies. These techniques have the advantage 
of an unbiased comprehensive approach, and they are increasingly 
cost-effective. Analysis of cell-free DNA (cfDNA; also referred to as 
“liquid biopsy”) present in body fluids is playing a growing role for 
minimally invasive diagnostics and disease monitoring. Genomic 
tests are also widely used for the detection of pathogens and for the 
identification of viral or bacterial sequence variations.
CHAPTER 479
Principles of Human Genetics 
The integration of genomic tests into clinical medicine is asso­
ciated with a number of ongoing challenges related to variable 
sensitivities of the tests, bioinformatics analyses, storage and shar­
ing of data, and the difficulty of interpreting all genetic variants 
identified with comprehensive testing. The discovery of incidental 
(or secondary) findings that are unrelated to the indication for the 
sequencing analysis, but indicators of other disorders of potential 
relevance for patient care can pose a difficult ethical dilemma. 
It can lead to the detection of undiagnosed medically action­
able genetic conditions but can also reveal deleterious mutations 
that cannot be influenced, as numerous sequence variants are of 
unknown significance.
A general algorithm for the approach to mutational analysis in 
patients with a suspected genetic disorder and (advanced) malig­
nancies is outlined in Fig. 479-17. The importance of a detailed 
characterization of the clinical phenotype cannot be overempha­
sized. This is the step where one should also consider the possibil­
ity of genetic heterogeneity and phenocopies. If obvious candidate 
genes are suggested by the phenotype, they can be analyzed directly. 
After identification of a mutation, it is essential to demonstrate that 
it segregates with the phenotype. The functional characterization of 
novel mutations remains labor intensive and may require analyses 
in vitro or in transgenic models in order to document the relevance 
of the genetic alteration.
Prenatal diagnosis of numerous genetic diseases in instances with 
a high risk for certain disorders is possible by direct DNA analysis. 
Amniocentesis involves the removal of a small amount of amniotic 
fluid, usually at 16 weeks of gestation. Cells can be collected and 
submitted for karyotype analyses, FISH, and mutational analysis 
of selected genes (Table 479-4). The main indications for amnio­
centesis include advanced maternal age (>35 years), presence of an 
abnormality of the fetus on ultrasound examination, an abnormal 
serum “quad” test (α fetoprotein, β human chorionic gonadotropin, 
inhibin-A, and unconjugated estriol), a family history of chromo­
somal abnormalities, or a Mendelian disorder amenable to genetic 
testing. Prenatal diagnosis can also be performed by chorionic villus 
sampling (CVS), in which a small amount of the chorion is removed 
by a transcervical or transabdominal biopsy. Chromosomes and 
DNA obtained from these cells can be submitted for cytogenetic 
and mutational analyses. CVS can be performed earlier in gesta­
tion (weeks 9–12) than amniocentesis, an aspect that may be of 
relevance when termination of pregnancy is a consideration. Later 
in pregnancy, beginning at ~18 weeks of gestation, percutaneous 
umbilical blood sampling (PUBS; cordocentesis) permits collection 
of fetal blood for analysis. Prenatal cfDNA allows DNA analy­
ses from the mother and fetus from a maternal blood sample to 
screen for certain chromosomal abnormalities and fetal sex. These 
approaches enable screening for clinically relevant and deleterious 
alleles inherited from the parents, as well as for de novo germline 
mutations, and they have the potential to identify genetic disorders 
in the prenatal setting.
In combination with in vitro fertilization (IVF) techniques, it is 
possible to perform genetic diagnoses in a single cell removed from 
the four- to eight-cell embryo or to analyze the first polar body 
from an oocyte. Preconceptual diagnosis thereby avoids therapeutic 
abortions but is costly and labor intensive. It should be empha­
sized that excluding a specific disorder by any of these approaches 
is never equivalent to the assurance of having a normal child.

Characterization of phenotype
Familial or sporadic genetic disorder
PART 16
Genes, the Environment, and Disease
Pedigree analysis
Gene unknown
Gene known or
candidate genes
Targeted sequencing
Deep sequencing of DNA
Deep sequencing of RNA (RNAseq)
Deep sequencing
(Linkage analysis and
sequencing of linked region)
Mutational analysis
Determine functional
properties of identified
mutations in vitro and in vivo
Genetic counseling
Testing of other family members
Therapy integrating genetic
and genomic information
Treatment based
on pathophysiology
FIGURE 479-17  Approach to genetic disease.
Postnatal indications for cytogenetic analyses in infants or chil­
dren include multiple congenital anomalies, suspicion of a known 
cytogenetic syndrome, developmental delay, dysmorphic features, 
autism, short stature, and disorders of sexual development, among 
others (Table 479-4).
Mutations in certain cancer susceptibility genes such as BRCA1 
and BRCA2 may identify individuals with an increased risk for the 
development of malignancies and result in risk-reducing interven­
tions. The detection of cytogenetic alterations and mutations is an 
important diagnostic and prognostic tool in leukemias, and it has 
also transformed the management of solid tumors. In addition to 
providing diagnostic information, mutational analysis can inform 
the choice of targeted therapies (“actionable mutations”), character­
ize the mutational load, identify gene signatures associated with 
effective immunotherapies, and be used for surveillance.
The demonstration of the presence or absence of mutations and 
polymorphisms is also relevant for the field of pharmacogenom­
ics, including the identification of differences in drug treatment 
response or metabolism as a function of genetic background
Gene therapy through the introduction of a normal gene or 
the ability to make site-specific modifications to the human 
genome has, so far, limited clinical application. However, several 
gene transfer methods have now been approved for clinical use, 
for example, for the treatment of Leber congenital amaurosis, 
B-cell acute lymphoblastic leukemia, spinal muscular atrophy, 
and hereditary transthyretin-mediated amyloidosis. Genome edit­
ing (or gene editing) with CRISPR-Cas9 is a promising novel 
approach for the treatment of various diseases, for example cystic 
fibrosis, certain cancers, hemophilia, and sickle cell disease. The 
first therapies using this technology for the treatment of sickle cell 
disease were approved by the U.S. Food and Drug Administration 
in 2023 (Chap. 483). 
ETHICAL ISSUES
Determination of the association of genetic defects with disease, 
comprehensive data of an individual’s genome, and studies of genetic 
variation raise many ethical and legal issues. Genetic information 
is generally regarded as sensitive information that should not be 

Patient with (advanced) cancer
Tumor biopsy: Somatic analysis
Peripheral cells: Germline analysis
DNA and RNA extraction
Bioinformatics
Tumor board
readily accessible without explicit consent (genetic privacy). The 
disclosure of genetic information may risk possible discrimination 
by insurers or employers. The scientific components of the Human 
Genome Project have been paralleled by efforts to examine ethical, 
social, and legal implications. An important milestone emerging 
from these endeavors is the Genetic Information Nondiscrimination 
Act (GINA), signed into law in 2008, which aims to protect asymp­
tomatic individuals against the misuse of genetic information for 
health insurance and employment. It does not, however, protect the 
symptomatic individual. Provisions of the U.S. Patient Protection 
and Affordable Care Act, effective in 2014, have, in part, filled this 
gap and prohibit exclusion from, or termination of, health insurance 
based on personal health status. Potential threats to the maintenance 
of genetic privacy include the increasing integration of genomic 
data into electronic medical records, compelled disclosures of health 
records, and direct-to-consumer genetic testing.
It is widely accepted that identifying disease-causing genes can 
lead to improvements in diagnosis, treatment, and prevention. 
However, the information gleaned from genotypic results can have 
quite different impacts, depending on the availability of strategies 
to modify the course of disease. For example, the identification of 
mutations that cause MEN 2 or hemochromatosis allows specific 
interventions for affected family members. On the other hand, at 
present, the identification of an Alzheimer’s or Huntington’s disease 
gene does not currently alter therapy and outcomes. Most genetic 
disorders are likely to fall into an intermediate category where the 
opportunity for prevention or treatment is significant but limited. 
However, the progress in this area is unpredictable, as underscored 
by the finding that angiotensin II receptor blockers appear to slow 
disease progression in Marfan’s syndrome. Genetic test results can 
generate anxiety in affected individuals and family members. Com­
prehensive sequence analyses are particularly challenging because 
most individuals can be expected to harbor several serious reces­
sive gene mutations. Moreover, the sensitivity of comprehensive 
sequence analyses is not always greater, for example, if CNV analy­
sis is not integrated. Genetic manipulation and patient selection for 
gene therapy approaches have raised ethical controversy and safety 
concerns that remain unresolved.