Human Molecular Genetics

by Strachan, Tom; Read, Andrew P.

• ISBN13: 9780815341826
• ISBN10: 0815341822
• Edition: 3rd
• Format: Hardcover
• Copyright: 2003-11-21
• Publisher: Garland Science

Summary

Following the completion of the Human Genome Project the content and organization of the third edition of Human Molecular Genetics has been thoroughly revised. * Part One (Chapters 1-7) covers basic material on DNA structure and function, chromosomes, cells and development, pedigree analysis and the basic techniques used in the laboratory. * Part Two (Chapters 8-12) discusses the various genome sequencing projects and the insights they provide into the organization, expression, variation and evolution of our genome. * Part Three (Chapters 13-18) focuses on mapping, identifying and diagnosing the genetic causes of mendelian and complex diseases and cancer. * Part Four (Chapters 19-21) looks at the wider horizons of functional genomics, proteomics, bioinformatics, animal models and therapy. There are new chapters on cells and development and on functional genomics. The sections on complex diseases have been completely rewritten and reorganized, as hasthe chapter on Genome Projects. Other changes include a new section on molecular phylogenetics (Chapter 12) and the introduction of 'Ethics Boxes' to discuss some of the implications of the new knowledge. Virtually every page has been revised and updated to take account of the stunning developments of the past four years since the publication of the last edition of Human Molecular Genetics. features: * Integration of Human Genome Project data throughout the book * Two new chapters 'Cells and Development' (Chapter 3) and 'Beyond the Genome Project: Functional Genomics, Proteomics and Bioinformatics' (Chapter 19) * Completely rewritten and reorganized coverage of complex disease genetics * Increased emphasis on gene function and on applications of genetic knowledge, including ethical issues * More prominence given to novel approaches to treating disease, such as cell-based therapies, pharmacogenomics, and personalized medicine * Special topic boxes that include detailedcoverage of ethical, legal and social issues, including eugenics, genetic testing and discrimination, germ-line gene therapy and genetic enhancement, and human cloning * Contains two indices: a general index and one that contains names of diseases and disorders.

Author Biography

Andrew Read is Professor of Human Genetics at Manchester University.

Table of Contents

Abbreviations	xxiii
Preface	xxvii
Supplementary learning aids	xxviii
Before we start -- Intelligent use of the Internet	xxix
PART ONE: The Basics	1	(204)
DNA structure and gene expression	3	(30)
Building blocks and chemical bonds in DNA, RNA and polypeptides	4	(4)
DNA, RNA and polypeptides are large polymers defined by a linear sequence of simple repeating units	4	(2)
Covalent bonds confer stability; weaker noncovalent bonds facilitate intermolecular associations and stabilize structure	6	(2)
DNA structure and replication	8	(5)
The structure of DNA is an antiparallel double helix	8	(2)
Examples of the importance of hydrogen bonding in nucleic acids and proteins	10	(1)
DNA replication is semi-conservative and synthesis of DNA strands is semi-discontinuous	10	(1)
The DNA replication machinery in mammalian cells is complex	10	(2)
Major classes of proteins used in the DNA replication machinery	12	(1)
Viral genomes are frequently maintained by RNA replication rather than DNA replication	13	(1)
RNA transcription and gene expression	13	(6)
The flow of genetic information in cells is almost exclusively one way: DNA RNA protein	13	(2)
Only a small fraction of the DNA in complex organisms is expressed to give a protein or RNA product	15	(1)
During transcription genetic information in some DNA segments (genes) specifies RNA	16	(1)
Cis-acting regulatory elements and trans-acting transcription factors are required in eukaryotic gene expression	17	(2)
Tissue-specific gene expression involves selective activation of specific genes	19	(1)
RNA processing	19	(4)
RNA splicing removes nonessential RNA sequences from the primary transcript	19	(3)
Specialized nucleotides are added to the 5' and 3' ends of most RNA polymerase II transcripts	22	(1)
Translation, post-translational processing and protein structure	23	(10)
During translation mRNA is decoded on ribosomes to specify the synthesis of polypeptides	23	(2)
The genetic code is degenerate and not quite a universal code	25	(1)
Post-translational modificatins include chemical modifications of some amino acids and polypeptide cleavage	26	(2)
Protein secretion and intracellular export is controlled by specific localization signals or by chemical modifications	28	(1)
Protein structure is highly varied and not easily predicted from the amino acid sequence	29	(4)
Chromosome structure and function	33	(26)
Ploidy and the cell cycle	34	(1)
Structure and function of chromosome	34	(6)
Packaging of DNA into chromosomes requires multiple hierarchies of DNA folding	35	(1)
Individual chromosomes occupy nonoverlapping territories in an interphase nucleus	35	(1)
Chromosomes as functioning organelles: the pivotal role of the centromere	36	(1)
The mitotic spindle and its components	37	(1)
Chromosomes as functioning organelles: origins of replication	38	(1)
Chromosomes as functioning organelles: the telomeres	39	(1)
Heterochromatin and euchromatin	40	(1)
Mitosis and meiosis are the two types of cell division	40	(4)
Mitosis is the normal form of cell division	40	(1)
Meiosis is a specialized form of cell division giving rise to sperm and egg cells	41	(3)
X-Y pairing and the pseudoautosomal regions	44	(1)
Studying human chromosomes	44	(7)
Mitotic chromosomes can be seen in any dividing cell, but meiotic chromosomes are hard to study in humans	44	(4)
Chromosome banding	48	(1)
Molecular cytogenetics: chromosome FISH	48	(1)
Human chromosome nomenclature	49	(1)
Chromosome painting, molecular karyotyping and comparative genome hybridization	49	(2)
Chromosome abnormalities	51	(8)
Types of chromosomal abnormality	51	(1)
Numerical chromosomal abnormalities involve gain or loss of complete chromosomes	52	(1)
Nomenclature of chromosome abnormalities	53	(1)
Structural chromosomal abnormalities result from misrepair of chromosome breaks or from malfunction of the recombination system	54	(3)
Apparently normal chromosomal complements may be pathogenic if they have the wrong parental origin	57	(2)
Cells and development	59	(42)
The structure and diversity of cells	60	(6)
Prokaryotes and eukaryotes represent the fundamental division of cellular life forms	60	(1)
Cell size and shape can vary enormously, but rates of diffusion fix some upper limits	61	(1)
In multicellular organisms, there is a fundamental distinction between somatic cells and the germ line	61	(1)
Intracellular organization of animal cells	62	(2)
The cytoskeleton: the key to cell movement and cell shape and a major framework for intracellular transport	64	(1)
In multicellular organisms, no two cells carry exactly the same DNA sequence	64	(1)
Cells from multicellular organisms can be studied in situ or in culture	65	(1)
Cell interactions	66	(5)
Communication between cells involves the perception of signaling molecules by specific receptors	66	(1)
Activated receptors initiate signal transduction pathways that may involve enzyme cascades or second messengers, and result in the activation or inhibition of transcription factors	67	(1)
The organization of cells to form tissues requires cell adhesion	67	(3)
The extracellular matrix provides a scaffold for all tissues in the body and is also an important source of signals that control cell behavior	70	(1)
An overview of development	71	(1)
The specialization of cells during development	72	(7)
Cell specialization involves an irreversible series of hierarchical decisions	72	(1)
Animal models of development	73	(1)
The choice between alternative fates may depend on lineage or position	73	(1)
Twinning in human embryos	74	(1)
Stem cells are self-renewing progenitor cells	74	(1)
Where our tissues come from -- the developmental hierarchy in mammals	75	(1)
The diversity of human cells	76	(1)
A variety of tissue stem cells are known to exist but much remains to be learned about them	77	(1)
Embryonic stem (ES) cells have the potential to form any tissue	78	(1)
The differentiation potential of tissue stem cells is controversial	79	(1)
Pattern formation in development	79	(2)
Emergence of the body plan is dependent on axis specification and polarization	80	(1)
Homeotic mutations reveal the molecular basis of positional identity	80	(1)
Pattern formation often depends on signal gradients	80	(1)
Morphogenesis	81	(5)
Morphogenesis can be driven by changes in cell shape and size	81	(1)
Polarizing the mammalian embryo -- signals and gene products	82	(1)
Major morphogenetic changes in the embryo result from diferential cell affinity	82	(3)
Cell proliferation and programmed cell death (apoptosis) are important morphogenetic mechanisms	85	(1)
Early human development: fertilization to gastrulation	86	(8)
Fertilization activates the egg and brings together the nuclei of sperm and egg to form a unique individual	86	(1)
Cleavage partitions the zygote into many smaller cells	87	(1)
Only a small percentage of the cells in the early mammalian embryo gives rise to the mature organism	88	(1)
Implantation	88	(1)
Gastrulation is a dynamic process whereby cells of the epiblast give rise to the three germ layers	88	(1)
Extra-embryonic membranes and the placenta	89	(4)
Sex determination: genes and the environment in development	93	(1)
Neural development	94	(3)
The nervous system develops after the ectoderm is induced to differentiate by the underlying mesoderm	94	(1)
Pattern formation in the neural tube involves the coordinated expression of genes along two axes	94	(1)
Neuronal differentiation involves the combinatorial activity of transcription factors	95	(2)
Conservation of developmental pathways	97	(4)
Many human diseases are caused by the failure of normal developmental processes	97	(1)
Developmental processes are highly conserved at both the single gene level and the level of complete pathways	98	(3)
Genes in pedigrees and populations	101	(20)
Monogenic versus multifactorial inheritance	102	(1)
Mendelian pedigree patterns	102	(4)
Dominance and recessiveness are properties of characters, not genes	102	(1)
There are five basic Mendelian pedigree patterns	102	(2)
Characteristics of the Mendelian patterns of inheritance	104	(1)
The mode of inheritance can rarely be defined unambiguously in a single pedigree	104	(1)
One gene--one enzyme does not imply one gene--one syndrome	105	(1)
Mitochondrial inheritance gives a recognizable matrilineal pedigree pattern	106	(1)
The complementation test to discover whether two recessive characters are determined by allelic genes	106	(1)
Complications to the basic Mendelian pedigree patterns	106	(5)
Common recessive conditions can give a pseudo-dominant pedigree pattern	106	(1)
Failure of a dominant condition to manifest is called nonpenetrance	106	(1)
Many conditions show variable expression	107	(2)
For imprinted genes, expression depends on parental origin	109	(1)
Male lethality may complicate X-linked pedigrees	109	(1)
New mutations often complicate pedigree interpretation, and can lead to mosaicism	109	(2)
Genetics of multifactorial characters: the polygenic-threshold theory	111	(6)
Some history	111	(1)
Polygenic theory of quantitative traits	112	(2)
Two common misconceptions about regression to the mean	114	(1)
Partitioning of variance	115	(1)
Polygenic theory of discontinuous characters	115	(1)
Counseling in non-Mendelian conditions uses empiric risks	116	(1)
Factors affecting gene frequencies	117	(4)
There can be a simple relation between gene frequencies and genotype frequencies	117	(1)
Genotype frequencies can be used (with caution) to calculate mutation rates	117	(1)
Hardy-Weinberg equilibrium genotype frequencies for allele frequencies p(A1) and q (A2)	117	(1)
The Hardy-Weinberg distribution can be used (with caution) to calculate carrier frequencies and simple risks for counseling	118	(1)
Mutation-selection equilibrium	118	(1)
Heterozygote advantage can be much more important than recurrent mutation for determining the frequency of a recessive disease	118	(1)
Selection in favor of heterozygotes for CF	119	(2)
Amplifying DNA: PCR and cell-based DNA cloning	121	(34)
The importance of DNA cloning	122	(1)
PCR: basic features and applications	123	(6)
Principles of basic PCR and reverse transcriptase (RT) PCR	123	(1)
A glossary of PCR methods	124	(1)
PCR has two major limitations: short sizes and low yields of products	125	(2)
General applications of PCR	127	(1)
Some PCR reactions are designed to permit multiple amplification products and to amplify previously uncharacterized sequences	128	(1)
Principles of cell-based DNA cloning	129	(9)
An overview of cell-based DNA cloning	129	(1)
Restriction endonucleases and modification-restriction systems	129	(1)
Restriction endonucleases enable the target DNA to be cut into manageable pieces which can be joined to similarly cut vector molecules	130	(3)
Introducing recombinant DNA into recipient cells provides a method for fractionating a complex starting DNA population	133	(1)
DNA libraries are a comprehensive set of DNA clones representing a complex starting DNA population	133	(2)
Recombinant screening is often achieved by insertional inactivation of a marker gene	135	(3)
Nonsense suppressor mutations	138	(1)
The importance of sequence tagged sites (STSs)	138	(1)
Cloning systems for amplifying different sized fragments	138	(6)
Standard plasmid vectors provide a simple way of cloning small DNA fragments in bacterial (and simple eukaryotic) cells	139	(1)
Lambda and cosmid vectors provide an efficient means of cloning moderately large DNA fragments in bacterial cells	140	(2)
Large DNA fragments can be cloned in bacterial cells using vectors based on bacteriophage P1 and F factor plasmids	142	(1)
Yeast artificial chromosomes (YACs) enable cloning of megabase fragments	143	(1)
Cloning systems for producing single-stranded and mutagenized DNA	144	(3)
Single-stranded DNA for use in DNA sequencing is obtained using M13 or phagemid vectors or by linear PCR amplification	144	(2)
Oligonucleotide mismatch mutagenesis can create a predetermined single nucleotide change in any cloned gene	146	(1)
PCR-based mutagenesis includes coupling of desired sequences or chemical groups to a target sequence and site-specific mutagenesis	146	(1)
Cloning systems designed to express genes	147	(8)
Large amounts of protein can be produced by expression cloning in bacterial cells	147	(3)
Phage display is a form of expression cloning in which proteins are expressed on bacterial cell surfaces	150	(1)
Eukaryotic gene expression is carried out with greater fidelity in eukaryotic cell lines	150	(2)
Transferring genes into cultured animal cells	152	(3)
Nucleic acid hybridization: principles and applications	155	(26)
Preparation of nucleic acid probes	156	(5)
Nucleic acids can conveniently be labeled in vitro by incorporation of modified nucleotides	156	(1)
Nucleic acids can be labeled by isotopic and nonisotopic methods	157	(2)
Principles of autoradiography	159	(2)
Principles of nucleic acid hybridization	161	(7)
Nucleic acid hybridization is a method for identifying closely related molecules within two nucleic acid populations	161	(3)
Fluorescence labeling and detection systems	164	(1)
The kinetics of DNA reassociation are defined by the product of DNA concentration and time (Cot)	164	(2)
A glossary of nucleic acid hybridization	166	(1)
A wide variety of nucleic acid hybridization assays can be used	167	(1)
Nucleic acid hybridization assays using cloned DNA probes to screen uncloned nucleic acid populations	168	(6)
Dot-blot hybridization, a rapid screening method, often employs allele-specific oligonucleotide probes	168	(1)
Standard and reverse nucleic acid hybridization assays	169	(1)
Southern and Northern blot hybridizations detect nucleic acids that have been size-fractionated by gel electrophoresis	169	(2)
Pulsed field gel electrophoresis extends Southern hybridization to include detection of very large DNA molecules	171	(1)
In in situ hybridization probes are hybridized to denatured DNA of a chromosome preparation or RNA of a tissue section fixed on a glass slide	172	(2)
Hybridization assays using cloned target DNA and microarrays	174	(7)
Colony blot and plaque lift hybridization are methods for screening separated bacterial colonies or plaques	174	(1)
Gridded high density arrays of transformed cell clones or DNA clones has greatly increased the efficiency of DNA library screening	175	(1)
DNA microarray technology has enormously extended the power of nucleic acid hybridization	175	(6)
Analyzing DNA and gene structure, variation and expression	181	(24)
Sequencing and genotyping DNA	182	(4)
Standard DNA sequencing involves enzymatic DNA synthesis using base-specific dideoxynucleotide chain terminators	182	(1)
Producing single-stranded DNA sequencing templates	182	(1)
Automated DNA sequencing and microarray-based re-sequencing	183	(1)
Basic genotyping of restriction site polymorphisms and variable number of tandem repeat polymorphisms	183	(3)
Identifying genes in cloned DNA and establishing their structure	186	(4)
Common classes of DNA polymorphism which are amenable to simple genotyping methods	187	(1)
Exon trapping identifies expressed sequences by using an artificial RNA splicing assay	187	(1)
cDNA selection identifies expressed sequences genomic clones by heteroduplex formation	188	(1)
Achieving full-length cDNA sequences: overlapping clone sets, and RACE-PCR amplification	188	(1)
Mapping transcription start sites and defining exon-intron boundaries	189	(1)
Studying gene expression	190	(15)
Principles of expression screening	190	(2)
Database homology searching	192	(1)
Hybridization-based gene expression analyses: from single gene analyses to whole genome expression screening	193	(4)
PCR-based gene expression analyses: RT-PCR and mRNA differential display	197	(1)
Protein expression screens typically use highly specific antibodies	198	(2)
Obtaining antibodies	200	(2)
Autofluorescent protein tags provided a powerful way of tracking subcellular localization of proteins	202	(3)
PART TWO: The human genome and its relationship to other genomes	205	(190)
Genome projects and model organisms	207	(32)
The ground-breaking importance of genome projects	208	(2)
Genome projects prepared the way for systematic studies of the Universe within	208	(1)
The medical and scientific benefits of the genome projects are expected to be enormous	208	(1)
A genomics glossary	209	(1)
Background and organization of the Human Genome Project	210	(2)
DNA polymorphisms and new DNA cloning technologies paved the way for sequencing our genome	210	(1)
The Human Genome Project was mainly conducted in large genome centers with high-throughput sequencing capacity	210	(2)
How the human genome was mapped and sequenced	212	(14)
The first useful human genetic maps were based on microsatellite markers	212	(1)
Human gene and DNA segment nomenclature	212	(1)
Major milestones in mapping and sequencing the human genome	213	(1)
The first high resolution physical maps of the human genome were based on clone contings and STS landmarks	213	(2)
Hybrid cell mapping	215	(2)
The final stage of the Human Genome Project was crucially dependent on BAC/PAC clone contigs	217	(1)
Physical mapping by building clone contigs	218	(2)
The first high density human gene maps were based on EST markers	220	(1)
Co-operation, competition and controversy in the genome projects	220	(1)
The draft human genome sequence suggested 30 000-35 000 human genes, but getting a precise total is difficult	221	(3)
The final stages of the Human Genome Project: gene annotation and gene ontology	224	(1)
Analyses of human genome sequence variation are important for anthropological and medical research	225	(1)
Without proper safeguards, the Human Genome Project could lead to discrimination against carriers of disease genes and to a resurgence of eugenics	225	(1)
Genome projects for model organisms	226	(13)
There is a huge diversity of prokaryotic genome projects	226	(1)
The S.cerevisiae genome project was the first of many successful protist genome projects	226	(1)
Model unicellular organisms	227	(1)
The Caenorhabditis elegans genome project was the first animal genome project to be completed	228	(1)
Metazoan genome projects are mostly focusing on models of development and disease	229	(1)
Model multicellular animals for understanding development, disease and gene function	230	(9)
Organization of the human genome	239	(36)
General organization of the human genome	240	(7)
An overview of the human genome	240	(1)
The mitochondrial genome consists of a small circular DNA duplex which is densely packed with genetic information	241	(1)
Genome copy number variation in human cells	242	(1)
The limited autonomy of the mitochondrial genome	243	(1)
The nuclear genome consists of 24 different DNA molecules corresponding to the 24 different human chromosomes	244	(1)
The human genome contains about 30 000--35 000 unevenly distributed genes but precise numbers are uncertain	245	(1)
DNA methylation and CpG islands	246	(1)
Organization, distribution and function of human RNA genes	247	(6)
A total of about 1200 human genes encode rRNA or tRNA and are mostly organized into large gene clusters	247	(2)
Small nuclear RNA and small nucleolar RNA are encoded by mostly dispersed, moderately large gene families	249	(1)
Anticodon specificity of eukaryotic cytoplasmic tRNAs	249	(1)
MicroRNAs and other novel regulatory RNAs are challenging preconceptions on the extent of RNA function	250	(3)
Organization, distribution and function of human polypeptide-encoding genes	253	(12)
Human genes show enormous variation in size and internal organization	253	(1)
Functionally similar genes are occasionally clustered in the human genome, but are more often dispersed over different chromosomes	254	(1)
Human genome and human gene statistics	255	(1)
Overlapping genes, genes-within-genes and polycistronic transcription units are occasionally found in the human genome	256	(1)
Polypeptide-encoding gene families can be classified according to the degree and extent of sequence relatedness in family members	257	(2)
Genes in human gene families may be organized into small clusters, widely dispersed or both	259	(3)
Pseudogenes, truncated gene copies and gene fragments are commonly found in multigene families	262	(3)
Human proteome classification has begun but the precise functions of many human proteins remain uncertain	265	(1)
Tandemly repeated noncoding DNA	265	(3)
Satellite DNA consists of very long arrays of tandem repeats and can be separated from bulk DNA by density gradient centrifugation	265	(2)
Minisatellite DNA is composed of moderately sized arrays of tandem repeats and is often located at or close to telomeres	267	(1)
Microsatellite DNA consists of short arrays of simple tandem repeats and is dispersed throughout the human genome	268	(1)
Interespersed repetitive noncoding DNA	268	(7)
Transposon-derived repeats make up > 40% of the human genome and mostly arose through RNA intermediates	268	(2)
Some human LINE1 elements are actively transposing and enable transposition of SINES, processed pseudogenes and retrogenes	270	(1)
Alu repeats occur more than once every 3 kb in the human genome and may be subject to positive selection	270	(5)
Human gene expression	275	(40)
An overview of gene expression in human cells	276	(1)
Spatial and temporal restriction of gene expression in mammalian cells	276	(1)
Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA	277	(14)
Histone modification and chromatin remodeling facilitate access to chromatin by DNA-binding factors	278	(1)
Ubiquitous transcription factors are required for transcription by RNA polymerases I and III	279	(1)
Transcription by RNA polymerase II requires complex sets of cis-acting regulatory sequences and tissue-specific transcription factors	280	(2)
Transcription factors contain conserved structural motifs that permit DNA binding	282	(1)
Classes of cis-acting sequence elements involved in regulating transcription of polypeptide-encoding genes	283	(2)
A variety of mechanisms permit transcriptional regulation of gene expression in response to external stimuli	285	(3)
Translational control of gene expression can involve recognition of UTR regulatory sequences by RNA-binding proteins	288	(3)
Alternative transcription and processing of individual genes	291	(3)
The use of alternative promoters can generate tissue-specific isoforms	291	(1)
Human genes are prone to alternative splicing and alternative polyadenylation	292	(1)
RNA editing is a rare form of processing whereby base-specific changes are introduced into RNA	293	(1)
Alternative splicing can alter the functional properties of a protein	293	(1)
Differential gene expression: origins through asymmetry and perpetuation through epigenetic mechanisms such as DNA methylation	294	(4)
Selective gene expression in cells of mammalian embryos most likely develops in response to short range cell-cell signaling events	295	(1)
DNA methylation is an important epigenetic factor in perpetuating gene repression in vertebrate cells	295	(2)
Animal DNA methylation may provide defense against transposons as well as regulating gene expression	297	(1)
Long range control of gene expression and imprinting	298	(8)
Chromatin structure may exert long-range control over gene expression	298	(1)
Expression of individual genes in gene clusters may be co-ordinated by a common locus control region	299	(1)
Some human genes show selective expression of only one of the two parental alleles	300	(1)
Genomic imprinting involves differences in the expression of alleles according to parent of origin	301	(1)
Mechanisms resulting in monoallelic expression from biallelic genes in human cells	302	(1)
The nonequivalence of the maternal and paternal genomes	302	(1)
The mechanism of genomic imprinting is unclear but a key component appears to be DNA methylation	303	(2)
X chromosome inactivation in mammals involves very long range cis-acting repression of gene expression	305	(1)
The unique organization and expression of Ig and TCR genes	306	(9)
DNA rearrangements in B and T cells generate cell-specific exons encoding Ig and TCR variable regions	308	(1)
Heavy chain class switching involves joining of a single VDJ exon to alternative constant region transcription units	309	(1)
The monospecificity of Igs and TCRs is due to allelic and light chain exclusion	310	(5)
Instability of the human genome: mutation and DNA repair	315	(36)
An overview of mutation, polymorphism, and DNA repair	316	(1)
Simple mutations	316	(13)
Mutations due to errors in DNA replication and repair are frequent	316	(1)
Classes of genetic polymorphisms and sequence variation	317	(1)
The frequency of individual base substitutions is nonrandom according to substitution class	318	(1)
The frequency and spectrum of mutations in coding DNA differs from that in noncoding DNA	318	(1)
Mechanisms that affect the population frequency of alleles	319	(1)
The location of base substitutions in coding DNA is nonrandom	320	(1)
Classes of single base substitution in polypeptide-encoding DNA	321	(1)
Substitution rates vary considerably between different genes and between different gene components	322	(1)
The substitution rate can vary in different chromosomal regions and in different lineages	323	(3)
Sex differences in mutation rate and the question of male-driven evolution	326	(3)
Genetic mechanisms which result in sequence exchanges between repeats	329	(2)
Replication slippage can cause VNTR polymorphism at short tandem repeats (microsatellites)	329	(1)
Large units of tandemly repeated DNA are prone to insertion/deletion as a result of unequal crossover or unequal sister chromatid exchanges	329	(1)
Gene conversion events may be relatively frequent in tandemly repetitive DNA	329	(2)
Pathogenic mutations	331	(6)
There is a high deleterious mutation rate in hominids	332	(1)
The mitochondrial genome is a hotspot for pathogenic mutations	333	(1)
Most splicing mutations alter a conserved sequence needed for normal splicing, but some occur in sequences not normally required for splicing	334	(2)
Mutations that introduce a premature termination codon often result in unstable mRNA but other outcomes are possible	336	(1)
The pathogenic potential of repeated sequences	337	(7)
Slipped strand mispairing of short tandem repeats predisposes to pathogenic deletions and frameshifting insertions	337	(1)
Unstable expansion of short tandem repeats can cause a variety of diseases but the mutational mechanism is not well understood	337	(2)
Tandemly repeated and clustered gene families may be prone to pathogenic unequal crossover and gene conversion-like events	339	(1)
Interspersed repeats often predispose to large deletions and duplications	340	(2)
Pathogenic inversions can be produced by intrachromatid recombination between inverted repeats	342	(1)
DNA sequence transposition is not uncommon and can cause disease	343	(1)
DNA repair	344	(7)
DNA repair usually involves cutting out and resynthesizing a whole area of DNA surrounding the damage	345	(1)
DNA repair systems share components and processes with the transcription and recombination machinery	345	(2)
Hypersensitivity to agents that damage DNA is often the result of an impaired cellular response to DNA damage, rather than defective DNA repair	347	(4)
Our place in the tree of life	351	(44)
Evolution of gene structure and duplicated genes	352	(9)
Spliceosomal introns probably originated from group II introns and first appeared in early eukaryotic cells	352	(1)
Complex genes can evolve by intragenic duplication, often as a result of exon duplication	352	(1)
Intron groups	353	(1)
Exon shuffling can bring together new combinations of protein domains	353	(1)
Gene duplication has played a crucially important role in the evolution of multicellular organisms	354	(1)
The globin superfamily has evolved by a process of gene duplications, gene conversions, and gene loss/inactivation	354	(1)
Symmetrical exons and intron phases	355	(2)
Gene duplication mechanisms and paralogy	357	(3)
Retrotransposition can permit exon shuffling and is an important contributor to gene evolution	360	(1)
Evolution of chromosomes and genomes	361	(11)
The mitochondrial genome may have originated following endocytosis of a prokaryotic cell by a eukaryotic cell precursor	361	(1)
The universal tree of life and horizontal gene transfer	362	(1)
Reduced selection pressure caused the mitochondrial genetic code to diverge	363	(1)
The evolution of vertebrate genomes may have involved whole genome duplication	363	(1)
There have been numerous major chromosome rearrangements during the evolution of mammalian genomes	364	(2)
Segmental duplication in primate lineages and the evolutionary instability of pericentromeric and subtelomeric sequences	366	(1)
The human X and Y chromosomes exhibit substantial regions of sequence homology, including common pseudoautosomal regions	367	(1)
Human sex chromosomes evolved from autosomes and diverged due to periodic regional suppression of recombination	368	(3)
Sex chromosome differentiation results in progressive Y chromosome degeneration and X chromosome inactivation	371	(1)
Molecular phylogenetics and comparative genomics	372	(5)
Molecular phylogenetics uses sequence alignments to construct evolutionary trees	372	(2)
New computer programs align large scale and whole genome sequences, aiding evolutionary analyses and identification of conserved sequenes	374	(1)
Gene number is generally proportional to biological complexity	375	(1)
The extent of progressive protein specialization is being revealed by proteome comparisons	376	(1)
What makes us human?	377	(8)
What makes us different from mice?	378	(3)
What makes us different from our nearest relatives, the great apes?	381	(2)
A glossary of common metazoan phylogenetic groups and terms	383	(2)
Evolution of human populations	385	(10)
Genetic evidence has suggested a recent origin of modern humans from African populations	385	(2)
Human genetic diversity is low and is mostly due to variation within populations rather than between them	387	(2)
Coalescence analyses	389	(6)
PART THREE: Mapping and identifying disease genes and mutations	395	(142)
Genetic mapping of Mendelian characters	397	(18)
Recombinants and nonrecombinants	398	(4)
The recombination fraction is a measure of genetic distance	398	(1)
Recombination fractions do not exceed 0.5 however great the physical distance	398	(1)
Mapping functions define the relationship between recombination fraction and genetic distance	399	(1)
Chiasma counts and total map length	399	(1)
Physical vs. genetic maps: the distribution of recombinants	400	(2)
Genetic markers	402	(2)
Mapping human disease genes requires genetic markers	402	(1)
The heterozygosity or polymorphism information content measure how informative a marker is	402	(1)
The development of human genetic markers	403	(1)
DNA polymorphisms are the basis of all current genetic markers	403	(1)
Informative and uniformative meioses	404	(1)
Two-point mapping	404	(3)
Scoring recombinants in human pedigrees is not always simple	404	(1)
Computerized lod score analysis is the best way to analyze complex pedigrees for linkage between Mendelian characters	405	(1)
Calculation of lod scores for the families in Figure 13.6	406	(1)
Lod scores of +3 and -2 are the criteria for linkage and exclusion (for a single test)	406	(1)
For whole genome searches a genome-wide threshold of significance must be used	406	(1)
Multipoint mapping is more efficient than two-point mapping	407	(1)
Multipoint linkage can locate a disease locus on a framework of markers	407	(1)
Marker framework maps: the CEPH families	407	(1)
Bayesian calculation of linkage threshold	407	(1)
Multipoint disease-marker mapping	408	(1)
Fine-mapping using extended pedigrees and ancestral haplotypes	408	(3)
Autozygosity mapping can map recessive conditions efficiently in extended inbred families	408	(1)
Identifying shared ancestral segments allowed high-resolution mapping of the loci for cystic fibrosis and Nijmegen breakage syndrome	409	(2)
Standard lod score analysis is not without problems	411	(4)
Errors in genotyping and misdiagnoses can generate spurious recombinants	411	(1)
Computational difficulties limit the pedigrees that can be analyzed	412	(1)
Locus heterogeneity is always a pitfall in human gene mapping	413	(1)
Meiotic mapping has limited resolution	413	(1)
Characters whose inheritance is not Mendelian are not amenable to mapping by the methods described in this chapter	413	(2)
Identifying human disease genes	415	(20)
Principles and strategies in identifying disease genes	416	(1)
Position-independent strategies for identifying disease genes	416	(2)
Identifying a disease gene through knowing the protein product	416	(2)
Identifying the disease gene through an animal model	418	(1)
Identification of a disease gene using position-independent DNA sequence knowledge	418	(1)
Positional cloning	418	(5)
The first step is to define the candidate region as tightly as possible	419	(1)
A contig of clones must be established across the candidate region	419	(1)
A transcript map defines all genes within the candidate region	420	(1)
Genes from the candidate region must be prioritized for mutation testing	421	(1)
Transcript mapping: laboratory methods that supplement database analysis for identifying expressed sequences within genomic clones	421	(1)
The special relevance of mouse mutants	422	(1)
Use of chromosomal abnormalities	423	(5)
Patients with a balanced chromosomal abnormality and an unexplained phenotype are interesting	423	(1)
Mapping mouse genes	423	(2)
Patients with two Mendelian conditions, or a Mendelian condition plus mental retardation, may have a chromosomal deletion	425	(1)
Pointers to the presence of chromosome abnormalities	426	(1)
Position effects -- a pitfall in disease gene identification	427	(1)
Confirming a candidate gene	428	(1)
Mutation screening to confirm a candidate gene	428	(1)
CGH for detecting submicroscopic chromosomal imbalances	428	(1)
Once a candidate gene is confirmed, the next step is to understand its function	429	(1)
Eight examples illustrate various ways disease genes have been identified	429	(6)
Direct identification of a gene through a chromosome abnormality: Sotos syndrome	429	(1)
Pure transcript mapping: Treacher Collins syndrome	430	(1)
Large-scale sequencing and search for homologs: branchio-oto-renal syndrome	430	(1)
Positional candidates defined by function: rhodopsin and fibrillin	431	(1)
A positional candidate identified through comparison of the human and mouse maps: PAX3 and Waardenburg syndrome	431	(1)
Inference from function in vitro: Fanconi anemia	431	(1)
Inference from function in vivo: myosin 15 and DFNB3 deafness	431	(1)
Inference from the expression pattern: otoferlin	431	(4)
Mapping and identifying genes conferring susceptibility to complex diseases	435	(26)
Deciding whether a non-Mendelian character is genetic: the role of family, twin and adoption studies	436	(1)
The λ value is a measure of familial clustering	436	(1)
The importance of shared family environment	436	(1)
Twin studies suffer from many limitations	436	(1)
Adoption studies: the gold standard for disentangling genetic and environmental factors	437	(1)
Segregation analysis allows analysis of characters that are anywhere on the spectrum between purely Mendelian and purely polygenic	437	(2)
Bias of ascertainment is often a problem with family data: the example of autosomal recessive conditions	438	(1)
Complex segregation analysis is a general method for estimating the most likely mix of genetic factors in pooled family data	438	(1)
Linkage analysis of complex characters	439	(3)
Standard lod score analysis is usually inappropriate for non-Mendelian characters	439	(1)
Correcting the segregation ratio	439	(1)
Non-parametric linkage analysis does not require a genetic model	440	(1)
Shared segment analysis in families: affected sib pair and affected pedigree member analysis	441	(1)
Thresholds of significance are an important consideration in analysis of complex diseases	442	(1)
Association studies and linkage disequilibrium	442	(5)
Why associations happen	442	(1)
Association is in principle quite distinct from linkage, but where the family and the population merge, linkage and association merge	443	(1)
Measures of linkage disequilibrium	443	(1)
Many studies show islands of linkage disequilibrium separated by recombination hotspots	444	(1)
Design of association studies	445	(1)
The transmission disequilibrium test (TDT) to determine whether marker allele M1 is associated with a disease	446	(1)
Linkage and association: complementary techniques	447	(1)
Identifying the susceptibility alleles	447	(1)
Sample sizes needed to find a disease susceptibility locus by a whole genome scan using either affected sib pairs (ASP) or the transmission disequilibrium test (TDT)	447	(1)
Eight examples illustrate the varying success of genetic dissection of complex diseases	448	(9)
Breast cancer: identifying a Mendelian subset has led to important medical advances, but does not explain the causes of the common sporadic disease	448	(2)
Hirschsprung disease: an oligogenic disease	450	(1)
Alzheimer disease: genetic factors are important both in the common late-onset form and in the rare Mendelian early-onset forms, but they are different genes, acting in different ways	450	(1)
Type 1 diabetes mellitus: still the geneticist's nightmare?	451	(1)
Alzheimer disease, ApoE testing and discrimination	452	(1)
Type 2 diabetes: two susceptibility factors, one so common as to be undetectable by linkage; the other very complex and in certain populations only	453	(2)
Inflammatory bowel disease: a clear-cut susceptibility gene identified	455	(1)
Schizophrenia: the special problems of psychiatric or behavioral disorders	455	(1)
Obesity: genetic analysis of a quantitative trait	456	(1)
Overview and summary	457	(4)
Why is it so difficult?	457	(1)
If it all works out and we identify susceptibility alleles---then what?	457	(4)
Molecular pathology	461	(26)
Introduction	462	(1)
The convenient nomenclature of A and a alleles hides a vast diversity of DNA sequences	462	(1)
A first classification of mutations is into loss of function vs. gain of function mutations	462	(3)
For molecular pathology, the important thing is not the sequence of a mutant allele but its effect	462	(1)
The main classes of mutation	462	(1)
Nomenclature for describing sequence changes	463	(1)
Loss of function is likely when point mutations in a gene produce the same pathological change as deletions	463	(1)
A nomenclature for describing the effect of an allele	463	(1)
Gain of function is likely when only a specific mutation in a gene produces a given pathology	464	(1)
Deciding whether a DNA sequence change is pathogenic can be difficult	465	(1)
Loss of function mutations	465	(4)
Many different changes to a gene can cause loss of function	465	(1)
Hemoglobinopathies	465	(1)
Guidelines for assessing the significance of a DNA sequence change	466	(1)
In haploinsufficiency a 50% reduction in the level of gene function causes an abnormal phenotype	467	(2)
Mutations in proteins that work as dimers or multimers sometimes produce dominant negative effects	469	(1)
Epigenetic modification can abolish gene function even without a DNA sequence change	469	(1)
Gain of function mutations	469	(2)
Acquisition of a novel function is rare in inherited disease but common in cancer	469	(1)
Overexpression may be pathogenic	470	(1)
Qualitative changes in a gene product can cause gain of function	471	(1)
Molecular pathology: from gene to disease	471	(7)
For loss of function mutations the phenotypic effect depends on the residual level of gene function	471	(1)
Molecular pathology of Prader-Willi and Angelman syndromes	472	(2)
Loss of function and gain of function mutations in the same gene will cause different diseases	474	(1)
Variability within families is evidence of modifier genes or chance effects	475	(1)
Unstable expanding repeats -- a novel cause of disease	476	(2)
Protein aggregation is a common pathogenic mechanism in gain of function diseases	478	(1)
For mitochondrial mutations, heteroplasmy and instability complicate the relationship between genotype and phenotype	478	(1)
Molecular pathology: from disease to gene	478	(2)
The gene underlying a disease may not be the obvious one	479	(1)
Locus heterogeneity is the rule rather than the exception	479	(1)
Mutations in different members of a gene family can produce a series of related or overlapping syndromes	479	(1)
Clinical and molecular classifications are alternative tools for thinking about diseases, and each is valid in its own sphere	480	(1)
Molecular pathology of chromosomal disorders	480	(7)
Microdeletion syndromes bridge the gap between single gene and chromosomal syndromes	480	(3)
The major effects of chromosomal aneuploidies may be caused by dosage imbalances in a few identifiable genes	483	(4)
Cancer genetics	487	(22)
Introduction	488	(1)
The evolution of cancer	488	(1)
Oncogenes	489	(3)
The history of oncogenes	489	(1)
Two ways of making a series of successive mutations more likely	489	(1)
The functions of oncogenes	490	(1)
Activation of proto-oncogenes	490	(2)
Tumor suppressor genes	492	(5)
The retinoblastoma paradigm	492	(5)
Loss of heterozygosity (LoH) screening is widely used for trying to identify TS gene locations	497	(1)
Tumor suppressor genes are often silenced epigenetically by methylation	497	(1)
Stability of the genome	497	(4)
Chromosomal instability	497	(2)
DNA repair defects and DNA-level instability	499	(1)
Hereditary nonpolyposis colon cancer and microsatellite instability	499	(1)
p53 and apoptosis	500	(1)
Control of the cell cycle	501	(1)
The G1--S checkpoint	501	(1)
Integrating the data: pathways and capabilities	502	(2)
Pathways in colorectal cancer	502	(1)
A successful tumor must acquire six specific capabilities	503	(1)
What use is all this knowledge?	504	(5)
Genetic testing in individuals and populations	509	(28)
Introduction	510	(1)
The choice of material to test: DNA, RNA or protein	510	(1)
Scanning a gene for mutations	511	(4)
Methods based on sequencing	511	(1)
Methods based on detecting mismatches or heteroduplexes	511	(1)
Methods based on single-strand conformation analysis	512	(1)
Methods based on translation: the protein truncation test	513	(1)
Methods for detecting deletions	513	(1)
Methods for detecting DNA methylation patterns	514	(1)
Testing for a specified sequence change	515	(6)
Many simple methods are available for genotyping a specified variant	516	(2)
Multiplex amplifiable probe hybridization (MAPH)	518	(1)
Methods for high-throughput genotyping	519	(1)
Genetic testing for triplet repeat diseases	519	(2)
Geographical origin is an important consideration for some tests	521	(1)
Gene tracking	521	(8)
Gene tracking involves three logical steps	521	(3)
Two methods for high-throughput genotyping	524	(1)
Recombination sets a fundamental limit on the accuracy of gene tracking	524	(1)
Calculating risks in gene tracking	524	(3)
The logic of gene tracking	527	(1)
The special problems of Duchenne muscular dystrophy	528	(1)
Population screening	529	(3)
Acceptable screening programs must fit certain criteria	529	(1)
Use of Bayes' theorem for combining probabilities	529	(1)
Specificity and sensitivity measure the technical performance of a screening test	530	(1)
Organization of a genetic screening program	531	(1)
DNA profiling can be used for identifying individuals and determining relationships	532	(5)
A variety of different DNA polymorphisms have been used for profiling	532	(2)
DNA profiling can be used to determine the zygosity of twins	534	(1)
DNA profiling can be used to disprove or establish paternity	534	(1)
DNA profiling is a powerful tool for forensic investigations	535	(1)
The Prosecutor's Fallacy	535	(2)
PART FOUR: New horizons: into the 21st century	537	(94)
Beyond the genome project: functional genomics, proteomics and bioinformatics	539	(36)
An overview of functional genomics	540	(1)
The information obtained from the structural phase of the Human Genome Project is of limited use without functional annotation	540	(1)
The functions of individual genes can be described at the biochemical, cellular and whole-organism levels	540	(1)
Functional relationships among genes must be studied at the levels of the transcriptome and proteome	540	(1)
The function of glucokinase	541	(1)
High-throughput analysis techniques and bioinformatics are the enabling technologies of functional genomics	541	(1)
Functional annotation by sequence comparison	541	(4)
Tentative gene functions can be assigned by sequence comparison	541	(2)
Consensus search methods can extend the number of homologous relationships identified	543	(1)
Similarities and differences between genomes indicate conserved and functionally important sequences	543	(1)
Comparative genomics can be exploited to identify and characterize human disease genes	544	(1)
A stubborn minority of genes resist functional annotation by homology searching	545	(1)
Global mRNA profiling (transcriptomics)	545	(8)
Transcriptome analysis reveals how changes in patterns of gene expression coordinate the biochemical activities of the cell in health and disease	545	(1)
Direct sequence sampling is a statistical method for determining the relative abundances of different transcripts	546	(1)
Sequence sampling techniques for the global analysis of gene expression	547	(1)
DNA microarrays use multiplex hybridization assays to measure the abundances of thousands of transcripts simultaneously	548	(2)
The analysis of DNA array data involves the creation of a distance matrix and the clustering of related datapoints using reiterative algorithms	550	(2)
DNA arrays have been used to study global gene expression in human cell lines, tissue biopsies and animal disease models	552	(1)
Proteomics	553	(19)
Proteomics encompasses the analysis of protein expression, protein structure and protein interactions	553	(1)
Expression proteomics has flourished through the combination of two major technology platforms: two-dimensional gel electrophoresis (2DGE) and mass spectrometry	554	(1)
Protein chips	554	(3)
Mass spectrometry in proteomics	557	(1)
Expression proteomics has been used to study changes in the proteome associated with disease and toxicity	558	(1)
Protein structures provide important functional information	559	(3)
There are many different ways to study individual protein interactions	562	(1)
Determination of protein structures	563	(1)
High throughput interaction screening using library-based methods	564	(3)
Structural classification of proteins	567	(4)
The challenge of interaction proteomics is to assemble a functional interaction map of the cell	571	(1)
Information about protein interactions with small ligands can improve our understanding of biomolecular processes and provides a rational basis for the design of drugs	572	(1)
Summary	572	(3)
Genetic manipulation of cells and animals	575	(34)
An overview of gene transfer technology	576	(1)
Principles of gene transfer	576	(18)
Gene transfer can be used to introduce new, functional DNA sequences into cultured animal cells either transiently or stably	576	(1)
The production of transgenic animals requires stable gene transfer to the germ line	577	(1)
Methods of gene transfer to animal cells in culture	578	(1)
Selectable markers for animal cells	579	(3)
Isolation and manipulation of mammalian embryonic stem cells	582	(2)
The control of transgene expression is an important consideration in any gene transfer experiment	584	(2)
Gene transfer can also be used to produce defined mutations and disrupt the expression of endogenous genes	586	(2)
Gene targeting allows the production of animals carrying defined mutations in every cell	588	(1)
Site-specific recombination allows conditional gene inactivation and chromosome engineering	589	(2)
Transgenic strategies can be used to inhibit endogenous gene function	591	(3)
Using gene transfer to study gene expression and function	594	(5)
Gene expression and regulation can be investigated using reporter genes	594	(1)
Reporter genes for animal cells	595	(1)
Gene function can be investigated by generating loss-of-function and gain-of-function mutations and phenocopies	595	(2)
The large scale analysis of gene function by insertional mutagenesis and systematic RNA interference are cornerstones of functional genomics	597	(2)
Sophisticated vectors used for insertional mutagenesis	599	(1)
Creating disease models using gene transfer and gene targeting technology	599	(10)
Modeling disease pathogenesis and drug treatment in cell culture	599	(1)
It may be difficult to identify animal disease models generated spontaneously or induced by random mutagenesis	600	(2)
Mice have been widely used as animal models of human disease largely because specific mutations can be created at a predetermined locus	602	(1)
Loss-of-function mutations can be modeled by gene targeting, and gain-of-function mutations by the expression of dominant mutant genes	602	(1)
The potential of animals for modeling human disease	603	(1)
Increasing attention is being focused on the use of transgenic animals to model complex disorders	604	(1)
Mouse models of human disease may be difficult to construct because of a variety of human/mouse differences	605	(4)
New approaches to treating disease	609	(22)
Treatment of genetic disease is not the same as genetic treatment of disease	610	(1)
Treatment of genetic disease	610	(1)
Using genetic knowledge to improve existing treatments and develop new versions of conventional treatments	610	(6)
Pharmacogenetics promises to increase the effectiveness of drugs and reduce dangerous side effects	610	(1)
Drug companies have invested heavily in genomics to try to identify new drug targets	611	(1)
Cell-based treatments promise to transform the potential of transplantation	611	(2)
Recombinant proteins and vaccines	613	(1)
The ethics of human cloning	614	(2)
Principles of gene therapy	616	(1)
Methods for inserting and expressing a gene in a target cell or tissue	616	(8)
Genes can be transferred to the recipient cells in the laboratory (ex vivo) or within the patient's body (in vivo)	616	(1)
Constructs may be designed to integrate into the host cell chromosomes or to remain as episomes	616	(1)
Germ line versus somatic gene therapy	617	(2)
1995 NIH Panel report on gene therapy (Orkin-Motulsky report)	619	(1)
Designer babies	619	(1)
Viruses are the most commonly used vectors for gene therapy	619	(3)
Nonviral vector systems avoid many of the safety problems of recombinant viruses, but gene transfer rates are generally low	622	(2)
Methods for repairing or inactivating a pathogenic gene in a cell or tissue	624	(1)
Repairing a mutant allele by homologous recombination	624	(1)
Inhibition of translation by antisense oligonucleotides	624	(1)
Selective destruction or repair of mRNA by a ribozyme	625	(1)
Selective inhibition of the mutant allele by RNA interference (RNAi)	625	(1)
Some examples of attempts at human gene therapy	625	(6)
The first definite success: a cure for X-linked severe combined immunodeficiency	626	(1)
Attempts at gene therapy for cystic fibrosis	626	(1)
Attempts at gene therapy for Duchenne muscular dystrophy	627	(1)
Gene therapy for cancer	628	(1)
Gene therapy for infectious disease: HIV	628	(3)
Glossary	631	(14)
Disease index	645	(2)
Index	647