Human Molecular Genetics, 2nd Edition,9780471330615

Human Molecular Genetics, 2nd Edition

by ;
Edition: 2nd
ISBN13: 9780471330615
ISBN10: 0471330612
Format: Paperback
Pub. Date: 1999-01-01
Publisher(s): Wiley-Liss
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Summary

"The Art of Human Molecular Genetics 3 "CD-ROM contains the complete set of figures from the book for presentation. The figures are available in JPEG and PowerPoint format.

Author Biography

Tom Strachan BSc PhD, FMedSci: Professor of Human Molecular Genetics and Scientific Director, Institute of Human Genetics University of Newcastle, Newcastle-upon-Tyne, UK Andrew P. Read MA PhD FRCPath FMedSci: Professor of Human Genetics University of Manchester, Manchester UK

Table of Contents

Abbreviations xiii
Preface to the first edition xv
Preface to the second edition xvii
Before we start - genetic data and the Internet xix
All students of human molecular genetics should be using the Internet xix
The World Wide Web is the primary way of using the Internet xix
Useful Internet starting points for human molecular genetics xxi
The World Wide Web gives access to most human genetic data xxi
Comprehensive DNA and protein sequence databases cover all organisms xxi
OMIM is the standard database of human mendelian characters xxi
Medline is the main way to locate published papers on a topic xxiii
Searching for a web page xxiii
DNA structure and gene expression
1(26)
Building blocks and chemical bonds in DNA, RNA and polypeptides
1(4)
DNA structure and replication
5(4)
Examples of the importance of hydrogen bonding in nucleic acids and proteins
5(4)
RNA transcription and gene expression
9(5)
RNA processing
14(4)
Translation, post-translational processing and protein structure
18(9)
Chromosomes in cells
27(28)
Organization and diversity of cells
27(3)
Anatomy of animal cells
29(1)
Development
30(4)
A brief outline of animal development
31(1)
The diversity of human cells
32(2)
Structure and function of chromosomes
34(4)
Mitosis and meiosis are the two types of cell division
38(5)
Studying human chromosomes
43(4)
Chromosome banding
44(1)
Chromosome nomenclature
45(2)
Chromosome abnormalities
47(8)
Nomenclature of chromosome abnormalities
47(8)
Genes in pedigrees
55(16)
Mendelian pedigree patterns
55(5)
Mendelian pedigree patterns
57(1)
The complementation test to discover whether two recessive characters are determined by allelic genes
58(2)
Complications to the basic pedigree patterns
60(4)
Factors affecting gene frequencies
64(3)
Hardy-Weinberg equilibrium genotype frequencies for allele frequencies p (A1) and q (A2)
65(1)
The Hardy-Weinberg distribution can be used (with caution) to calculate carrier frequencies and simple risks for counseling
66(1)
Mutation-selection equilibrium
66(1)
Selection in favor of heterozygotes for cystic fibrosis
67(1)
Nonmendelian characters
67(4)
Cell-based DNA cloning
71(24)
Fundamentals of DNA technology and the importance of DNA cloning
71(1)
Principles of cell-based DNA cloning
72(10)
Restriction endonucleases and modification-restriction systems
75(7)
Oligonucleotide linkers
82(1)
Nonsense suppressor mutations
82(1)
Vector systems for cloning different sizes of DNA fragments
82(6)
Cloning systems for preparing single-stranded DNA and for studying gene expression
88(7)
Nucleic acid hybridization assays
95(24)
Preparation of nucleic acid probes
95(5)
Principles of autoradiography
100(1)
Principles of nucleic acid hybridization
100(6)
Fluorescence labeling and detection systems
102(4)
Competition hybridization and Cot-1 DNA
106(1)
Nucleic acid hybridization assays using cloned DNA probes to screen uncloned nucleic acid populations
106(8)
Standard and reverse nucleic acid hybridization assays
107(7)
Nucleic acid hybridization assays using cloned target DNA, and microarray hybridization technology
114(5)
Evolution and applications of DNA microarrays (`DNA chips')
117(2)
PCR, DNA sequencing and in vitro mutagenesis
119(20)
Basic features of PCR
119(4)
Proofreading by DNA polymerase-associated 3' ⇒ 5' exonuclease activity
122(1)
Applications of PCR
123(6)
DNA sequencing
129(6)
In vitro site-specific mutagenesis
135(4)
Organization of the human genome
139(30)
General organization of the human genome
139(5)
The limited autonomy of the mitochondrial genome
141(3)
Organization and distribution of human genes
144(7)
Human gene organization
150(1)
Human multigene families and repetitive coding DNA
151(8)
Pseudogenes and gene fragments
157(2)
Extragenic repeated DNA sequences and transposable elements
159(10)
Classes of mammalian sequence which undergo transposition through an RNA intermediate
165(4)
Human gene expression
169(40)
An overview of gene expression in human cells
169(1)
Spatial and temporal restriction of gene expression in mammalian cells
170(1)
Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA
170(13)
Classes of cis-acting sequence elements involved in regulating transcription of polypeptide-encoding genes
174(9)
Alternative transcription and processing of individual genes
183(5)
The classical view of a gene is no longer valid
185(1)
Alternative splicing can alter the functional properties of a protein
186(2)
Asymmetry as a means of establishing differential gene expression and DNA methylation as means of perpetuating differential expression
188(6)
CpG islands
190(4)
Long-range control of gene expression and imprinting
194(7)
Mechanisms resulting in monoallelic expression from biallelic genes in human (mammalian) cells
196(1)
The nonequivalence of the maternal and paternal genomes
197(4)
The unique organization and expression of Ig and TCR genes
201(8)
Instability of the human genome: mutation and DNA repair
209(32)
An overview of mutation, polymorphism, and DNA repair
209(1)
Simple mutations
210(7)
Mechanisms which affect the population frequency of alleles
212(1)
Classes of single base substitution in polypeptide-encoding DNA
213(4)
Genetic mechanisms which result in sequence exchanges between repeats
217(5)
Pathogenic mutations
222(5)
How are new mitochondrial mutations fixed (i.e. achieve a frequency of 100% in a population)?
224(3)
The pathogenic potential of repeated sequences
227(8)
DNA repair
235(6)
Physical and transcript mapping
241(28)
Low resolution physical mapping
241(7)
Selecting for the chromosome contents of hybrids
242(5)
Chromosome painting
247(1)
High resolution physical mapping: chromatin and DNA fiber FISH and restriction mapping
248(4)
Assembly of clone contigs
252(8)
The importance of sequence tagged sites (STSs)
259(1)
Constructing transcript maps and identifying genes in cloned DNA
260(9)
Commonly used methods for identifying genes in cloned DNA
261(8)
Genetic mapping of mendelian characters
269(14)
Recombinants and nonrecombinants
269(2)
Genetic markers
271(3)
The development of human genetic markers
273(1)
Informative and uninformative meioses
274(1)
Two-point mapping
274(3)
Calculation of lod scores
276(1)
Bayesian calculation of linkage threshold
277(1)
Multipoint mapping is more efficient than two-point mapping
277(2)
Standard lod score analysis is not without problems
279(4)
Genetic mapping of complex characters
283(12)
Parametric linkage analysis and complex diseases
283(1)
Nonparametric linkage analysis does not require a genetic model
284(2)
Association is in principle quite distinct from linkage, but where the family and the population merge, linkage and association merge
286(2)
The transmission disequilibrium test (TDT)
288(1)
Linkage disequilibrium as a mapping tool
288(2)
Thresholds of significance are an important consideration in analysis of complex diseases
290(3)
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)
292(1)
Strategies for complex disease mapping usually involve a combination of linkage and association techniques
293(2)
Genome projects
295(20)
The history, organization, goals and value of the Human Genome Project
295(2)
Genetic and physical mapping of the human genome
297(10)
Human gene and DNA segment nomenclature
299(7)
Cooperation, competition and controversy in the genome projects
306(1)
Model organism and other genome projects
307(3)
Model organisms for which genome projects are considered particularly relevant to the Human Genome Project
308(2)
Life in the post-genome (sequencing) era
310(5)
Our place in the tree of life
315(36)
Evolution of the mitochondrial genome and the origin of eukaryotic cells
315(3)
The three kingdoms of life
317(1)
Evolution of the eukaryotic nuclear genome: genome duplication and large-scale chromosomal alterations
318(4)
Paralogy, orthology and homology
320(2)
Evolution of the human sex chromosomes
322(7)
Evolution of human DNA sequence families and DNA organization
329(5)
Evolution of gene structure
334(3)
Intron groups and intron phases
336(1)
What makes us human? Comparative mammalian genome organization and the evolution of modern humans
337(14)
Identifying human disease genes
351(26)
Principles and strategies in identifying disease genes
351(1)
Position-independent strategies for identifying disease genes
351(5)
In positional cloning, disease genes are identified using only knowledge of their approximate chromosomal location
356(10)
Transcript mapping: how to identify expressed sequences within genomic clones from a candidate region
358(2)
Pointers to the presence of large-scale mutations
360(1)
Position effects - a pitfall in disease gene identification
360(6)
Positional candidate strategies identify candidate genes by a combination of their map position and expression, function or homology
366(6)
Mapping mouse genes
369(3)
Confirming a candidate gene
372(5)
Molecular pathology
377(24)
Introduction
377(1)
The main classes of mutation
377(1)
There are rules for the nomenclature of mutations and databases of mutations
377(1)
A nomenclature for describing the effect of an allele
378(1)
Nomenclature for describing mutations
378(1)
A first classification of mutations is into loss of function vs gain of function mutations
378(2)
Loss of function mutations
380(5)
Guidelines for deciding whether a DNA sequence change is pathogenic
380(2)
Hemoglobinopathies
382(1)
Molecular pathology of Prader-Willi and Angelman syndromes
383(2)
Gain of function mutations
385(4)
Unstable expanding repeats - a novel cause of disease
386(2)
Laboratory diagnosis of fragile X
388(1)
Molecular pathology: from gene to disease
389(4)
Molecular pathology: from disease to gene
393(2)
Molecular pathology of chromosomal disorders
395(6)
Genetic testing in individuals and populations
401(26)
Direct testing is like any other path lab investigation: a sample from the patient is tested to see if it is normal or abnormal
401(14)
Gene tracking
415(3)
Gene tracking: four stages in the investigation of a late-onset autosomal dominant disease where direct mutation detection is not possible
416(2)
Use of Bayes' theorem for combining probabilities
418(1)
Population screening
418(4)
DNA profiling can be used for identifying individuals and determining relationships
422(5)
Cancer genetics
427(18)
Cancer is the natural end-state of multicellular organisms
427(1)
Mutations in cancer cells typically affect a limited number of pathways
427(1)
Two ways of making a series of successive mutations more likely
427(1)
Oncogenes
428(2)
Activation of proto-oncogenes
430(4)
Tumor suppressor genes
434(4)
Two-hit mechanisms may explain patchy mendelian phenotypes
436(2)
Control of the cell cycle
438(2)
Control of the integrity of the genome
440(2)
The multistep evolution of cancer
442(3)
Complex diseases: theory and results
445(20)
Deciding whether a nonmendelian character is genetic: the role of family, twin and adoption studies
445(2)
Genetic differences between identical twins
446(1)
Polygenic theory of quantitative traits
447(3)
Two common misconceptions about regression to the mean
448(2)
Partitioning of variance
450(1)
Polygenic theory of discontinuous characters
450(2)
Segregation analysis allows analysis of characters that are anywhere on the spectrum between purely mendelian and purely polygenic
452(3)
Correcting the segregation ratio
453(2)
Seven examples illustrate the varying success of genetic dissection of complex diseases
455(6)
Applications of genetic insights into complex diseases
461(4)
Studying human gene structure, expression and function using cultured cells and cell extracts
465(26)
Gene structure and transcript mapping studies
465(6)
Obtaining gene clones for studying human gene structure, expression and function
466(5)
Studying gene expression using cultured cells or cell extracts
471(9)
Obtaining antibodies
478(2)
Confocal fluorescence microscopy
480(1)
Identifying regulatory sequences through the use of reporter genes and DNA-protein interactions
480(5)
Methods for transferring genes into cultured animal cells
481(4)
Investigating gene function by identifying interactions between a protein and other macromolecules
485(6)
Genetic manipulation of animals
491(24)
An overview of genetic manipulation of animals
491(1)
The creation and applications of transgenic animals
492(5)
Isolation and manipulation of mammalian embryonic stem cells
495(2)
Use of mouse embryonic stem cells in gene targeting and gene trapping
497(5)
Creating animal models of disease using transgenic technology and gene targeting
502(6)
The potential of animals for modeling human disease
505(3)
Manipulating animals by somatic cell nuclear transfer
508(7)
Gene therapy and other molecular genetic-based therapeutic approaches
515(30)
Principles of molecular genetic-based therapies and treatment with recombinant proteins or genetically engineered vaccines
515(5)
General gene therapy strategies
516(2)
Treatment using conventional animal or human products can be hazardous
518(2)
The technology of classical gene therapy
520(6)
Cell therapy
521(5)
Therapeutics based on targeted inhibition of gene expression and mutation correction in vivo
526(4)
Gene therapy for inherited disorders
530(5)
Gene therapy for neoplastic disorders and infectious disease
535(4)
The ethics of human gene therapy
539(6)
Glossary 545(12)
Indexes 557

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