Human molecular genetics / Tom Strachan and Andrew P. Read.

Format:

Book

Author/Creator:

Strachan, T.

Contributor:

Read, Andrew P., 1939-

Language:

English

Subjects (All):

Human molecular genetics.

Molecular Biology.

Medical Subjects:

Molecular Biology.

Physical Description:

xxiii, 576 pages : illustrations (some color) ; 28 cm

Edition:

Second edition.

Place of Publication:

New York : Wiley-Liss, 1999.

Contents:

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

Box 1 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

Chapter 1 DNA structure and gene expression 1

1.1 Building blocks and chemical bonds in DNA, RNA and polypeptides 1

1.2 DNA structure and replication 5

Box 1.1 Examples of the importance of hydrogen bonding in nucleic acids and proteins 5

1.3 RNA transcription and gene expression 9

1.4 RNA processing 14

1.5 Translation, post-translational processing and protein structure 18

Chapter 2 Chromosomes in cells 27

2.1 Organization and diversity of cells 27

Box 2.1 Anatomy of animal cells 29

2.2 Development 30

Box 2.2 A brief outline of animal development 31

Box 2.3 The diversity of human cells 32

2.3 Structure and function of chromosomes 34

2.4 Mitosis and meiosis are the two types of cell division 38

2.5 Studying human chromosomes 43

Box 2.4 Chromosome banding 44

Box 2.5 Chromosome nomenclature 45

2.6 Chromosome abnormalities 47

Box 2.6 Nomenclature of chromosome abnormalities 47

Chapter 3 Genes in pedigrees 55

3.1 Mendelian pedigree patterns 55

Box 3.1 Mendelian pedigree patterns 57

Box 3.2 The complementation test to discover whether two recessive characters are determined by allelic genes 58

3.2 Complications to the basic pedigree patterns 60

3.3 Factors affecting gene frequencies 64

Box 3.3 Hardy-Weinberg equilibrium genotype frequencies for allele frequencies p (A[subscript 1]) and q (A[subscript 2]) 65

Box 3.4 The Hardy-Weinberg distribution can be used (with caution) to calculate carrier frequencies and simple risks for counseling 66

Box 3.5 Mutation-selection equilibrium 66

Box 3.6 Selection in favor of heterozygotes for cystic fibrosis 67

3.4 Nonmendelian characters 67

Chapter 4 Cell-based DNA cloning 71

4.1 Fundamentals of DNA technology and the importance of DNA cloning 71

4.2 Principles of cell-based DNA cloning 72

Box 4.1 Restriction endonucleases and modification-restriction systems 75

Box 4.2 Oligonucleotide linkers 82

Box 4.3 Nonsense suppressor mutations 82

4.3 Vector systems for cloning different sizes of DNA fragments 82

4.4 Cloning systems for preparing single-stranded DNA and for studying gene expression 88

Chapter 5 Nucleic acid hybridization assays 95

5.1 Preparation of nucleic acid probes 95

Box 5.1 Principles of autoradiography 100

5.2 Principles of nucleic acid hybridization 100

Box 5.2 Fluorescence labeling and detection systems 102

Box 5.3 Competition hybridization and Cot-1 DNA 106

5.3 Nucleic acid hybridization assays using cloned DNA probes to screen uncloned nucleic acid populations 106

Box 5.4 Standard and reverse nucleic acid hybridization assays 107

5.4 Nucleic acid hybridization assays using cloned target DNA, and microarray hybridization technology 114

Box 5.5 Evolution and applications of DNA microarrays ('DNA chips') 117

Chapter 6 PCR, DNA sequencing and in vitro mutagenesis 119

6.1 Basic features of PCR 119

Box 6.1 Proofreading by DNA polymerase-associated 3' => 5' exonuclease activity 122

6.2 Applications of PCR 123

6.3 DNA sequencing 129

6.4 In vitro site-specific mutagenesis 135

Chapter 7 Organization of the human genome 139

7.1 General organization of the human genome 139

Box 7.1 The limited autonomy of the mitochondrial genome 141

7.2 Organization and distribution of human genes 144

Box 7.2 Human gene organization 150

7.3 Human multigene families and repetitive coding DNA 151

Box 7.3 Pseudogenes and gene fragments 157

7.4 Extragenic repeated DNA sequences and transposable elements 159

Box 7.4 Classes of mammalian sequence which undergo transposition through an RNA intermediate 165

Chapter 8 Human gene expression 169

8.1 An overview of gene expression in human cells 169

Box 8.1 Spatial and temporal restriction of gene expression in mammalian cells 170

8.2 Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA 170

Box 8.2 Classes of cis-acting sequence elements involved in regulating transcription of polypeptide-encoding genes 174

8.3 Alternative transcription and processing of individual genes 183

Box 8.3 The classical view of a gene is no longer valid 185

Box 8.4 Alternative splicing can alter the functional properties of a protein 186

8.4 Asymmetry as a means of establishing differential gene expression and DNA methylation as means of perpetuating differential expression 188

Box 8.5 CpG islands 190

8.5 Long-range control of gene expression and imprinting 194

Box 8.6 Mechanisms resulting in monoallelic expression from biallelic genes in human (mammalian) cells 196

Box 8.7 The nonequivalence of the maternal and paternal genomes 197

8.6 The unique organization and expression of Ig and TCR genes 201

Chapter 9 Instability of the human genome: mutation and DNA repair 209

9.1 An overview of mutation, polymorphism, and DNA repair 209

9.2 Simple mutations 210

Box 9.1 Mechanisms which affect the population frequency of alleles 212

Box 9.2 Classes of single base substitution in polypeptide-encoding DNA 213

9.3 Genetic mechanisms which result in sequence exchanges between repeats 217

9.4 Pathogenic mutations 222

Box 9.3 How are new mitochondrial mutations fixed (i.e.

achieve a frequency of 100% in a population)? 224

9.5 The pathogenic potential of repeated sequences 227

9.6 DNA repair 235

Chapter 10 Physical and transcript mapping 241

10.1 Low resolution physical mapping 241

Box 10.1 Selecting for the chromosome contents of hybrids 242

Box 10.2 Chromosome painting 247

10.2 High resolution physical mapping: chromatin and DNA fiber FISH and restriction mapping 248

10.3 Assembly of clone contigs 252

Box 10.3 The importance of sequence tagged sites (STSs) 259

10.4 Constructing transcript maps and identifying genes in cloned DNA 260

Box 10.4 Commonly used methods for identifying genes in cloned DNA 261

Chapter 11 Genetic mapping of mendelian characters 269

11.1 Recombinants and nonrecombinants 269

11.2 Genetic markers 271

Box 11.1 The development of human genetic markers 273

Box 11.2 Informative and uninformative meioses 274

11.3 Two-point mapping 274

Box 11.3 Calculation of lod scores 276

Box 11.4 Bayesian calculation of linkage threshold 277

11.4 Multipoint mapping is more efficient than two-point mapping 277

11.5 Standard lod score analysis is not without problems 279

Chapter 12 Genetic mapping of complex characters 283

12.1 Parametric linkage analysis and complex diseases 283

12.2 Nonparametric linkage analysis does not require a genetic model 284

12.3 Association is in principle quite distinct from linkage, but where the family and the population merge, linkage and association merge 286

Box 12.1 The transmission disequilibrium test (TDT) 288

12.4 Linkage disequilibrium as a mapping tool 288

12.5 Thresholds of significance are an important consideration in analysis of complex diseases 290

Box 12.2 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

12.6 Strategies for complex disease mapping usually involve a combination of linkage and association techniques 293

Chapter 13 Genome projects 295

13.1 The history, organization, goals and value of the Human Genome Project 295

13.2 Genetic and physical mapping of the human genome 297

Box 13.1 Human gene and DNA segment nomenclature 299

Box 13.2 Cooperation, competition and controversy in the genome projects 306

13.3 Model organism and other genome projects 307

Box 13.3 Model organisms for which genome projects are considered particularly relevant to the Human Genome Project 308

13.4 Life in the post-genome (sequencing) era 310

Chapter 14 Our place in the tree of life 315

14.1 Evolution of the mitochondrial genome and the origin of eukaryotic cells 315

Box 14.1 The three kingdoms of life 317

14.2 Evolution of the eukaryotic nuclear genome: genome duplication and large-scale chromosomal alterations 318

Box 14.2 Paralogy, orthology and homology 320

14.3 Evolution of the human sex chromosomes 322

14.4 Evolution of human DNA sequence families and DNA organization 329

14.5 Evolution of gene structure 334

Box 14.3 Intron groups and intron phases 336

14.6 What makes us human? Comparative mammalian genome organization and the evolution of modern humans 337

Chapter 15 Identifying human disease genes 351

15.1 Principles and strategies in identifying disease genes 351

15.2 Position-independent strategies for identifying disease genes 351

15.3 In positional cloning, disease genes are identified using only knowledge of their approximate chromosomal location 356

Box 15.1 Transcript mapping: how to identify expressed sequences within genomic clones from a candidate region 358

Box 15.2 Pointers to the presence of large-scale mutations 360

Box 15.3 Position effects - a pitfall in disease gene identification 360

15.4 Positional candidate strategies identify candidate genes by a combination of their map position and expression, function or homology 366

Box 15.4 Mapping mouse genes 369

15.5 Confirming a candidate gene 372

Chapter 16 Molecular pathology 377

Box 16.1 The main classes of mutation 377

16.2 There are rules for the nomenclature of mutations and databases of mutations 377

Box 16.2 A nomenclature for describing the effect of an allele 378

Box 16.3 Nomenclature for describing mutations 378

16.3 A first classification of mutations is into loss of function vs gain of function mutations 378

16.4 Loss of function mutations 380

Box 16.4 Guidelines for deciding whether a DNA sequence change is pathogenic 380

Box 16.5 Hemoglobinopathies 382

Box 16.6 Molecular pathology of Prader-Willi and Angelman syndromes 383

16.5 Gain of function mutations 385

Box 16.7 Unstable expanding repeats - a novel cause of disease 386

Box 16.8 Laboratory diagnosis of fragile X 388

16.6 Molecular pathology: from gene to disease 389

16.7 Molecular pathology: from disease to gene 393

16.8 Molecular pathology of chromosomal disorders 395

Chapter 17 Genetic testing in individuals and populations 401

17.1 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

17.2 Gene tracking 415

Box 17.1 Gene tracking: four stages in the investigation of a late-onset autosomal dominant disease where direct mutation detection is not possible 416

Box 17.2 Use of Bayes' theorem for combining probabilities 418

17.3 Population screening 418

17.4 DNA profiling can be used for identifying individuals and determining relationships 422

Chapter 18 Cancer genetics 427

18.1 Cancer is the natural end-state of multicellular organisms 427

18.2 Mutations in cancer cells typically affect a limited number of pathways 427

Box 18.1 Two ways of making a series of successive mutations more likely 427

18.3 Oncogenes 428

18.4 Activation of proto-oncogenes 430

18.5 Tumor suppressor genes 434

Box 18.2 Two-hit mechanisms may explain patchy mendelian phenotypes 436

18.6 Control of the cell cycle 438

18.7 Control of the integrity of the genome 440

18.8 The multistep evolution of cancer 442

Chapter 19 Complex diseases: theory and results 445

19.1 Deciding whether a nonmendelian character is genetic: the role of family, twin and adoption studies 445

Box 19.1 Genetic differences between identical twins 446

19.2 Polygenic theory of quantitative traits 447

Box 19.2 Two common misconceptions about regression to the mean 448

Box 19.3 Partitioning of variance 450

19.3 Polygenic theory of discontinuous characters 450

19.4 Segregation analysis allows analysis of characters that are anywhere on the spectrum between purely mendelian and purely polygenic 452

Box 19.4 Correcting the segregation ratio 453

19.5 Seven examples illustrate the varying success of genetic dissection of complex diseases 455

19.6 Applications of genetic insights into complex diseases 461

Chapter 20 Studying human gene structure, expression and function using cultured cells and cell extracts 465

20.1 Gene structure and transcript mapping studies 465

Box 20.1 Obtaining gene clones for studying human gene structure, expression and function 466

20.2 Studying gene expression using cultured cells or cell extracts 471

Box 20.2 Obtaining antibodies 478

Box 20.3 Confocal fluorescence microscopy 480

20.3 Identifying regulatory sequences through the use of reporter genes and DNA-protein interactions 480

Box 20.4 Methods for transferring genes into cultured animal cells 481

20.4 Investigating gene function by identifying interactions between a protein and other macromolecules 485

Chapter 21 Genetic manipulation of animals 491

21.1 An overview of genetic manipulation of animals 491

21.2 The creation and applications of transgenic animals 492

Box 21.1 Isolation and manipulation of mammalian embryonic stem cells 495

21.3 Use of mouse embryonic stem cells in gene targeting and gene trapping 497

21.4 Creating animal models of disease using transgenic technology and gene targeting 502

Box 21.2 The potential of animals for modeling human disease 505

21.5 Manipulating animals by somatic cell nuclear transfer 508

Chapter 22 Gene therapy and other molecular genetic-based therapeutic approaches 515

22.1 Principles of molecular genetic-based therapies and treatment with recombinant proteins or genetically engineered vaccines 515

Box 22.1 General gene therapy strategies 516

Box 22.2 Treatment using conventional animal or human products can be hazardous 518

22.2 The technology of classical gene therapy 520

Box 22.3 Cell therapy 521

22.3 Therapeutics based on targeted inhibition of gene expression and mutation correction in vivo 526

22.4 Gene therapy for inherited disorders 530

22.5 Gene therapy for neoplastic disorders and infectious disease 535

22.6 The ethics of human gene therapy 539.

Notes:

Includes bibliographical references and index.

ISBN:

0471330612

OCLC:

41580663