Handbook of statistical genetics / edited by D.J. Balding, M. Bishop, C. Cannings.

Format:

Book

Contributor:

Balding, D. J.

Bishop, M. J. (Martin J.)

Cannings, C. (Christopher), 1942-

Series:

Wiley series in proability and statistics.

Wiley series in proability and statistics

Language:

English

Subjects (All):

Genetics--Statistical methods--Handbooks, manuals, etc.

Genetics.

Statistics as Topic.

Genetics--Statistical methods.

Medical Subjects:

Genetics.

Statistics as Topic.

Genre:

Handbooks and manuals.

Physical Description:

xxvi, 863 pages : illustrations ; 26 cm.

Place of Publication:

New York : John Wiley, 2001.

Contents:

Part 1 Bioinformatics 1

1 Chromosome Maps / T.P. Speed, H. Zhao 3

1.2 Genetic Maps 5

1.3 Physical Maps 20

1.4 Radiation Hybrid Mapping 27

1.5 Other Physical Mapping Approaches 31

1.6 Gene Maps 31

1.7 Programs for Physical Mapping 31

2 Statistical Significance in Biological Sequence Comparison / W.R. Pearson, T.C. Wood 39

2.2 Statistical Significance and Biological Significance 40

2.3 Estimating Statistical Significance for Local Similarity Searches 43

2.4 Summary: Exploiting Statistical Estimates 61

3 Probabilistic Models for the Study of Protein Evolution / J.L. Thorne, N. Goldman 67

3.2 The Dayhoff Model 68

3.3 Amino Acid Composition 70

3.4 Heterogeneity of Replacement Rates Among Sites 71

3.5 Protein Structure 72

3.6 Variation of Preferred Residues Among Sites 74

3.7 Models with a Physicochemical Basis 75

3.8 Codon-Based Models 76

3.9 Covariation Among Sites 77

4 Statistical Approaches in Eukaryotic Gene Prediction / V. Solovyev 83

4.1 Structural Organization and Expression of Eukaryotic Genes 83

4.2 Methods of Functional Signal Recognition 86

4.3 Performance Measures 89

4.4 Linear Discriminant Analysis 90

4.5 Prediction of Donor and Acceptor Splice Junctions 91

4.6 Identification of Promoter Regions in Human DNA 99

4.7 Recognition of Polya Signals 105

4.8 Characteristics for Recognition of 3'-Processing Sites 106

4.9 Identification of Multiple Genes in Genomic Sequences 107

4.10 Discriminative and Probabilistic Approaches to Multiple Gene Prediction 108

4.11 Internal Exon Recognition 111

4.12 Recognition of Flanking Exons 112

4.13 Performance of Gene Identification Programs 114

4.14 Using Protein Similarity Information to Improve Gene Prediction 116

4.15 Annotation of Sequences from Genome Sequencing Projects 117

4.16 Infogene: A Gene-Centered Database of Known and Predicted Genes 119

5 Protein Structure / W.R. Taylor 129

5.2 Basic Principles 130

5.3 Structure Comparison and Classification 133

5.4 Protein Structure Prediction 143

Part 2 Population Genetics 151

6 Mathematical Models in Population Genetics / C. Neuhauser 153

6.1 A Brief History of the Role of Selection 153

6.2 Mutation, Random Genetic Drift, and Selection 154

6.3 The Diffusion Approximation 158

6.4 The Infinite Allele Model 163

6.5 Other Models of Mutation and Selection 166

6.6 Coalescent Theory 167

6.7 Detecting Selection 173

7 Coalescent Theory / M. Nordborg 179

7.2 The Coalescent 180

7.3 Generalizing the Coalescent 186

7.4 Geographical Structure 190

7.5 Segregation 192

7.6 Recombination 195

7.7 Selection 200

7.8 Neutral Mutations 205

8 Inference Under the Coalescent / M. Stephens 213

8.2 The Likelihood and the Coalescent 218

8.3 Importance Sampling 220

8.4 Markov Chain Monte Carlo 224

9 Inferences from Spatial Population Genetics / F. Rousset 239

9.2 Models in Spatial Population Genetics 241

9.3 Methods of Inference 243

9.4 Inference Under the Different Models 249

9.5 Spatial Analyses in Practice 256

9.6 Software 258

Appendix A Analysis of Variance and Probabilities of Identity 259

Appendix B Likelihood Analysis of the Island Model 263

10 Analysis of Population Subdivision / L. Excoffier 271

10.2 The Fixation Index F 272

10.3 Wright's F-Statistics in Hierarchic Subdivisions 274

10.4 Analysis of Genetic Subdivision Under an Analysis of Variance Framework 279

10.5 Relationship Between Different Definitions of Fixation Indexes 287

10.6 F-Statistics and Coalescence Times 290

10.7 Analysis of Molecular Data: The Amova Framework 291

10.8 Significance Testing 299

10.9 Related and Remaining Problems 301

11 Linkage Disequilibrium and Recombination / R.R. Hudson 309

11.2 Tests of Association 311

11.3 Properties of Linkage Disequilibrium Under Population Genetic Models 318

Part 3 Evolutionary Genetics 325

12 Adaptive Molecular Evolution / Z. Yang 327

12.2 Markov Model of Codon Substitution 329

12.3 Estimation of Synonymous and Non-Synonymous Substitution Rates Between Two Sequences 331

12.4 Likelihood Calculation on a Phylogeny 338

12.5 Detecting Adaptive Evolution Along Lineages 339

12.6 Inferring Amino Acid Sites Under Diversifying Selection 343

12.7 Limitations of Current Methods 347

12.8 Computer Software 348

13 Genome Evolution / J.F.Y. Brookfield 351

13.2 The Structure and Function of Genomes 353

13.3 The Organization of Genomes 359

13.4 Population Genetics and the Genome 364

13.5 Population Genetics of Mobile DNAs 366

14 Virus Evolution / Y. Suzuki, A. Wyndham, T. Gojobori 377

14.1 Introduction: HIV as a Model for Virus Evolution 377

14.3 Evolutionary Rate 380

14.4 Natural Selection 387

14.5 Phylogenetic Relationships Between HIV and SIV Members 390

14.6 Recombination 392

14.7 The Molecular Clock and Divergence Dates 394

14.8 Population Dynamics and Models 397

15 Application of the Likelihood Function in Phylogenetic Analysis / J.P. Huelsenbeck, J.P. Bollback 415

15.2 History 417

15.3 Likelihood Function 418

15.4 Developing an Intuition of Likelihood 424

15.5 Method of Maximum Likelihood 426

15.6 Bayesian Inference 429

15.7 Markov Chain Monte Carlo 431

15.8 Assessing Uncertainty of Phylogenies 435

15.9 Hypothesis Testing and Model Choice 436

15.10 Comparative Analysis 437

16 Phylogenetics: Parsimony and Distance Methods / D. Penny, M. Hendy 445

16.3 Theoretical Background 456

16.4 Methods for Inferring Evolutionary Trees 466

16.5 Search Strategies 478

Part 4 Genetic Epidemiology 485

17 Nonparametric Linkage / P. Holmans 487

17.2 Pros and Cons of Model-Free Methods 488

17.3 Model-Free Methods for Dichotomous Traits 489

17.4 Model-Free Methods for Quantitative Traits 498

18 The Transmission/Disequilibrium Test / W.J. Ewens, R.S. Spielman 507

18.2 The Case-Control Test 508

18.3 The Transmission/Disequilibrium Test 509

18.4 Statistical Properties of the TDT 510

18.5 The TDT as a Test of Association 512

18.6 Generalizations of the TDT: More than Two Marker Alleles 513

18.7 Generalizations of the TDT: Unaffected Sibs 514

18.8 The S-TDT Used as a Test of Association 517

19 Population Association / D. Clayton 519

19.2 Measures of Association 520

19.3 Case-Control Studies 522

19.4 Tests for Association 524

19.5 Logistic Regression and Log-Linear Models 527

19.6 Stratification and Matching 529

19.7 Unmeasured Confounding 532

19.8 Multiple Alleles 534

19.9 Haplotype Analysis 537

20 Linkage Analysis / E.A. Thompson 541

20.2 The Early Years 542

20.3 The Development of Human Genetic Linkage Analysis 544

20.4 The Pedigree Years: Segregation and Linkage Analysis 546

20.5 Likelihood and Location Score Computation 548

20.6 Linkage Analysis of Complex Traits 553

20.7 Map Estimation, Map Uncertainty, and the Meiosis Model 556

20.8 The Future 559

Part 5 Animal and Plant Breeding 565

21 Quantitative Trait Loci in Inbred Lines / R.C. Jansen 567

21.2 Segregation Analysis 570

21.3 Dissecting Quantitative Variation with the Aid of Molecular Markers 575

21.4 QTL Detection Strategies 585

22 Mapping Quantitative Trait Loci in Outbred Pedigrees / I. Hoeschele 599

22.2 Linkage Mapping via Least Squares or Maximum Likelihood and Fixed Effects Models 601

22.3 Linkage Mapping via Residual Maximum Likelihood and Random Effects Models 605

22.4 Linkage Mapping via Bayesian Methodology 614

22.5 Genotype Sampling in Complex Pedigrees 625

22.6 Fine Mapping of Quantitative Trait Loci 636

23 Inferences About Breeding Values / D. Gianola 645

23.2 Landmarks 646

23.3 Future Developments 664

24 Marker-Assisted Selection and Introgression / J.C.

Whittaker 673

24.2 Marker-Assisted Selection: Inbred Line Crosses 674

24.3 Marker-Assisted Selection: Outbred Populations 681

24.4 Marker-Assisted Introgression 686

Part 6 Applications 695

25 Ethics in the Use of Statistics in Genetics / D. Beyleveld 697

25.2 What is Ethics? 698

25.3 Normative Moral Theories and Institutionalized Consensus 700

25.4 Uses of Statistics 709

26 Forensics / B.S. Weir 721

26.2 Principles of Interpretation 722

26.3 Profile Probabilities 724

26.4 Mixtures 730

26.5 Sampling Issues 733

26.6 Other Forensic Issues 735

27 Pharmacogenetics / N.J. Schork, D. Fallin, H.K. Tiwari, M.A. Schork 741

27.1 Introduction: The Scope of Pharmacogenetics 742

27.2 General Issues in the Pharmacogenetic Analysis of Clinical Trials 743

27.3 Phenotypic and Outcome Assessment via Mixture Distribution Analysis 746

27.4 Optimal Genotyping Protocols via Extreme Sampling 749

27.5 Multilocus and Haplotype Analysis 752

27.6 Assessing Sample Homogeneity 755

27.7 Sequential Pharmacogenetic Designs 757

28 Statistical Basis of Risk Calculations / R. Chakraborty 765

28.2 Concept of Risk in the Formulation of Bayesian Inference 766

28.3 Various Stages of Risk Estimation 767

28.4 Major Advances in Estimating the Conditional Probability 768

28.5 Use of Genetic Data in Other Types of Risk Estimation 772

29 Conservation Genetics / M.A. Beaumont 779

29.2 Estimating Effective Population Size 780

29.3 Hybridization 798

30 Genetic History of the Human Species / J.H. Relethford 813

30.2 Models of Modern Human Origins 814

30.3 Gene Trees 818

30.4 African Genetic Diversity 824

30.5 Genetic Distances Between Living Human Populations 828

30.6 Genetic Demography of the Human Species 832.

Notes:

Includes bibliographical references and index.

ISBN:

0471860948

OCLC:

44578885