Second Edition features the latest tools for uncovering the genetic basis of human disease The Second Edition of this landmark publication brings together a team of leading experts in the field to thoroughly update the publication. Readers will discover the tremendous advances made in human genetics in the seven years that have elapsed since the First Edition. Once again, the editors have assembled a comprehensive introduction to the strategies, designs, and methods of analysis for the discovery of genes in common and genetically complex traits. The growing social, legal, and ethical issues surrounding the field are thoroughly examined as well.
Rather than focusing on technical details or particular methodologies, the editors take a broader approach that emphasizes concepts and experimental design. Readers familiar with the First Edition will find new and cutting-edge material incorporated into the text:
- Updated presentations of bioinformatics, multiple comparisons, sample size requirements, parametric linkage analysis, case-control and family-based approaches, and genomic screening
- New methods for analysis of gene-gene and gene-environment interactions
- A completely rewritten and updated chapter on determining genetic components of disease
- New chapters covering molecular genomic approaches such as microarray and SAGE analyses using single nucleotide polymorphism (SNP) and cDNA expression data, as well as quantitative trait loci (QTL) mapping
The editors, two of the world's leading genetic epidemiologists, have ensured that each chapter adheres to a consistent and high standard. Each one includes all-new discussion questions and practical examples. Chapter summaries highlight key points, and a list of references for each chapter opens the door to further investigation of specific topics.
Molecular biologists, human geneticists, genetic epidemiologists, and clinical and pharmaceutical researchers will find the Second Edition a helpful guide to understanding the genetic basis of human disease, with its new tools for detecting risk factors and discovering treatment strategies.
Table of Contents:
Foreword xv
Preface xvii
Contributors xix
1. Basic Concepts in Genetics and Linkage Analysis 1
Elizabeth C. Melvin and Marcy C. Speer
Introduction 1
Historical Contributions 2
Segregation and Linkage Analysis 2
Hardy–Weinberg Equilibrium 5
DNA, Genes, and Chromosomes 5
Structure of DNA 5
Genes and Alleles 9
Genes and Chromosomes 10
Inheritance Patterns in Mendelian Disease 13
Genetic Changes Associated with Disease/Trait Phenotypes 14
Point Mutations 14
Deletion/Insertion Mutations 17
Novel Mechanisms of Mutation: Unstable DNA and Trinucleotide Repeats 18
Susceptibility Versus Causative Genes 19
Genes, Mitosis, and Meiosis 23
When Genes and Chromosomes Segregate Abnormally 25
Ordering and Spacing of Loci by Mapping Techniques 26
Physical Mapping 26
Genetic Mapping 29
Interference and Genetic Mapping 30
Meiotic Breakpoint Mapping 31
Disease Gene Discovery 31
Information Content in a Pedigree 41
Disease Gene Localization 42
Extensions to Complex Disease 45
Summary 45
References 46
2. Defining Disease Phenotypes 51
Arthur S. Aylsworth
Introduction 51
Exceptions to Traditional Mendelian Inheritance Patterns 52
Pseudodominant Transmission of a Recessive 53
Pseudorecessive Transmission of a Dominant 54
Mosaicism 55
Mitochondrial Inheritance 56
Incomplete Penetrance and Variable Expressivity 58
Genomic Imprinting 61
Phenocopies and Other Environmentally Related Effects 63
Heterogeneity 64
Genetic Heterogeneity 64
Phenotypic Heterogeneity 65
Complex Inheritance 67
Polygenic and Multifactorial Models 67
Role of Environment 70
Role of Chance in Phenotype Expression 70
Phenotype Definition 71
Classification of Disease 71
Nonsyndromic Phenotypes 72
Syndromic Phenotypes 72
Associations and Syndromes of Unknown Cause 73
Importance of Chromosomal Rearrangements in Mapping 74
Qualitative (Discontinuous) and Quantitative (Continuous) Traits 74
Defining Phenotypes for Analysis of Complex Genetic Disorders 75
Select Most Biologically Meaningful Phenotype 75
Partition Phenotype or Dataset by Cause and Associated Pathology 75
Summary: Approach to Phenotype Definition 80
Resources for Information about Clinical Genetics and
Phenotype Definition 82
References 82
3. Determining Genetic Component of a Disease 91
Allison Ashley-Koch
Introduction 91
Study Design 92
Selecting a Study Population 93
Ascertainment 94
Approaches to Determining the Genetic Component of a Disease 99
Cosegregation with Chromosomal Abnormalities and Other Genetic Disorders 100
Familial Aggregation 101
Twin and Adoption Studies 104
Recurrence Risk in Relatives of Affected Individuals 105
Heritability 107
Segregation Analysis 108
Summary 110
References 111
4. Patient and Family Participation in Genetic Research Studies 117
Chantelle Wolpert, Amy Baryk Crunk, and Susan Estabrooks Hahn
Introduction 117
Step 1: Preparing to Initiate a Family Study 118
Confidentiality 118
Certificate of Confidentiality 119
Need for a Family Studies Director 119
Working with Human Subjects 122
Step 2: Ascertainment of Families for Studies 124
Family Recruitment 124
Informed Consent and Family Participation 128
Step 3: Data Collection 131
Confirmation of Diagnosis 131
Art of Field Studies 132
Special Issues in Family Studies 133
Step 4: Family Follow-Up 135
Need for Additional Medical Services 135
Duty to Recontact Research Participants 136
Maintaining Contact with Participants 137
Guidelines for Releasing Genetic Information 137
Genetic Testing of Children 139
Genetic Discrimination 139
DNA Banking 141
Future Considerations 142
Appendix 142
References 148
5. Collection of Biological Samples for DNA Analysis 153
Jeffery M. Vance
Establishing Goals of Collection 153
Types of DNA Sample Collection 153
Venipuncture (Blood) 153
Buccal Samples 155
Dried Blood 156
Tissue 156
DNA Extraction and Processing 157
Blood 157
Quantitation 157
Tissue Culture 159
Buccal Brushes 160
Dried Blood Cards 161
Fixed Tissue 161
Whole-Genome Amplification 161
Sample Management 162
Informed Consent/Security 164
References 164
6. Methods of Genotyping 167
Jeffery M. Vance
Brief Historical Review of Markers Used for Genotyping 167
Restriction Fragment Length Polymorphisms 167
Variable Number of Tandem Repeat Markers 168
Short Tandem Repeats or Microsatellites 168
Single-Nucleotide Polymorphisms 168
Sources of Markers 168
Restriction Fragment Length Polymorphisms 169
Microsatellites 169
Single-Nucleotide Polymorphisms 171
PCR and Genotyping 171
Laboratory and Methodology Optimization 171
Optimization of Reagents 172
“I Can’t Read a Marker, What Should I Do?” 173
Marker Separation 175
Manual or Nonsequencer Genotyping 175
Loading Variants 176
DNA Pooling and Homozygosity Mapping 177
Detection Methods 178
Radioactive Methods (32P or 33P) 178
Silver Stain 178
Fluorescence 179
SNP Detection 181
DNA Array or “Chip” 181
Oligonucleotide Ligation Assay 181
Fluorescent Polarization 182
Taqman 182
Single-Base-Pair Extension 184
Pyrosequencing 184
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Spectrometry 184
Invader and PCR-Invader Assays 184
Single-Strand Conformational Polymorphism 186
Denaturing High-Pressure Liquid Chromatography 186
Data Management 186
Objectivity 187
Genotype Integrity 187
Scoring 187
Standards 187
Quality Control 188
References 189
7. Data Analysis Issues in Expression Profiling 193
Simon Lin and Michael Hauser
Introduction 193
Serial Analysis of Gene Expression 194
Analysis of SAGE Libraries 195
Microarray Analysis 196
Data Preparation 197
Expression Data Matrix 198
Dimension Reduction of Features 198
Measures of Similarity between Objects 200
Unsupervised Machine Learning: Clustering 201
Supervised Machine Learning 204
Data Visualization 207
Other Types of Gene Expression Data Analysis 207
Biological Applications of Expression Profiling 209
References 212
8. Information Management 219
Carol Haynes and Colette Blach
Information Planning 220
Needs Assessment 220
Information Flow 222
Plan Logical Database Model 223
Hardware and Software Requirements 225
Software Selection 226
System Administration 226
Database Administration 226
Database Implementation 227
Conversion 227
Performance Tuning 228
Data Integrity 228
User Interfaces 231
Security 231
Transmission Security 231
System Security 233
Patient Confidentiality 233
Pedigree Plotting and Data Manipulation Software 234
Summary 235
9. Quantitative Trait Linkage Analysis 237
Jason H. Moore
Introduction to Quantitative Traits 237
Genetic Architecture 238
Study Design 240
Haseman–Elston Regression 240
Multipoint IBD Method 242
Variance Component Linkage Analysis 243
Nonparametric Methods 246
Future Directions 247
Summary 249
References 250
10. Advanced Parametric Linkage Analysis 255
Silke Schmidt
Two-Point Analysis 256
Example of LOD Score Calculation and Interpretation 259
Effects of Misspecified Model Parameters in LOD Score Analysis 260
Impact of Misspecified Disease Allele Frequency 261
Impact of Misspecified Mode of Inheritance 262
Impact of Misspecified Disease Penetrances 263
Impact of Misspecified Marker Allele Frequency 264
Control of Scoring Errors 265
Genetic Heterogeneity 266
Multipoint Analysis 269
Practical Approaches for Model-Based Linkage Analysis of Complex Traits 273
Affecteds-Only Analysis 274
Maximized Maximum LOD Score 275
Heterogeneity LOD 275
MFLINK 276
Summary 277
References 277
11. Nonparametric Linkage Analysis 283
Elizabeth R. Hauser, Jonathan Haines, and David E. Goldgar
Introduction 283
Background and Historical Framework 284
Identity by State and Identity by Descent 286
Measures of Familiality 289
Qualitative Traits 289
Measuring Genetic Effects in Quantitative Traits 293
Summary of Basic Concepts 295
Methods for Nonparametric Linkage Analysis 295
Tests for Linkage Using Affected Sibling Pairs (ASPs) 295
Methods Incorporating Affected Relative Pairs 301
Power Analysis and Experimental Design Considerations for Qualitative Traits 311
Nonparametric Quantitative Trait Linkage Analysis 314
Power and Sampling Considerations for Mapping Quantitative Trait Loci 316
Examples of Application of Sibpair Methods for Mapping Complex Traits 318
Additional Considerations in Nonparametric Linkage Analysis 319
WPC Analysis 319
Software Available for Nonparametric Linkage Analysis 322
Summary 323
References 323
12. Linkage Disequilibrium and Association Analysis 329
Eden R. Martin
Introduction 329
Linkage Disequilibrium 330
Measures of Allelic Association 330
Causes of Allelic Association 331
Mapping Genes Using Linkage Disequilibrium 334
Tests for Association 335
Case–Control Tests 335
Family-Based Tests of Association 340
Analysis of Haplotype Data 345
Association Tests for Quantitative Traits 347
Association and Genomic Screening 347
Special Populations 348
Summary 349
References 349
13. Sample Size and Power 355
Yi-Ju Li, Susan Shao, and Marcy Speer
Introduction 355
Power Studies for Linkage Analysis: Mendelian Disease 358
Information Content of Pedigrees 358
Computer Simulation Methods 359
Definitions for Power Assessments 363
Power Studies for Linkage Analysis: Complex Disease 365
Discrete Traits 367
Quantitative Traits 373
Power Studies for Association Analysis 376
Transmission/Disequilibrium Test for Discrete Traits 378
Transmission/Disequilibrium Test for Quantitative Traits 380
Case–Control Study Design 380
DNA Pooling 381
Genomic Screening Strategies for Association Studies 381
Simulation of Linkage and Association Program 382
Summary 383
Appendix 13.1: Example of Monte Carlo Simulation Assuming That Trait and Marker Loci Are Unlinked to Each Other 384
Appendix 13.2: Example LOD Score Results for Pedigree in Figure 13.2 385
Appendix 13.3: Example of Simulation of Genetic Marker Genotypes Conditional on Trait Phenotypes Allowing for Complete and Reduced Penetrance 386
References 393
14. Complex Genetic Interactions 397
William K. Scott and Joellen M. Schildkraut
Introduction 397
Evidence for Complex Genetic Interactions Genetic Heterogeneity 398
Genetic Heterogeneity 398
Gene–Gene Interaction (Epistasis) 399
Gene–Environment Interaction 400
Analytic Approaches to Detection of Complex Interactions 401
Segregation Analysis 402
Linkage Analysis 402
Association Analysis 406
Potential Biases 414
Conclusion 415
References 415
15. Genomics and Bioinformatics 423
Judith E. Stenger and Simon G. Gregory
Introduction 423
Era of the Genome 423
Mapping the Human Genome 424
Genetic Mapping 425
Radiation Hybrid Mapping 427
Physical Mapping 428
Public Data Repositories and Genome Browsers 432
Single-Nucleotide Polymorphisms 434
SNP Discovery 435
Utilizing SNPs 436
Computational SNP Resources 437
Model Organisms 438
Identifying Candidate Genes by Genomic Convergence 439
De Novo Annotation of Genes 440
Software Suites 441
Online Sequence Analysis Resources 441
Understanding Molecular Mechanisms of Disease 442
Assigning Gene Function 442
Looking Beyond Genome Sequence 444
Other Databases 445
Summary 446
References 448
16. Designing a Study for Identifying. Genes in Complex Traits 455
Jonathan L. Haines and Margaret A. Pericak-Vance
Introduction 455
Components of a Disease Gene Discovery Study 457
Define Phenotype 459
Develop Study Design 460
Analysis 463
Follow-Up 464
Keys to a Successful Study 465
Foster Interaction of Necessary Expertise 465
Develop Careful Study Design 466
References 467
Index 469
About the Author :
JONATHAN L. HAINES is Director of the Program in Human Genetics, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine. His research into the localization and identification of genes involved in human disease includes studying Alzheimer's disease, multiple sclerosis, Parkinson's disease, autism, macular degeneration, and other complex diseases. MARGARET A. PERICAK-VANCE is Director of the Center for Human Genetics and Chief of the Section of Medical Genetics in the Department of Medicine, Duke University School of Medicine. She is a founding Fellow of the American College of Medical Genetics. Her research interests include the integration of genomic and statistical technologies and their application to diseases of importance to public health, with an emphasis on neurologic diseases.
