Genetic Analysis of Complex Diseases

William K. Scott, PhD, is Professor at the University of Miami Leonard M. Miller School of Medicine where he teaches design and analysis of human genomic studies. He has authored over 200 peer-reviewed articles on the genetic epidemiology of complex traits.Marylyn D. Ritchie, PhD, is Professor in the Department of Genetics at the University of Pennsylvania, Perelman School of Medicine. She is also the Director of the Center for Translational Bioinformatics in the Institute for Biomedical Informatics. She has authored over 350 peer-reviewed articles on statistical genetics, translational bioinformatics and biomedical informatics.

• List of Contributors xvForeword xvii1 Designing a Study for Identifying Genes in Complex Traits 1William K. Scott, Marylyn D. Ritchie, Jonathan L. Haines,and Margaret A. Pericak-VanceIntroduction 1Components of a Disease Gene Discovery Study 3Define Disease Phenotype 4Clinical Definition 4Determining that a Trait Has a Genetic Component 5Identification of Datasets 5Develop Study Design 5Family-Based Studies 6Population-Based Studies 6Approaches for Gene Discovery 7Analysis 7Genomic Analysis 7Statistical Analysis 8Bioinformatics 8Follow-up 8Variant Detection 8Replication 9Functional Studies 9Keys to a Successful Study 10Foster Interaction of Necessary Expertise 10Develop Careful Study Design 11References 112 Basic Concepts in Genetics 13 Kayla Fourzali, Abigail Deppen, and Elizabeth HeiseIntroduction 13Historical Contributions 13Segregation and Linkage Analysis 13Hardy–Weinberg Equilibrium 14DNA, Genes, and Chromosomes 17Structure of DNA 17Genes and Alleles 19Genes and Chromosomes 20Genes, Mitosis, and Meiosis 22When Genes and Chromosomes Segregate Abnormally 25Inheritance Patterns in Mendelian Disease 25Autosomal Recessive 25Autosomal Dominant 25X-linked Inheritance 28Mitochondrial Inheritance 29Y-linked 29Genetic Changes Associated with Disease/ Trait Phenotypes 29Mutations Versus Polymorphisms 29Point Mutations 30Sickle Cell Anemia 30Achondroplasia 30Deletion/Insertion Mutations 31Duchenne and Becker Muscular Dystrophy 31Cystic Fibrosis 31Charcot-Marie- Tooth Disease 31Nucleotide Repeat Disorders 32Susceptibility Versus Causative Genes 32Summary 34References 343 Determining the Genetic Component of a Disease 36Allison Ashley Koch and Evadnie RampersaudIntroduction 36Study Design 37Selecting a Study Population 37Population-Based 38Clinic-Based 38Ascertainment 38Single Affected Individual 39Relative Pairs 40Extended Families 40Healthy or Unaffected Controls 41Ascertainment Bias 42Approaches to Determining the Genetic Component of a Disease 44Co-segregation with Chromosomal Abnormalities and Other Genetic Disorders 44Familial Aggregation 44Family History Approach 44Example of Calculating Attributable Fraction 46Correlation Coefficients 46Twin and Adoption Studies 47Recurrence Risk in Relatives of Affected Individuals 48Heritability 49Example Using Correlation Coefficients to Calculate Heritability 50Segregation Analysis 51Summary 52References 534 Study Design for Genetic Studies 58Dana C. Crawford and Logan DumitrescuIntroduction 58Selecting a Study Population 58Family- Based Studies (Linkage) 59Family- Based Studies (Association) 60Studies of Unrelated Individuals (Association) 61Cohort Studies 61Cross- Sectional Studies 66Case– Control Studies 66Other Study Designs 68Biobanks 69Other Biobanks 71Biospecimens for Biobanks 72Summary 73References 745 Responsible Conduct of Research in Genetic Studies 79Susan Estabrooks Hahn, Adam Buchanan, Chantelle Wolpert,and Susan H. BlantonIntroduction 79Research Regulations and Genetics Research 80Addressing Pertinent ELSI in Genetic Research 83Genetic Discrimination 83Privacy and Confidentiality 84Certificate of Confidentiality 85Coding Data and Samples 85Secondary Subjects 86Future Use of Samples/Data Sharing 87Handling of Research Results 88CLIA Regulations: Separation of Research and Clinical Laboratories 89Releasing Children’s Genetic Research Results 90DNA Ownership 90DNA Banking 90Family Coercion 91Practical Methods for Efficient High-Quality Genetic Research Services 91The Investigator as the Genetic Study Coordinator 92Time Spent 92Recruitment 93Support Groups and Organizations 93Referrals from Health Care Providers 93Research Databases and the Internet 94Institution Databases 94Medical Clinics 94Recruitment by Family Members 95Informed Consent 95Vulnerable Populations 96Minors 97Persons with Cognitive Impairment 97Data and Sample Collection 97Sample Collection 97Confirmation of Diagnosis 98The Art of Field Studies 99Referring for Additional Medical Services 99Maintaining Contact with Participants 100Future Considerations 100References 1006 Linkage Analysis 105Susan H. BlantonDisease Gene Discovery 107Ability to Detect Linkage 116Real World Example of LOD Score Calculation and Interpretation 117Disease Gene Localization 120Multipoint Analysis 121Effects of Misspecified Model Parameters in LOD Score Analysis 124Impact of Incorrect Disease Allele Frequency 124Impact of Incorrect Mode of Inheritance 125Impact of Incorrect Disease Penetrance 125Impact of Incorrect Marker Allele Frequency 126Control of Scoring Errors 127Genetic Heterogeneity 128Practical Approach for Model-Based Linkage Analysis of Complex Traits 131Nonparametric Linkage Analysis 133Identity by State and Identity by Descent 134Methods for Nonparametric Linkage Analysis 136Tests for Linkage Using Affected Sibling Pairs (ASP) 137Test Based on Identity by State 137Tests Based on Identity by Descent in ASPs 138Simple Tests 138Tests Applicable When IBD Status Cannot Be Determined 139Multipoint Affected Sib-Pair Methods 141Handling Sibships with More Than 2 Affected Siblings 142Methods Incorporating Affected Relative Pairs 142NPL Analysis 143Fitting Population Parameters 145Power Analysis and Experimental Design Considerations for Qualitative Traits 147Factors Influencing Power of Sib-pair Methods 147The Example of Testicular Cancer 148Examples of Sib-Pair Methods for Mapping Complex Traits 150Mapping Quantitative Traits 151Measuring Genetic Effects in Quantitative Traits 152Study Design for Quantitative Trait Linkage Analysis 154Haseman–Elston Regression 155Variance Components Linkage Analysis 156Nonparametric Methods 158The Future 159Software Available 160References 1607 Data Management 169 Stephen D. Turner and William S. BushDeveloping a Data Organization Strategy 170A Brief Overview of Data Normalization 170Database Management System (DBMS) and Structured Query Language (SQL) 172Partitioning Data by Type 173Sequence-Level Data 174Sample-Level Data 174Database Implementation 175Hardware and Software Requirements 175Implementation and Performance Tuning 175Interacting with the Database Directly 176Security 177Other Tools for Data Management and Manipulation 177R 177PLINK 178SAMtools 178Workflow Management and Cloud Computing 178Conclusion 179References 1798 Linkage Disequilibrium and Association Analysis 182Eden R. Martin and Ren-HuaChungIntroduction 182Linkage Disequilibrium 182Measures of Allelic Association 183Causes of Allelic Association 184Mapping Genes Using Linkage Disequilibrium 186Tests of Association 187Case–Control Tests 188Test Statistics 188Measures of Disease Association and Impact 189Assessing Confounding Bias 191Family-Based Tests of Association 192The Transmission/Disequilibrium Test 192Tests Using Unaffected Sibling Controls 194Tests Using Extended Pedigrees 195Regression and Likelihood-Based Methods 196Association Tests with Quantitative Traits 197Analysis of Haplotype Data 197Genome-Wide Association Studies (GWAS) 198Special Populations 199HapMap 2001000 Genomes Project 200Summary 201References 2019 Genome-Wide Association Studies 205 Jacob L. McCauley, Yogasudha Veturi, Shefali Setia Verma, and Marylyn D. RitchieIntroduction 205Definition of GWAS 206Purpose of GWAS 206Design 206Technologies for High-Density Genotyping 206Discrete and Quantitative Trait Analysis 208Case–Control, Family-Based, and Cohort Study Designs 209Statistical Power for Association and Correction for Testing Multiple Hypotheses 211Data Analysis 212Quality Control on Genotyping Call Data 212Initial Genotyping Quality Control 213Sample-Level Quality Control 214SNP-Level Quality Control 215Software Programs for Quality Control 215Population Structure 216Imputation 219Genetic Association Testing 220Meta-Analysis and “Mega-Analysis” 221Whole-Genome Regression-Based GWAS 222Conclusion 222References 22210 Bioinformatics of Human Genetic Disease Studies 228Dale J. HedgesIntroduction 228Common Threads Genome Analysis 229A Brief Note on Study Design 229Data Format Manipulation 229Planning for Adequate Computational Resources 230Storage 231Processing and Memory 232Networking 232Genomics in the Cloud 232Processing and Analysis of Genomic Data 233Array-Based Data 233DNA Arrays and High-Throughput Genotyping 233Preprocessing and Initial Quality Control 234Genotype Calling 234Call Efficiency 235Data Cleaning and Additional Quality Control 236Inferring Structural Variation From SNP-based Array Data 236A Note on Statistical Analysis and Interpretation of Results 236Array-Based Analysis of Gene Expression 237Batch Effects and Data Normalization 237Differential Expression 238Classification and Clustering Methods 239Visualization of Expression Data 240Pathway and Network Analyses 240Direct Counting and Other Expression Assay Procedures 241Additional Uses for Oligonucleotide Arrays 242High-Throughput Sequencing Methods for Genomics 243Introduction 243High-Throughput Sequencing for Genotype Inference 244Expression Analysis from High-Throughput Sequencing Data – RNA-Seq 252ChIP-Seq and Methylation-based Sequences 255Bioinformatics Resources 256Annotation of Genomic Data 257Genome Browsers as Versatile Tools 258Bioinformatics Frameworks and Workflows 259Crowdsourcing and Troubleshooting 260Data Sharing 260References 26111 Complex Genetic Interactions/Data Mining/Dimensionality Reduction 265William S. Bush and Stephen D. TurnerHuman Diseases Are Complex 265Complexity of Biological Systems 266Genetic Heterogeneity 267Statistical and Mathematical Concepts of Complex Genetic Models 268Analytic Approaches to the Detection of Complex Interactions 270Linkage Analysis/Genomic Sharing 270Association Analysis 270Genome‐Wide Association Analysis 272Conclusion 273References 27312 Sample Size, Power, and Data Simulation 278Sarah A. Pendergrass and Marylyn D. RitchieIntroduction 278Sample Size and Power 279Power Calculations and Simulation 282Power Studies for Association Analysis 282Software for Calculating Power for Association Studies, Family- or Population-Based 283PGA: Power for Genetic Association Analyses 283Fine-Mapping Power Calculator 284Quanto 284PAWE: Power for Association with Errors 284PAWE-3D 284GPC: Genetic Power Calculator 284CaTS 284INPower 284Software for Calculating Power for Transmission Disequilibrium Testing (TDT) and Affected Sib-Pair Testing (ASP) 284GPC: Genetic Power Calculator 284TDT-PC: Transmission Disequilibrium Test Power Calculator 284TDTASP 285TDTPOWER 285ASP/ASPSHARE 285Simulation Software for Association Study Power Assessment 285Backward and Forward Model Simulations 285Coalescent Model Simulation – Short Genetic Sequences 286Larger Coalescent Simulated Models 286Forward Model Simulations – Short Genetic Sequences 286Forward Model Simulations – Large Genetic Sequences 286Resampling Simulation Tools 287Software for Simulation of Phenotypic Data 287Power Simulations for Linkage Analysis 288Definitions for Power Assessments for Linkage Analysis 288Computer Simulation Methods for Linkage Analysis of Mendelian Disease 289SIMLINK 289SLINK: Simulation Program for Linkage Analysis 289SUP: Slink Utility Program 290ALLEGRO 290MERLIN: Multipoint Engine for Rapid Likelihood Inference 290SimPED 290Power Studies for Linkage Analysis – Complex Disease 290Inclusion of Unaffected Siblings 291Affected Relative Pairs of Other Types 291Other Considerations 291Genomic Screening Strategies: One-Stage versus Two-Stage Designs 291Software for Designing Linkage Analysis Studies of Complex Disease 292SIMLA 292Quantitative Traits 292Extreme Discordant Pairs 292Sampling Consideration for the Variance Component Method 293Software for Designing Linkage Analysis Studies for Quantitative Traits 294SOLAR: Sequential Oligogenic Linkage Analysis Routines 294MERLIN: Multipoint Engine for Rapid Likelihood Inference 294SimuPOP 294Summary 294References 294Index 298