{"product_id":"genetic-analysis-of-complex-disease-isbn-9781118123911","title":"Genetic Analysis of Complex Disease","description":"\u003cb\u003eGenetic Analysis of Complex Diseases\u003c\/b\u003e \u003cp\u003e\u003cb\u003eAn up-to-date and complete treatment of the strategies, designs and analysis methods for studying complex genetic disease in human beings \u003c\/b\u003e \u003c\/p\u003e\u003cp\u003eIn the newly revised Third Edition of \u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e, a team of distinguished geneticists delivers a comprehensive introduction to the most relevant strategies, designs and methods of analysis for the study of complex genetic disease in humans. The book focuses on concepts and designs, thereby offering readers a broad understanding of common problems and solutions in the field based on successful applications in the design and execution of genetic studies.  \u003c\/p\u003e\u003cp\u003eThis edited volume contains contributions from some of the leading voices in the area and presents new chapters on high-throughput genomic sequencing, copy-number variant analysis and epigenetic studies. Providing clear and easily referenced overviews of the considerations involved in genetic analysis of complex human genetic disease, including sampling, design, data collection, linkage and association studies and social, legal and ethical issues.  \u003c\/p\u003e\u003cp\u003e\u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e also provides:  \u003c\/p\u003e\u003cul\u003e\n\u003cli\u003eA thorough introduction to study design for the identification of genes in complex traits\u003c\/li\u003e \u003cli\u003eComprehensive explorations of basic concepts in genetics, disease phenotype definition and the determination of the genetic components of disease\u003c\/li\u003e \u003cli\u003ePractical discussions of modern bioinformatics tools for analysis of genetic data\u003c\/li\u003e \u003cli\u003eReflecting on responsible conduct of research in genetic studies, as well as linkage analysis and data management\u003c\/li\u003e \u003cli\u003eNew expanded chapter on complex genetic interactions\u003c\/li\u003e\n\u003c\/ul\u003e \u003cp\u003eThis latest edition of \u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e is a must-read resource for molecular biologists, human geneticists, genetic epidemiologists and pharmaceutical researchers. It is also invaluable for graduate students taking courses in statistical genetics or genetic epidemiology. \u003c\/p\u003e\u003cp\u003eList of Contributors xv\u003c\/p\u003e \u003cp\u003eForeword xvii\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Designing a Study for Identifying Genes in Complex Traits \u003c\/b\u003e\u003cb\u003e1\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eWilliam K. Scott, Marylyn D. Ritchie, Jonathan L. Haines,and Margaret A. Pericak-Vance\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 1\u003c\/p\u003e \u003cp\u003eComponents of a Disease Gene Discovery Study 3\u003c\/p\u003e \u003cp\u003eDefine Disease Phenotype 4\u003c\/p\u003e \u003cp\u003eClinical Definition 4\u003c\/p\u003e \u003cp\u003eDetermining that a Trait Has a Genetic Component 5\u003c\/p\u003e \u003cp\u003eIdentification of Datasets 5\u003c\/p\u003e \u003cp\u003eDevelop Study Design 5\u003c\/p\u003e \u003cp\u003eFamily-Based Studies 6\u003c\/p\u003e \u003cp\u003ePopulation-Based Studies 6\u003c\/p\u003e \u003cp\u003eApproaches for Gene Discovery 7\u003c\/p\u003e \u003cp\u003eAnalysis 7\u003c\/p\u003e \u003cp\u003eGenomic Analysis 7\u003c\/p\u003e \u003cp\u003eStatistical Analysis 8\u003c\/p\u003e \u003cp\u003eBioinformatics 8\u003c\/p\u003e \u003cp\u003eFollow-up 8\u003c\/p\u003e \u003cp\u003eVariant Detection 8\u003c\/p\u003e \u003cp\u003eReplication 9\u003c\/p\u003e \u003cp\u003eFunctional Studies 9\u003c\/p\u003e \u003cp\u003eKeys to a Successful Study 10\u003c\/p\u003e \u003cp\u003eFoster Interaction of Necessary Expertise 10\u003c\/p\u003e \u003cp\u003eDevelop Careful Study Design 11\u003c\/p\u003e \u003cp\u003eReferences 11\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Basic Concepts in Genetics \u003c\/b\u003e\u003cb\u003e13 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eKayla Fourzali, Abigail Deppen, and Elizabeth Heise\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 13\u003c\/p\u003e \u003cp\u003eHistorical Contributions 13\u003c\/p\u003e \u003cp\u003eSegregation and Linkage Analysis 13\u003c\/p\u003e \u003cp\u003eHardy–Weinberg Equilibrium 14\u003c\/p\u003e \u003cp\u003eDNA, Genes, and Chromosomes 17\u003c\/p\u003e \u003cp\u003eStructure of DNA 17\u003c\/p\u003e \u003cp\u003eGenes and Alleles 19\u003c\/p\u003e \u003cp\u003eGenes and Chromosomes 20\u003c\/p\u003e \u003cp\u003eGenes, Mitosis, and Meiosis 22\u003c\/p\u003e \u003cp\u003eWhen Genes and Chromosomes Segregate Abnormally 25\u003c\/p\u003e \u003cp\u003eInheritance Patterns in Mendelian Disease 25\u003c\/p\u003e \u003cp\u003eAutosomal Recessive 25\u003c\/p\u003e \u003cp\u003eAutosomal Dominant 25\u003c\/p\u003e \u003cp\u003eX-linked Inheritance 28\u003c\/p\u003e \u003cp\u003eMitochondrial Inheritance 29\u003c\/p\u003e \u003cp\u003eY-linked 29\u003c\/p\u003e \u003cp\u003eGenetic Changes Associated with Disease\/ Trait Phenotypes 29\u003c\/p\u003e \u003cp\u003eMutations Versus Polymorphisms 29\u003c\/p\u003e \u003cp\u003ePoint Mutations 30\u003c\/p\u003e \u003cp\u003eSickle Cell Anemia 30\u003c\/p\u003e \u003cp\u003eAchondroplasia 30\u003c\/p\u003e \u003cp\u003eDeletion\/Insertion Mutations 31\u003c\/p\u003e \u003cp\u003eDuchenne and Becker Muscular Dystrophy 31\u003c\/p\u003e \u003cp\u003eCystic Fibrosis 31\u003c\/p\u003e \u003cp\u003eCharcot-Marie- Tooth Disease 31\u003c\/p\u003e \u003cp\u003eNucleotide Repeat Disorders 32\u003c\/p\u003e \u003cp\u003eSusceptibility Versus Causative Genes 32\u003c\/p\u003e \u003cp\u003eSummary 34\u003c\/p\u003e \u003cp\u003eReferences 34\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Determining the Genetic Component of a Disease \u003c\/b\u003e\u003cb\u003e36\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eAllison Ashley Koch and Evadnie Rampersaud\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 36\u003c\/p\u003e \u003cp\u003eStudy Design 37\u003c\/p\u003e \u003cp\u003eSelecting a Study Population 37\u003c\/p\u003e \u003cp\u003ePopulation-Based 38\u003c\/p\u003e \u003cp\u003eClinic-Based 38\u003c\/p\u003e \u003cp\u003eAscertainment 38\u003c\/p\u003e \u003cp\u003eSingle Affected Individual 39\u003c\/p\u003e \u003cp\u003eRelative Pairs 40\u003c\/p\u003e \u003cp\u003eExtended Families 40\u003c\/p\u003e \u003cp\u003eHealthy or Unaffected Controls 41\u003c\/p\u003e \u003cp\u003eAscertainment Bias 42\u003c\/p\u003e \u003cp\u003eApproaches to Determining the Genetic Component of a Disease 44\u003c\/p\u003e \u003cp\u003eCo-segregation with Chromosomal Abnormalities and Other Genetic Disorders 44\u003c\/p\u003e \u003cp\u003eFamilial Aggregation 44\u003c\/p\u003e \u003cp\u003eFamily History Approach 44\u003c\/p\u003e \u003cp\u003eExample of Calculating Attributable Fraction 46\u003c\/p\u003e \u003cp\u003eCorrelation Coefficients 46\u003c\/p\u003e \u003cp\u003eTwin and Adoption Studies 47\u003c\/p\u003e \u003cp\u003eRecurrence Risk in Relatives of Affected Individuals 48\u003c\/p\u003e \u003cp\u003eHeritability 49\u003c\/p\u003e \u003cp\u003eExample Using Correlation Coefficients to Calculate Heritability 50\u003c\/p\u003e \u003cp\u003eSegregation Analysis 51\u003c\/p\u003e \u003cp\u003eSummary 52\u003c\/p\u003e \u003cp\u003eReferences 53\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Study Design for Genetic Studies \u003c\/b\u003e\u003cb\u003e58\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eDana C. Crawford and Logan Dumitrescu\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 58\u003c\/p\u003e \u003cp\u003eSelecting a Study Population 58\u003c\/p\u003e \u003cp\u003eFamily- Based Studies (Linkage) 59\u003c\/p\u003e \u003cp\u003eFamily- Based Studies (Association) 60\u003c\/p\u003e \u003cp\u003eStudies of Unrelated Individuals (Association) 61\u003c\/p\u003e \u003cp\u003eCohort Studies 61\u003c\/p\u003e \u003cp\u003eCross- Sectional Studies 66\u003c\/p\u003e \u003cp\u003eCase– Control Studies 66\u003c\/p\u003e \u003cp\u003eOther Study Designs 68\u003c\/p\u003e \u003cp\u003eBiobanks 69\u003c\/p\u003e \u003cp\u003eOther Biobanks 71\u003c\/p\u003e \u003cp\u003eBiospecimens for Biobanks 72\u003c\/p\u003e \u003cp\u003eSummary 73\u003c\/p\u003e \u003cp\u003eReferences 74\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Responsible Conduct of Research in Genetic Studies \u003c\/b\u003e\u003cb\u003e79\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSusan Estabrooks Hahn, Adam Buchanan, Chantelle Wolpert,\u003c\/i\u003e\u003ci\u003eand Susan H. Blanton\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 79\u003c\/p\u003e \u003cp\u003eResearch Regulations and Genetics Research 80\u003c\/p\u003e \u003cp\u003eAddressing Pertinent ELSI in Genetic Research 83\u003c\/p\u003e \u003cp\u003eGenetic Discrimination 83\u003c\/p\u003e \u003cp\u003ePrivacy and Confidentiality 84\u003c\/p\u003e \u003cp\u003eCertificate of Confidentiality 85\u003c\/p\u003e \u003cp\u003eCoding Data and Samples 85\u003c\/p\u003e \u003cp\u003eSecondary Subjects 86\u003c\/p\u003e \u003cp\u003eFuture Use of Samples\/Data Sharing 87\u003c\/p\u003e \u003cp\u003eHandling of Research Results 88\u003c\/p\u003e \u003cp\u003eCLIA Regulations: Separation of Research and Clinical Laboratories 89\u003c\/p\u003e \u003cp\u003eReleasing Children’s Genetic Research Results 90\u003c\/p\u003e \u003cp\u003eDNA Ownership 90\u003c\/p\u003e \u003cp\u003eDNA Banking 90\u003c\/p\u003e \u003cp\u003eFamily Coercion 91\u003c\/p\u003e \u003cp\u003ePractical Methods for Efficient High-Quality Genetic Research Services 91\u003c\/p\u003e \u003cp\u003eThe Investigator as the Genetic Study Coordinator 92\u003c\/p\u003e \u003cp\u003eTime Spent 92\u003c\/p\u003e \u003cp\u003eRecruitment 93\u003c\/p\u003e \u003cp\u003eSupport Groups and Organizations 93\u003c\/p\u003e \u003cp\u003eReferrals from Health Care Providers 93\u003c\/p\u003e \u003cp\u003eResearch Databases and the Internet 94\u003c\/p\u003e \u003cp\u003eInstitution Databases 94\u003c\/p\u003e \u003cp\u003eMedical Clinics 94\u003c\/p\u003e \u003cp\u003eRecruitment by Family Members 95\u003c\/p\u003e \u003cp\u003eInformed Consent 95\u003c\/p\u003e \u003cp\u003eVulnerable Populations 96\u003c\/p\u003e \u003cp\u003eMinors 97\u003c\/p\u003e \u003cp\u003ePersons with Cognitive Impairment 97\u003c\/p\u003e \u003cp\u003eData and Sample Collection 97\u003c\/p\u003e \u003cp\u003eSample Collection 97\u003c\/p\u003e \u003cp\u003eConfirmation of Diagnosis 98\u003c\/p\u003e \u003cp\u003eThe Art of Field Studies 99\u003c\/p\u003e \u003cp\u003eReferring for Additional Medical Services 99\u003c\/p\u003e \u003cp\u003eMaintaining Contact with Participants 100\u003c\/p\u003e \u003cp\u003eFuture Considerations 100\u003c\/p\u003e \u003cp\u003eReferences 100\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Linkage Analysis \u003c\/b\u003e\u003cb\u003e105\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSusan H. Blanton\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eDisease Gene Discovery 107\u003c\/p\u003e \u003cp\u003eAbility to Detect Linkage 116\u003c\/p\u003e \u003cp\u003eReal World Example of LOD Score Calculation and Interpretation 117\u003c\/p\u003e \u003cp\u003eDisease Gene Localization 120\u003c\/p\u003e \u003cp\u003eMultipoint Analysis 121\u003c\/p\u003e \u003cp\u003eEffects of Misspecified Model Parameters in LOD Score Analysis 124\u003c\/p\u003e \u003cp\u003eImpact of Incorrect Disease Allele Frequency 124\u003c\/p\u003e \u003cp\u003eImpact of Incorrect Mode of Inheritance 125\u003c\/p\u003e \u003cp\u003eImpact of Incorrect Disease Penetrance 125\u003c\/p\u003e \u003cp\u003eImpact of Incorrect Marker Allele Frequency 126\u003c\/p\u003e \u003cp\u003eControl of Scoring Errors 127\u003c\/p\u003e \u003cp\u003eGenetic Heterogeneity 128\u003c\/p\u003e \u003cp\u003ePractical Approach for Model-Based Linkage Analysis of Complex Traits 131\u003c\/p\u003e \u003cp\u003eNonparametric Linkage Analysis 133\u003c\/p\u003e \u003cp\u003eIdentity by State and Identity by Descent 134\u003c\/p\u003e \u003cp\u003eMethods for Nonparametric Linkage Analysis 136\u003c\/p\u003e \u003cp\u003eTests for Linkage Using Affected Sibling Pairs (ASP) 137\u003c\/p\u003e \u003cp\u003eTest Based on Identity by State 137\u003c\/p\u003e \u003cp\u003eTests Based on Identity by Descent in ASPs 138\u003c\/p\u003e \u003cp\u003eSimple Tests 138\u003c\/p\u003e \u003cp\u003eTests Applicable When IBD Status Cannot Be Determined 139\u003c\/p\u003e \u003cp\u003eMultipoint Affected Sib-Pair Methods 141\u003c\/p\u003e \u003cp\u003eHandling Sibships with More Than 2 Affected Siblings 142\u003c\/p\u003e \u003cp\u003eMethods Incorporating Affected Relative Pairs 142\u003c\/p\u003e \u003cp\u003eNPL Analysis 143\u003c\/p\u003e \u003cp\u003eFitting Population Parameters 145\u003c\/p\u003e \u003cp\u003ePower Analysis and Experimental Design Considerations for Qualitative Traits 147\u003c\/p\u003e \u003cp\u003eFactors Influencing Power of Sib-pair Methods 147\u003c\/p\u003e \u003cp\u003eThe Example of Testicular Cancer 148\u003c\/p\u003e \u003cp\u003eExamples of Sib-Pair Methods for Mapping Complex Traits 150\u003c\/p\u003e \u003cp\u003eMapping Quantitative Traits 151\u003c\/p\u003e \u003cp\u003eMeasuring Genetic Effects in Quantitative Traits 152\u003c\/p\u003e \u003cp\u003eStudy Design for Quantitative Trait Linkage Analysis 154\u003c\/p\u003e \u003cp\u003eHaseman–Elston Regression 155\u003c\/p\u003e \u003cp\u003eVariance Components Linkage Analysis 156\u003c\/p\u003e \u003cp\u003eNonparametric Methods 158\u003c\/p\u003e \u003cp\u003eThe Future 159\u003c\/p\u003e \u003cp\u003eSoftware Available 160\u003c\/p\u003e \u003cp\u003eReferences 160\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Data Management \u003c\/b\u003e\u003cb\u003e169 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eStephen D. Turner and William S. Bush\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eDeveloping a Data Organization Strategy 170\u003c\/p\u003e \u003cp\u003eA Brief Overview of Data Normalization 170\u003c\/p\u003e \u003cp\u003eDatabase Management System (DBMS) and Structured Query Language (SQL) 172\u003c\/p\u003e \u003cp\u003ePartitioning Data by Type 173\u003c\/p\u003e \u003cp\u003eSequence-Level Data 174\u003c\/p\u003e \u003cp\u003eSample-Level Data 174\u003c\/p\u003e \u003cp\u003eDatabase Implementation 175\u003c\/p\u003e \u003cp\u003eHardware and Software Requirements 175\u003c\/p\u003e \u003cp\u003eImplementation and Performance Tuning 175\u003c\/p\u003e \u003cp\u003eInteracting with the Database Directly 176\u003c\/p\u003e \u003cp\u003eSecurity 177\u003c\/p\u003e \u003cp\u003eOther Tools for Data Management and Manipulation 177\u003c\/p\u003e \u003cp\u003eR 177\u003c\/p\u003e \u003cp\u003ePLINK 178\u003c\/p\u003e \u003cp\u003eSAMtools 178\u003c\/p\u003e \u003cp\u003eWorkflow Management and Cloud Computing 178\u003c\/p\u003e \u003cp\u003eConclusion 179\u003c\/p\u003e \u003cp\u003eReferences 179\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Linkage Disequilibrium and Association Analysis \u003c\/b\u003e\u003cb\u003e182\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eEden R. Martin and Ren-HuaChung\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 182\u003c\/p\u003e \u003cp\u003eLinkage Disequilibrium 182\u003c\/p\u003e \u003cp\u003eMeasures of Allelic Association 183\u003c\/p\u003e \u003cp\u003eCauses of Allelic Association 184\u003c\/p\u003e \u003cp\u003eMapping Genes Using Linkage Disequilibrium 186\u003c\/p\u003e \u003cp\u003eTests of Association 187\u003c\/p\u003e \u003cp\u003eCase–Control Tests 188\u003c\/p\u003e \u003cp\u003eTest Statistics 188\u003c\/p\u003e \u003cp\u003eMeasures of Disease Association and Impact 189\u003c\/p\u003e \u003cp\u003eAssessing Confounding Bias 191\u003c\/p\u003e \u003cp\u003eFamily-Based Tests of Association 192\u003c\/p\u003e \u003cp\u003eThe Transmission\/Disequilibrium Test 192\u003c\/p\u003e \u003cp\u003eTests Using Unaffected Sibling Controls 194\u003c\/p\u003e \u003cp\u003eTests Using Extended Pedigrees 195\u003c\/p\u003e \u003cp\u003eRegression and Likelihood-Based Methods 196\u003c\/p\u003e \u003cp\u003eAssociation Tests with Quantitative Traits 197\u003c\/p\u003e \u003cp\u003eAnalysis of Haplotype Data 197\u003c\/p\u003e \u003cp\u003eGenome-Wide Association Studies (GWAS) 198\u003c\/p\u003e \u003cp\u003eSpecial Populations 199\u003c\/p\u003e \u003cp\u003eHapMap 200\u003c\/p\u003e \u003cp\u003e1000 Genomes Project 200\u003c\/p\u003e \u003cp\u003eSummary 201\u003c\/p\u003e \u003cp\u003eReferences 201\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Genome-Wide Association Studies \u003c\/b\u003e\u003cb\u003e205 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eJacob L. McCauley, Yogasudha Veturi, Shefali Setia Verma, and Marylyn D. Ritchie\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 205\u003c\/p\u003e \u003cp\u003eDefinition of GWAS 206\u003c\/p\u003e \u003cp\u003ePurpose of GWAS 206\u003c\/p\u003e \u003cp\u003eDesign 206\u003c\/p\u003e \u003cp\u003eTechnologies for High-Density Genotyping 206\u003c\/p\u003e \u003cp\u003eDiscrete and Quantitative Trait Analysis 208\u003c\/p\u003e \u003cp\u003eCase–Control, Family-Based, and Cohort Study Designs 209\u003c\/p\u003e \u003cp\u003eStatistical Power for Association and Correction for Testing Multiple Hypotheses 211\u003c\/p\u003e \u003cp\u003eData Analysis 212\u003c\/p\u003e \u003cp\u003eQuality Control on Genotyping Call Data 212\u003c\/p\u003e \u003cp\u003eInitial Genotyping Quality Control 213\u003c\/p\u003e \u003cp\u003eSample-Level Quality Control 214\u003c\/p\u003e \u003cp\u003eSNP-Level Quality Control 215\u003c\/p\u003e \u003cp\u003eSoftware Programs for Quality Control 215\u003c\/p\u003e \u003cp\u003ePopulation Structure 216\u003c\/p\u003e \u003cp\u003eImputation 219\u003c\/p\u003e \u003cp\u003eGenetic Association Testing 220\u003c\/p\u003e \u003cp\u003eMeta-Analysis and “Mega-Analysis” 221\u003c\/p\u003e \u003cp\u003eWhole-Genome Regression-Based GWAS 222\u003c\/p\u003e \u003cp\u003eConclusion 222\u003c\/p\u003e \u003cp\u003eReferences 222\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Bioinformatics of Human Genetic Disease Studies \u003c\/b\u003e\u003cb\u003e228\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eDale J. Hedges\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 228\u003c\/p\u003e \u003cp\u003eCommon Threads Genome Analysis 229\u003c\/p\u003e \u003cp\u003eA Brief Note on Study Design 229\u003c\/p\u003e \u003cp\u003eData Format Manipulation 229\u003c\/p\u003e \u003cp\u003ePlanning for Adequate Computational Resources 230\u003c\/p\u003e \u003cp\u003eStorage 231\u003c\/p\u003e \u003cp\u003eProcessing and Memory 232\u003c\/p\u003e \u003cp\u003eNetworking 232\u003c\/p\u003e \u003cp\u003eGenomics in the Cloud 232\u003c\/p\u003e \u003cp\u003eProcessing and Analysis of Genomic Data 233\u003c\/p\u003e \u003cp\u003eArray-Based Data 233\u003c\/p\u003e \u003cp\u003eDNA Arrays and High-Throughput Genotyping 233\u003c\/p\u003e \u003cp\u003ePreprocessing and Initial Quality Control 234\u003c\/p\u003e \u003cp\u003eGenotype Calling 234\u003c\/p\u003e \u003cp\u003eCall Efficiency 235\u003c\/p\u003e \u003cp\u003eData Cleaning and Additional Quality Control 236\u003c\/p\u003e \u003cp\u003eInferring Structural Variation From SNP-based Array Data 236\u003c\/p\u003e \u003cp\u003eA Note on Statistical Analysis and Interpretation of Results 236\u003c\/p\u003e \u003cp\u003eArray-Based Analysis of Gene Expression 237\u003c\/p\u003e \u003cp\u003eBatch Effects and Data Normalization 237\u003c\/p\u003e \u003cp\u003eDifferential Expression 238\u003c\/p\u003e \u003cp\u003eClassification and Clustering Methods 239\u003c\/p\u003e \u003cp\u003eVisualization of Expression Data 240\u003c\/p\u003e \u003cp\u003ePathway and Network Analyses 240\u003c\/p\u003e \u003cp\u003eDirect Counting and Other Expression Assay Procedures 241\u003c\/p\u003e \u003cp\u003eAdditional Uses for Oligonucleotide Arrays 242\u003c\/p\u003e \u003cp\u003eHigh-Throughput Sequencing Methods for Genomics 243\u003c\/p\u003e \u003cp\u003eIntroduction 243\u003c\/p\u003e \u003cp\u003eHigh-Throughput Sequencing for Genotype Inference 244\u003c\/p\u003e \u003cp\u003eExpression Analysis from High-Throughput Sequencing Data – RNA-Seq 252\u003c\/p\u003e \u003cp\u003eChIP-Seq and Methylation-based Sequences 255\u003c\/p\u003e \u003cp\u003eBioinformatics Resources 256\u003c\/p\u003e \u003cp\u003eAnnotation of Genomic Data 257\u003c\/p\u003e \u003cp\u003eGenome Browsers as Versatile Tools 258\u003c\/p\u003e \u003cp\u003eBioinformatics Frameworks and Workflows 259\u003c\/p\u003e \u003cp\u003eCrowdsourcing and Troubleshooting 260\u003c\/p\u003e \u003cp\u003eData Sharing 260\u003c\/p\u003e \u003cp\u003eReferences 261\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Complex Genetic Interactions\/Data Mining\/Dimensionality Reduction \u003c\/b\u003e\u003cb\u003e265\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eWilliam S. Bush and Stephen D. Turner\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eHuman Diseases Are Complex 265\u003c\/p\u003e \u003cp\u003eComplexity of Biological Systems 266\u003c\/p\u003e \u003cp\u003eGenetic Heterogeneity 267\u003c\/p\u003e \u003cp\u003eStatistical and Mathematical Concepts of Complex Genetic Models 268\u003c\/p\u003e \u003cp\u003eAnalytic Approaches to the Detection of Complex Interactions 270\u003c\/p\u003e \u003cp\u003eLinkage Analysis\/Genomic Sharing 270\u003c\/p\u003e \u003cp\u003eAssociation Analysis 270\u003c\/p\u003e \u003cp\u003eGenome‐Wide Association Analysis 272\u003c\/p\u003e \u003cp\u003eConclusion 273\u003c\/p\u003e \u003cp\u003eReferences 273\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Sample Size, Power, and Data Simulation \u003c\/b\u003e\u003cb\u003e278\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSarah A. Pendergrass and Marylyn D. Ritchie\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 278\u003c\/p\u003e \u003cp\u003eSample Size and Power 279\u003c\/p\u003e \u003cp\u003ePower Calculations and Simulation 282\u003c\/p\u003e \u003cp\u003ePower Studies for Association Analysis 282\u003c\/p\u003e \u003cp\u003eSoftware for Calculating Power for Association Studies, Family- or Population-Based 283\u003c\/p\u003e \u003cp\u003ePGA: Power for Genetic Association Analyses 283\u003c\/p\u003e \u003cp\u003eFine-Mapping Power Calculator 284\u003c\/p\u003e \u003cp\u003eQuanto 284\u003c\/p\u003e \u003cp\u003ePAWE: Power for Association with Errors 284\u003c\/p\u003e \u003cp\u003ePAWE-3D 284\u003c\/p\u003e \u003cp\u003eGPC: Genetic Power Calculator 284\u003c\/p\u003e \u003cp\u003eCaTS 284\u003c\/p\u003e \u003cp\u003eINPower 284\u003c\/p\u003e \u003cp\u003eSoftware for Calculating Power for Transmission Disequilibrium Testing (TDT) and Affected Sib-Pair Testing (ASP) 284\u003c\/p\u003e \u003cp\u003eGPC: Genetic Power Calculator 284\u003c\/p\u003e \u003cp\u003eTDT-PC: Transmission Disequilibrium Test Power Calculator 284\u003c\/p\u003e \u003cp\u003eTDTASP 285\u003c\/p\u003e \u003cp\u003eTDTPOWER 285\u003c\/p\u003e \u003cp\u003eASP\/ASPSHARE 285\u003c\/p\u003e \u003cp\u003eSimulation Software for Association Study Power Assessment 285\u003c\/p\u003e \u003cp\u003eBackward and Forward Model Simulations 285\u003c\/p\u003e \u003cp\u003eCoalescent Model Simulation – Short Genetic Sequences 286\u003c\/p\u003e \u003cp\u003eLarger Coalescent Simulated Models 286\u003c\/p\u003e \u003cp\u003eForward Model Simulations – Short Genetic Sequences 286\u003c\/p\u003e \u003cp\u003eForward Model Simulations – Large Genetic Sequences 286\u003c\/p\u003e \u003cp\u003eResampling Simulation Tools 287\u003c\/p\u003e \u003cp\u003eSoftware for Simulation of Phenotypic Data 287\u003c\/p\u003e \u003cp\u003ePower Simulations for Linkage Analysis 288\u003c\/p\u003e \u003cp\u003eDefinitions for Power Assessments for Linkage Analysis 288\u003c\/p\u003e \u003cp\u003eComputer Simulation Methods for Linkage Analysis of Mendelian Disease 289\u003c\/p\u003e \u003cp\u003eSIMLINK 289\u003c\/p\u003e \u003cp\u003eSLINK: Simulation Program for Linkage Analysis 289\u003c\/p\u003e \u003cp\u003eSUP: Slink Utility Program 290\u003c\/p\u003e \u003cp\u003eALLEGRO 290\u003c\/p\u003e \u003cp\u003eMERLIN: Multipoint Engine for Rapid Likelihood Inference 290\u003c\/p\u003e \u003cp\u003eSimPED 290\u003c\/p\u003e \u003cp\u003ePower Studies for Linkage Analysis – Complex Disease 290\u003c\/p\u003e \u003cp\u003eInclusion of Unaffected Siblings 291\u003c\/p\u003e \u003cp\u003eAffected Relative Pairs of Other Types 291\u003c\/p\u003e \u003cp\u003eOther Considerations 291\u003c\/p\u003e \u003cp\u003eGenomic Screening Strategies: One-Stage versus Two-Stage Designs 291\u003c\/p\u003e \u003cp\u003eSoftware for Designing Linkage Analysis Studies of Complex Disease 292\u003c\/p\u003e \u003cp\u003eSIMLA 292\u003c\/p\u003e \u003cp\u003eQuantitative Traits 292\u003c\/p\u003e \u003cp\u003eExtreme Discordant Pairs 292\u003c\/p\u003e \u003cp\u003eSampling Consideration for the Variance Component Method 293\u003c\/p\u003e \u003cp\u003eSoftware for Designing Linkage Analysis Studies for Quantitative Traits 294\u003c\/p\u003e \u003cp\u003eSOLAR: Sequential Oligogenic Linkage Analysis Routines 294\u003c\/p\u003e \u003cp\u003eMERLIN: Multipoint Engine for Rapid Likelihood Inference 294\u003c\/p\u003e \u003cp\u003eSimuPOP 294\u003c\/p\u003e \u003cp\u003eSummary 294\u003c\/p\u003e \u003cp\u003eReferences 294\u003c\/p\u003e \u003cp\u003eIndex 298\u003c\/p\u003e \u003cp\u003e\u003cb\u003eWilliam K. Scott, PhD,\u003c\/b\u003e 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.\u003c\/p\u003e \u003cp\u003e\u003cb\u003eMarylyn D. Ritchie, PhD,\u003c\/b\u003e 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.  \u003c\/p\u003e\u003cp\u003e\u003cb\u003eAn up-to-date and complete treatment of the strategies, designs and analysis methods for studying complex genetic disease in human beings \u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIn the newly revised Third Edition of \u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e, a team of distinguished geneticists delivers a comprehensive introduction to the most relevant strategies, designs and methods of analysis for the study of complex genetic disease in humans. The book focuses on concepts and designs, thereby offering readers a broad understanding of common problems and solutions in the field based on successful applications in the design and execution of genetic studies.  \u003c\/p\u003e\u003cp\u003eThis edited volume contains contributions from some of the leading voices in the area and presents new chapters on high-throughput genomic sequencing, copy-number variant analysis and epigenetic studies. Providing clear and easily referenced overviews of the considerations involved in genetic analysis of complex human genetic disease, including sampling, design, data collection, linkage and association studies and social, legal and ethical issues.  \u003c\/p\u003e\u003cp\u003e\u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e also provides:  \u003c\/p\u003e\u003cul\u003e\n\u003cli\u003eA thorough introduction to study design for the identification of genes in complex traits\u003c\/li\u003e \u003cli\u003eComprehensive explorations of basic concepts in genetics, disease phenotype definition and the determination of the genetic components of disease\u003c\/li\u003e \u003cli\u003ePractical discussions of modern bioinformatics tools for analysis of genetic data\u003c\/li\u003e \u003cli\u003eReflecting on responsible conduct of research in genetic studies, as well as linkage analysis and data management\u003c\/li\u003e \u003cli\u003eNew expanded chapter on complex genetic interactions\u003c\/li\u003e\n\u003c\/ul\u003e \u003cp\u003eThis latest edition of \u003ci\u003eGenetic Analysis of Complex Diseases\u003c\/i\u003e is a must-read resource for molecular biologists, human geneticists, genetic epidemiologists and pharmaceutical researchers. It is also invaluable for graduate students taking courses in statistical genetics or genetic epidemiology.\u003c\/p\u003e","brand":"Wiley-Blackwell","offers":[{"title":"Default Title","offer_id":47989278245093,"sku":"NP9781118123911","price":114.0,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9781118123911.jpg?v=1761783489","url":"https:\/\/k12savings.com\/products\/genetic-analysis-of-complex-disease-isbn-9781118123911","provider":"K12savings","version":"1.0","type":"link"}