Human population genomics : introduction to essential concepts and applications /
Kirk E. Lohmueller, Rasmus Nielsen, editors.
Bok Engelsk 2021 · Llibres electrònics
glg
| Medvirkende | |
|---|---|
| Omfang | 1 online resource (IX, 234 p. 51 illus., 20 illus. in color.)
|
| Utgave | 1st ed. 2021.
|
| Opplysninger | Intro -- Preface -- Contents -- Part I Population Genetic Theory -- 1 Coalescent Models -- 1.1 Aims and Clarifications -- 1.2 Introduction: Gene Genealogies Within a Population or Species -- 1.2.1 Organismal Pedigrees and Gene Genealogies -- 1.3 The Standard Neutral Model: The Kingman Coalescent -- 1.3.1 The Sampling Structure of Coalescent Gene Genealogies -- 1.3.2 Including Mutations in the Coalescent -- 1.4 Fundamental Predictions for Single Loci in Well-Mixed Populations -- 1.4.1 The Size and Shape of a Gene Genealogy -- 1.4.2 Levels and Patterns of Genetic Variation -- 1.4.3 Tests of the Standard Neutral Coalescent Based on Site Frequencies -- 1.5 Extensions of the Standard Model -- 1.5.1 Fluctuations in Population Size over Time -- 1.5.2 Population Subdivision and Migration -- 1.6 Conclusion: Current Challenges of Big Data -- References -- 2 Linkage Disequilibrium -- 2.1 Introduction -- 2.2 Tests of whether D == 0 -- 2.3 More than Two Alleles per Locus -- 2.4 More than Two Loci: Haplotype Blocks and the HapMap Project -- 2.5 Dynamics of D -- 2.6 Genetic Drift and LD -- 2.7 Genealogical Interpretation of LD -- 2.8 Natural Selection and LD -- 2.9 Genetic Hitchhiking -- 2.10 Population Subdivision -- 2.11 Conclusion -- References -- 3 Analysis of Population Structure -- 3.1 What Is Population Structure? -- 3.2 Individual-Based and Unsupervised Methods for Inferring Population Structure -- 3.2.1 Tree Construction Methods at the Individual Level -- 3.2.2 Principal Component Analysis and Related Approaches -- 3.2.3 Ancestry Component Estimation with Few Model Assumptions -- 3.3 Population-Based and Supervised Methods -- 3.3.1 Genetic Differentiation at the Population Level -- 3.3.1.1 FST -- 3.3.1.2 Other Measures of Genetic Distance -- 3.3.2 Formal Tests for Admixture Under a Population Tree-Model -- 3.3.3 More Advanced Modeling.. - 3.3.3.1 Population Graph Fitting -- 3.3.3.2 Isolation-Migration Models -- 3.3.3.3 Approximate Bayesian Computation -- 3.4 Summary and Guidelines -- References -- 4 Types of Natural Selection and Tests of Selection -- 4.1 Types of Selection and Their Effect on Linked Neutral Sites -- 4.1.1 Types of Selection -- 4.1.2 The Effect of Selection on Linked Neutral Sites -- 4.2 Tests of Selection -- 4.2.1 Tests of Selection Based on the Site Frequency Spectrum -- 4.2.1.1 Tajima's D -- 4.2.1.2 Fay and Wu's H -- 4.2.1.3 Likelihood Ratio Tests -- 4.2.2 Tests of Selection Based on Haplotypes -- 4.2.2.1 Extended Haplotype Homozygosity (EHH) -- 4.2.2.2 Integrated Haplotype Score (iHS) -- 4.2.2.3 Cross-Population EHH (XP-EHH) -- 4.2.3 Tests Based on both Diversity and Divergence:The McDonald-Kreitman Test -- 4.3 How to Choose a Specific Test of Selection? -- References -- Part II Association Studies and Medical Genetics -- 5 Methods for Association Studies -- 5.1 Introduction -- 5.2 Types of Association Studies -- 5.2.1 Candidate Gene Studies -- 5.2.2 Genome-Wide Association Studies -- 5.2.2.1 Background -- 5.2.2.2 Multistage Study Designs -- 5.2.2.3 Limitations -- 5.2.3 Mendelian Randomization -- 5.2.4 Transcriptome-Wide Association Studies -- 5.2.5 Replication and Meta-analysis -- 5.2.5.1 Replication -- 5.2.5.2 Meta-analysis -- 5.3 Design of Association Studies -- 5.3.1 Quantitative Versus Qualitative Traits -- 5.3.2 Subject Selection -- 5.3.3 Sample Size -- 5.4 Measurement of Genetic Information -- 5.4.1 Common Variants -- 5.4.2 Rare Variants -- 5.5 Data Analysis -- 5.5.1 Quality Control -- 5.5.2 Data Imputation -- 5.5.3 Analysis of Common Variants -- 5.5.4 Analysis of Rare Variants -- 5.5.5 Incorporating External Information into Association Study Analyses -- 5.5.5.1 Gene Set Analysis -- 5.5.5.2 Hierarchical Modeling -- 5.5.6 Interactions.. - 5.5.7 Incorporating Covariates -- 5.5.7.1 Population Stratification -- 5.5.7.2 Addressing Other Confounding -- 5.5.7.3 Improving Precision -- 5.5.8 Multiple Testing -- 5.5.8.1 Bonferroni and Number of Effective Independent Tests -- 5.5.8.2 Permutation Testing -- 5.5.8.3 False Discovery Rate -- 5.5.8.4 Bayesian Approach -- 5.6 Concluding Remarks -- References -- 6 Identity by Descent in the Mapping of Genetic Traits -- 6.1 Introduction -- 6.1.1 Identity by Descent -- 6.1.2 From Descent to Gene Mapping -- 6.1.3 Outline of the Chapter -- 6.2 Probabilities of IBD -- 6.2.1 IBD in Defined Relatives -- 6.2.2 IBD in Populations -- 6.2.3 Probabilities of Genotypic Data Given IBD -- 6.2.4 Probabilities of Phenotypic Data Given IBD -- 6.3 Inferring in Pedigrees and Populations -- 6.3.1 IBD Given Marker Data on Relatives -- 6.3.2 Monte Carlo Realization of IBD in Defined Pedigrees -- 6.3.3 Inference of Realized Kinship or Relatedness -- 6.3.4 IBD Given Marker Data in Populations -- 6.4 IBD-Based Genetic Mapping -- 6.4.1 Mapping from IBD in Pedigrees -- 6.4.2 IBD in Pedigree-Based Likelihoods -- 6.4.3 Mapping from IBD in Populations -- 6.4.4 Model-Based Mapping Likelihoods in Populations -- 6.5 Summary -- References -- 7 What Have We Learned from GWAS? -- 7.1 Introduction -- 7.2 Lessons over Eight Years of Association Studies (2006-2013) -- 7.2.1 Study Design, Quality Control, and the Search for Technical Biases -- 7.2.2 Addressing Confounding from Population Stratification -- 7.2.3 Threshold for Declaring Significant Genome-Wide Results -- 7.2.4 Best Practices for In Silico Statistical Imputation -- 7.2.5 Collecting Evidence Across Studies via Meta-Analysis -- 7.3 Uncovering the Biology and Architecture of Complex Traits -- 7.3.1 Complex Traits Are Differentially Complicated -- 7.3.2 The (Un)Explained Heritability for Complex Traits.. - 7.3.3 The Data Are Consistent with a Strong Polygenic Component -- 7.3.4 Complex Traits Share a Genetic Basis in Common Across Populations -- 7.3.5 The Identification of Unknown Mechanisms for Disease Pathogenesis -- 7.3.6 The Importance of Phenotypic Collection in Study Designs -- 7.3.7 Challenges with Interpreting the Distribution of Effects and Frequencies -- 7.3.8 Observational Epidemiology and Genetics Need Not Always Agree -- 7.4 What Lies Just Beyond the Horizon for GWAS? -- 7.4.1 Custom Genotyping Arrays Technologies for Genetic Studies -- 7.4.2 Analysis of Multiple Phenotypic Measurements and Outcomes -- 7.4.3 Genetic Fine Mapping for Complex Trait Loci -- 7.4.4 Genetic Studies of Complex Traits across Ethnicities -- 7.4.5 Integration of System-Based and "Omics" Approaches with Genetics -- 7.4.6 Uniting Findings from GWAS with Sequencing Studies -- 7.5 Closing Thoughts -- References -- Part III Human Evolutionary Population Genetics -- 8 Inferring Human Demographic History from Genetic Data -- 8.1 Introduction -- 8.2 Human Population Structure -- 8.3 Effective Population Size -- 8.4 Population Bottlenecks -- 8.5 Sex Ratio -- 8.6 Estimating Demographic Parameters -- 8.7 Ancient Admixture -- 8.8 Other Ancient DNA Studies -- 8.9 Conclusion -- References -- 9 Natural Selection, Genetic Variation, and Human Diversity -- 9.1 Introduction -- 9.2 Amount of Selection in the Human Genome -- 9.2.1 Balancing Selection -- 9.2.2 Negative Selection -- 9.2.3 Positive Selection -- 9.3 Demography and Selection -- 9.4 Empirical Studies of Positive Selection -- 9.4.1 Single Gene Studies -- 9.4.2 Genome-Wide Scans for Selection -- 9.4.2.1 Insights from Genome-Wide Scans -- 9.4.2.2 Improving Genome-Wide Scans -- 9.5 Selection and Population Differentiation -- 9.6 Conclusions -- References.. - This textbook provides a concise introduction and useful overview of the field of human population genomics, making the highly technical and contemporary aspects more accessible to students and researchers from various fields. Over the past decade, there has been a deluge of genetic variation data from the entire genome of individuals from many populations. These data have allowed an unprecedented look at human history and how natural selection has impacted humans during this journey. Simultaneously, there have been increased efforts to determine how genetic variation affects complex traits in humans. Due to technological and methodological advances, progress has been made at determining the architecture of complex traits. Split in three parts, the book starts with the basics, followed by more advanced and current research. The first part provides an introduction to essential concepts in population genetics, which are relevant for any organism. The second part covers the genetics of complex traits in humans. The third part focuses on applying these techniques and concepts to genetic variation data to learn about demographic history and natural selection in humans. This new textbook aims to serve as a gateway to modern human population genetics research for those new to the field. It provides an indispensable resource for students, researchers and practitioners from disparate areas of expertise.
|
| Emner | |
| Sjanger | |
| ISBN | 3-030-61646-0
|
