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| Summary of Commonly Used Notation | |
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| Overview of Genetic Epidemiology | |
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| The Process of Genetic Epidemiology | |
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| Descriptive Epidemiology and Hypothesis Generation | |
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| Familial Aggregation | |
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| Segregation Analysis | |
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| Linkage Analysis | |
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| Fine Mapping and Cloning | |
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| Candidate Gene Association Studies | |
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| Characterizing the Effects of Cloned Genes | |
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| Conclusions | |
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| Basic Concepts of Molecular Genetics | |
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| Chromosomes | |
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| Cell Division | |
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| Cell Cycle | |
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| Mitosis | |
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| Meiosis | |
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| Genetic Recombination | |
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| Meiotic Recombination | |
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| Mitotic Recombination | |
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| DNA | |
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| Gene Expression | |
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| Transcription | |
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| RNA Processing | |
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| Translation | |
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| Post-Translational Modification | |
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| DNA Polymorphism | |
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| Conclusions | |
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| Principles of Mendelian Inheritance | |
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| Basic Concepts | |
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| Mendelian Inheritance at a Single Locus | |
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| Classical Autosomal Dominant Inheritance | |
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| Classical Autosomal Recessive Inheritance | |
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| Classical X-Linked Inheritance | |
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| Multiallelic Loci | |
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| Mendelian Inheritance at Two Loci | |
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| Conclusions | |
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| Basic Epidemiologic and Statistical Principles | |
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| Basic Probability Theory | |
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| Basic Epidemiologic Principles | |
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| Study Designs | |
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| Measures of Disease Frequency and Association | |
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| Interpretation of Epidemiologic Associations | |
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| Maximum Likelihood | |
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| Generalized Estimating Equations | |
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| Markov Chain Monte Carlo Methods | |
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| Randomization Procedures | |
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| Conclusions | |
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| Familial Aggregation | |
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| Genetic Relationships and Gene Identity | |
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| Formal Derivation of [phi] and [Delta] | |
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| Familial Correlations of Continuous Phenotypes | |
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| Familial Risk of Disease | |
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| The Concept of Familial Risk | |
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| Design Principles | |
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| Analytical Approaches | |
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| Other Designs | |
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| Randomization Tests of Familial Clustering | |
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| Twin Studies | |
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| Adoption Studies | |
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| Approaches to Dependent Data | |
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| Genetic Models | |
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| Regressive Models | |
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| Frailty Models | |
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| Generalized Estimating Equations | |
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| Conclusions | |
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| Segregation Analysis | |
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| Design Issues | |
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| Ascertainment of Families | |
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| Sequential Sampling | |
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| Classical Methods for Sibships | |
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| Ascertainment Correction | |
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| Likelihood Methods for Pedigree Analysis | |
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| General Model | |
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| Polygenic and Mixed Models | |
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| Penetrance Models | |
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| The Elston-Stewart Peeling Algorithm | |
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| Hypothesis Testing | |
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| Alternative Methods | |
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| Gibbs Sampling | |
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| Generalized Estimating Equations | |
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| Applications to Breast Cancer | |
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| Conclusions | |
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| Linkage Analysis | |
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| Recombination and Map Functions | |
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| Direct Counting Methods | |
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| Relative Pair Methods | |
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| Identity by State and by Descent | |
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| Affected Sib Pair Methods | |
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| Affected Relative Pair Methods | |
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| Sib Pair Methods for Quantitative Traits | |
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| Generalized Estimating Equation Methods | |
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| Lod Score Methods | |
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| Two-Point Linkage | |
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| Joint Segregation and Linkage Analysis and the Mod Score | |
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| Multipoint Linkage and Ordering Loci | |
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| Genome-Wide Scans | |
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| Genetic Heterogeneity | |
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| Gibbs Sampling Methods | |
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| Design Issues | |
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| Power and Sample Size | |
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| Selection Bias and Misspecification | |
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| Fine Mapping and Cloning of BRCA1 | |
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| Conclusions | |
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| Principles of Population Genetics | |
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| Distribution of Genes at a Single Locus | |
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| Hardy-Weinberg Equilibrium in Large Populations | |
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| Genetic Drift in Finite Populations | |
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| Effects of Mutation and Selection | |
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| Distribution of Genes at Two Loci | |
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| Origins of Linkage Disequilibrium | |
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| Decay of Linkage Disequilibrium | |
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| Estimation of Linkage Disequilibrium | |
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| Evolution of Haplotypes | |
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| Ancestral Inference | |
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| Coalescent Trees | |
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| Ancestral Recombination Graphs | |
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| Conclusions | |
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| Testing Candidate Gene Associations | |
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| Distributions of Genes in Affected and Unaffected Individuals | |
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| Homogeneous Populations | |
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| Ethnically Stratified Populations | |
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| Families | |
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| Design Options for Association Studies | |
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| Cohort Study Designs | |
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| Case-Control Designs | |
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| Parental Controls and the Transmission/Disequilibrium Test | |
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| Family-Based Association Tests | |
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| Quantitative Traits | |
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| Conclusions | |
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| Linkage Disequilibrium Mapping | |
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| Recently Admixed Populations | |
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| Isolated Populations | |
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| Empiric Methods for Estimating the Location of a Disease Gene or Mutation | |
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| Haplotype Sharing Methods | |
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| Parametric Methods Based on the Coalescent | |
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| How Much Linkage Disequilibrium Is There in the Human Genome? | |
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| Haplotype Block Structure | |
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| Conclusions | |
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| Gene Characterization | |
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| Estimation of Genetic Risks | |
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| Cohort and Case-Control Designs Using Unrelated Subjects | |
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| Familial Cohort Study Designs | |
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| Multistage Sampling and Countermatching | |
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| Relative Efficiency of the Alternative Designs | |
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| Gene-Environment and Gene-Gene Interactions | |
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| Case-Control Designs | |
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| Case-Only Studies | |
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| Case-Parent Trios | |
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| Gene-Environment Interactions for Breast Cancer | |
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| Relative Efficiency of Alternative Designs for Interaction Effects | |
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| Estimation of Gene Frequencies and Carrier Probabilities | |
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| Searching for Additional Genes | |
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| Conclusions | |
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| Tying It All Together: the Genetic Epidemiology of Colorectal Cancer | |
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| History, Descriptive Epidemiology, and Familiality | |
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| Mechanistic Hypotheses | |
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| Models of Carcinogenesis | |
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| Cancer Genes | |
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| Genomic Instability | |
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| Familial Cancer Syndromes | |
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| Familial Adenomatous Polyposis | |
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| Hereditary Nonpolyposis Colorectal Cancer | |
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| Sporadic Cancers | |
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| Genetic Alterations in Colorectal Cancer | |
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| Pathways: Suppressor and Mutator | |
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| Metabolic Pathways | |
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| The Relationship Between Polyps and Colorectal Cancer | |
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| Discovery of Novel Colorectal Cancer Genes | |
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| Implications for Clinical Management | |
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| The Future | |
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| Genome-Wide Scans for Association and Interactions | |
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| Gene Expression Assays | |
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| DNA Methylation and Loss of Imprinting | |
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| Conclusions | |
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| Glossary | |
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| References | |
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| Index | |