Statistical Genetics and Genomics

  1. Association Studies
    1. Principles of Association Analysis
      1. Direct vs Indirect Association
        1. Causal Variants
          1. Tagging Variants
            1. Linkage Disequilibrium Patterns
            2. Study Design Considerations
              1. Population Selection
                1. Phenotype Definition
                  1. Sample Size Requirements
                  2. Types of Association Studies
                    1. Candidate Gene Studies
                      1. Genome-Wide Association Studies
                        1. Targeted Sequencing Studies
                      2. Case-Control Association Studies
                        1. Study Design
                          1. Case Definition and Ascertainment
                            1. Control Selection
                              1. Matching Strategies
                              2. Statistical Analysis
                                1. Contingency Table Analysis
                                  1. Chi-squared Tests
                                    1. Fisher's Exact Test
                                      1. Odds Ratios and Confidence Intervals
                                      2. Logistic Regression Models
                                        1. Single-Marker Analysis
                                          1. Covariate Adjustment
                                            1. Interaction Testing
                                          2. Quantitative Trait Association
                                            1. Linear Regression Models
                                              1. Additive Models
                                                1. Dominant and Recessive Models
                                                  1. Genotypic Models
                                                  2. Effect Size Estimation
                                                    1. Beta Coefficients
                                                      1. Variance Explained
                                                        1. Standardized Effect Sizes
                                                        2. Non-Normal Traits
                                                          1. Transformation Methods
                                                            1. Generalized Linear Models
                                                              1. Robust Regression Methods
                                                            2. Population Stratification
                                                              1. Causes and Consequences
                                                                1. Ancestry Differences
                                                                  1. Cryptic Relatedness
                                                                    1. Admixture Effects
                                                                    2. Detection Methods
                                                                      1. Genomic Control
                                                                        1. Principal Component Analysis
                                                                          1. Multidimensional Scaling
                                                                          2. Correction Methods
                                                                            1. Structured Association
                                                                              1. Linear Mixed Models
                                                                                1. Family-Based Controls

                                                                            Previous

                                                                            4. Linkage Analysis and Gene Mapping

                                                                            Go to top

                                                                            Next

                                                                            6. Genome-Wide Association Studies