Statistical Genetics and Genomics

  1. Genome-Wide Association Studies
    1. GWAS Study Design
      1. Phenotype Considerations
        1. Trait Definition and Measurement
          1. Phenotype Quality Control
            1. Covariate Selection
            2. Sample Collection
              1. Population Selection
                1. Sample Size Calculations
                  1. Power Analysis
                  2. Genotyping Strategy
                    1. SNP Array Selection
                      1. Coverage and Density
                        1. Imputation Strategies
                      2. Genotyping Technologies
                        1. SNP Arrays
                          1. Array Design Principles
                            1. Probe Selection
                              1. Signal Processing
                              2. Quality Control Procedures
                                1. Sample-Level QC
                                  1. SNP-Level QC
                                    1. Batch Effects
                                      1. Population Stratification Checks
                                    2. Statistical Analysis of GWAS
                                      1. Single-Marker Tests
                                        1. Linear Regression
                                          1. Logistic Regression
                                            1. Score Tests
                                            2. Genetic Models
                                              1. Additive Model
                                                1. Dominant Model
                                                  1. Recessive Model
                                                    1. Genotypic Model
                                                    2. Covariate Adjustment
                                                      1. Population Structure
                                                        1. Demographic Variables
                                                          1. Technical Covariates
                                                        2. Multiple Testing Correction
                                                          1. Bonferroni Correction
                                                            1. Calculation and Application
                                                              1. Conservative Nature
                                                              2. False Discovery Rate
                                                                1. Benjamini-Hochberg Procedure
                                                                  1. q-values
                                                                  2. Permutation Testing
                                                                    1. Empirical P-values
                                                                      1. Computational Considerations
                                                                      2. Genome-Wide Significance
                                                                        1. Standard Thresholds
                                                                          1. Suggestive Significance
                                                                        2. GWAS Results Interpretation
                                                                          1. Manhattan Plots
                                                                            1. Construction and Interpretation
                                                                              1. Significance Lines
                                                                              2. Q-Q Plots
                                                                                1. Expected vs Observed P-values
                                                                                  1. Inflation Assessment
                                                                                  2. Regional Association Plots
                                                                                    1. LocusZoom Plots
                                                                                      1. Linkage Disequilibrium Patterns
                                                                                      2. Effect Size Interpretation
                                                                                        1. Odds Ratios
                                                                                          1. Beta Coefficients
                                                                                            1. Variance Explained
                                                                                          2. Meta-Analysis of GWAS
                                                                                            1. Fixed Effects Models
                                                                                              1. Inverse Variance Weighting
                                                                                                1. Assumptions and Limitations
                                                                                                2. Random Effects Models
                                                                                                  1. Between-Study Heterogeneity
                                                                                                    1. DerSimonian-Laird Method
                                                                                                    2. Quality Control in Meta-Analysis
                                                                                                      1. Study Selection Criteria
                                                                                                        1. Harmonization of Phenotypes
                                                                                                          1. Population Matching

                                                                                                      Previous

                                                                                                      5. Association Studies

                                                                                                      Go to top

                                                                                                      Next

                                                                                                      7. Post-GWAS Analysis