Statistical Genetics and Genomics

  1. Advanced Statistical Methods
    1. Polygenic Risk Scores
      1. PRS Construction Methods
        1. Clumping and Thresholding
          1. Bayesian Methods
            1. Machine Learning Approaches
            2. SNP Selection Strategies
              1. P-value Thresholds
                1. LD Pruning
                  1. Functional Prioritization
                  2. Weighting Schemes
                    1. Effect Size Weighting
                      1. Inverse Variance Weighting
                        1. Bayesian Weighting
                        2. PRS Validation
                          1. Cross-Validation
                            1. Independent Validation
                              1. Transferability Across Populations
                              2. Clinical Applications
                                1. Risk Stratification
                                  1. Personalized Medicine
                                    1. Ethical Considerations
                                  2. Mendelian Randomization
                                    1. Principles and Assumptions
                                      1. Instrumental Variable Framework
                                        1. Three Core Assumptions
                                          1. Violation Detection
                                          2. Single-Instrument MR
                                            1. Wald Ratio Method
                                              1. Confidence Intervals
                                                1. Weak Instrument Bias
                                                2. Multiple-Instrument MR
                                                  1. Inverse Variance Weighted Method
                                                    1. MR-Egger Regression
                                                      1. Weighted Median Method
                                                      2. Two-Sample MR
                                                        1. Summary Statistics Approach
                                                          1. Data Harmonization
                                                            1. Population Matching
                                                            2. Sensitivity Analysis
                                                              1. Pleiotropy Detection
                                                                1. Outlier Detection
                                                                  1. Robust Methods
                                                                2. Transcriptome-Wide Association Studies
                                                                  1. Gene Expression Imputation
                                                                    1. Reference Panels
                                                                      1. Prediction Models
                                                                        1. Cross-Validation
                                                                        2. TWAS Statistical Framework
                                                                          1. Association Testing
                                                                            1. Multiple Testing Correction
                                                                              1. Conditional Analysis
                                                                              2. Integration with GWAS
                                                                                1. Colocalization Analysis
                                                                                  1. Fine-Mapping Integration
                                                                                    1. Causal Gene Identification
                                                                                  2. Multi-Omics Integration
                                                                                    1. Data Types and Platforms
                                                                                      1. Genomics Data
                                                                                        1. Transcriptomics Data
                                                                                          1. Epigenomics Data
                                                                                            1. Proteomics Data
                                                                                              1. Metabolomics Data
                                                                                              2. Integration Strategies
                                                                                                1. Early Integration
                                                                                                  1. Intermediate Integration
                                                                                                    1. Late Integration
                                                                                                    2. Network-Based Approaches
                                                                                                      1. Multi-Layer Networks
                                                                                                        1. Network Propagation
                                                                                                          1. Module Detection
                                                                                                          2. Machine Learning Methods
                                                                                                            1. Dimensionality Reduction
                                                                                                              1. Feature Selection
                                                                                                                1. Ensemble Methods