Statistical Genetics and Genomics

  1. Post-GWAS Analysis
    1. Fine-Mapping Strategies
      1. Statistical Fine-Mapping
        1. Conditional Analysis
          1. Stepwise Regression
            1. Bayesian Fine-Mapping
            2. Credible Sets
              1. 95% Credible Sets
                1. 99% Credible Sets
                  1. Interpretation and Limitations
                  2. Functional Fine-Mapping
                    1. Integration with Functional Data
                      1. Prioritization Strategies
                    2. Functional Annotation of Variants
                      1. Variant Effect Prediction
                        1. Coding Variants
                          1. Regulatory Variants
                            1. Splicing Variants
                            2. Annotation Databases
                              1. dbSNP
                                1. ClinVar
                                  1. GWAS Catalog
                                    1. RegulomeDB
                                    2. Functional Prediction Tools
                                      1. SIFT
                                        1. PolyPhen
                                          1. CADD Scores
                                            1. DANN Scores
                                          2. Expression Quantitative Trait Loci
                                            1. eQTL Study Design
                                              1. Tissue Selection
                                                1. Sample Size Considerations
                                                  1. Confounding Factors
                                                  2. cis-eQTL Analysis
                                                    1. Local Association Testing
                                                      1. Distance Thresholds
                                                        1. Multiple Testing Correction
                                                        2. trans-eQTL Analysis
                                                          1. Genome-Wide Testing
                                                            1. Network Analysis
                                                              1. Regulatory Pathways
                                                              2. Allele-Specific Expression
                                                                1. Detection Methods
                                                                  1. Phasing Requirements
                                                                    1. Interpretation Challenges
                                                                  2. Chromatin Interaction Analysis
                                                                    1. Chromosome Conformation Capture
                                                                      1. 3C Technology
                                                                        1. 4C and 5C Extensions
                                                                          1. Hi-C Method
                                                                          2. Chromatin Loops and Domains
                                                                            1. Topologically Associating Domains
                                                                              1. Loop Detection Algorithms
                                                                                1. Functional Interpretation
                                                                                2. Integration with GWAS
                                                                                  1. Promoter-Enhancer Interactions
                                                                                    1. Long-Range Regulation
                                                                                      1. Target Gene Identification
                                                                                    2. Gene Set and Pathway Analysis
                                                                                      1. Gene-Based Association Tests
                                                                                        1. VEGAS Method
                                                                                          1. MAGMA Analysis
                                                                                            1. Aggregation Strategies
                                                                                            2. Pathway Enrichment Analysis
                                                                                              1. Gene Ontology Analysis
                                                                                                1. KEGG Pathway Analysis
                                                                                                  1. Reactome Analysis
                                                                                                  2. Network-Based Analysis
                                                                                                    1. Protein-Protein Interactions
                                                                                                      1. Co-expression Networks
                                                                                                        1. Regulatory Networks

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                                                                                                    6. Genome-Wide Association Studies

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                                                                                                    8. Next-Generation Sequencing in Genetics