Cancer Genomics

  1. Cancer Genomic Landscapes
    1. Pan-Cancer Genomic Patterns
      1. Common Alterations Across Cancers
        1. Frequently Mutated Genes
          1. Recurrent Structural Variations
            1. Universal Cancer Pathways
            2. Cancer Type-Specific Patterns
              1. Tissue-Specific Mutations
                1. Organ-Specific Pathways
                  1. Histology-Dependent Alterations
                2. Driver Gene Identification
                  1. Statistical Approaches
                    1. Mutation Frequency Analysis
                      1. Functional Impact Scoring
                        1. Pathway Enrichment
                        2. Functional Validation
                          1. In Vitro Assays
                            1. In Vivo Models
                              1. Clinical Evidence
                              2. Core Cancer Pathways
                                1. Cell Cycle Control
                                  1. DNA Damage Response
                                    1. Growth Factor Signaling
                                      1. Apoptosis Regulation
                                    2. Mutational Processes
                                      1. Endogenous Mutational Processes
                                        1. Replication Errors
                                          1. Spontaneous DNA Damage
                                            1. Oxidative Stress
                                            2. Exogenous Mutational Processes
                                              1. UV Radiation
                                                1. Chemical Carcinogens
                                                  1. Viral Integration
                                                  2. DNA Repair Deficiency
                                                    1. Mismatch Repair Deficiency
                                                      1. Homologous Recombination Deficiency
                                                        1. Base Excision Repair Defects
                                                        2. Mutational Signatures
                                                          1. Signature Extraction
                                                            1. Signature Attribution
                                                              1. Clinical Applications
                                                            2. Tumor Evolution
                                                              1. Clonal Evolution Models
                                                                1. Linear Evolution
                                                                  1. Branched Evolution
                                                                    1. Neutral Evolution
                                                                    2. Phylogenetic Reconstruction
                                                                      1. Tree Building Methods
                                                                        1. Temporal Ordering
                                                                          1. Ancestral State Reconstruction
                                                                          2. Selection Pressures
                                                                            1. Positive Selection
                                                                              1. Negative Selection
                                                                                1. Neutral Drift
                                                                              2. Tumor Heterogeneity
                                                                                1. Intratumor Heterogeneity
                                                                                  1. Spatial Heterogeneity
                                                                                    1. Temporal Heterogeneity
                                                                                      1. Functional Heterogeneity
                                                                                      2. Subclonal Architecture
                                                                                        1. Clonal Deconvolution
                                                                                          1. Subclone Quantification
                                                                                            1. Evolution Dynamics
                                                                                            2. Clinical Implications
                                                                                              1. Treatment Resistance
                                                                                                1. Biomarker Reliability
                                                                                                  1. Sampling Strategies

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                                                                                              4. Bioinformatics and Data Analysis

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                                                                                              6. Clinical Applications