Cancer Genomics

  1. Major Resources and Databases
    1. Large-Scale Genomic Projects
      1. The Cancer Genome Atlas
        1. Project Overview
          1. Data Types
            1. Key Findings
            2. International Cancer Genome Consortium
              1. Global Collaboration
                1. Data Standards
                  1. Major Contributions
                  2. Pediatric Cancer Genome Project
                    1. Childhood Cancer Focus
                      1. Unique Findings
                        1. Clinical Impact
                      2. Public Data Repositories
                        1. Genomic Data Commons
                          1. Data Access
                            1. Analysis Tools
                              1. Harmonized Data
                              2. European Genome-phenome Archive
                                1. Controlled Access Data
                                  1. International Collaboration
                                    1. Data Sharing Policies
                                    2. Sequence Read Archive
                                      1. Raw Sequencing Data
                                        1. Data Submission
                                          1. Access Methods
                                        2. Variant and Mutation Databases
                                          1. Catalogue of Somatic Mutations in Cancer
                                            1. Mutation Data
                                              1. Gene Information
                                                1. Clinical Annotations
                                                2. ClinVar
                                                  1. Clinical Significance
                                                    1. Variant Interpretation
                                                      1. Evidence Levels
                                                      2. Database of Single Nucleotide Polymorphisms
                                                        1. Population Variants
                                                          1. Frequency Data
                                                            1. Functional Annotations
                                                          2. Analysis Platforms
                                                            1. cBioPortal for Cancer Genomics
                                                              1. Data Visualization
                                                                1. Analysis Tools
                                                                  1. Multi-study Comparisons
                                                                  2. Genome Aggregation Database
                                                                    1. Population Reference
                                                                      1. Constraint Metrics
                                                                        1. Variant Interpretation
                                                                        2. Ensembl Genome Browser
                                                                          1. Genome Annotation
                                                                            1. Comparative Genomics
                                                                              1. Variant Effect Prediction
                                                                            2. Clinical Databases
                                                                              1. OncoKB
                                                                                1. Therapeutic Implications
                                                                                  1. Evidence Levels
                                                                                    1. Clinical Annotations
                                                                                    2. CIViC
                                                                                      1. Clinical Interpretations
                                                                                        1. Community Curation
                                                                                          1. Evidence Summaries
                                                                                          2. Precision Medicine Knowledge Base
                                                                                            1. Treatment Guidelines
                                                                                              1. Drug Interactions
                                                                                                1. Clinical Trials

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                                                                                            6. Clinical Applications

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                                                                                            8. Challenges and Future Directions