Cancer Genomics

  1. Types of Genomic Alterations in Cancer
    1. Overview of Genomic Alterations
      1. Classification Systems
        1. Frequency Distributions
          1. Tissue-Specific Patterns
            1. Temporal Acquisition
            2. Point Mutations
              1. Single Nucleotide Variants
                1. Transition Mutations
                  1. Transversion Mutations
                    1. Mutational Mechanisms
                    2. Functional Consequences
                      1. Missense Mutations
                        1. Nonsense Mutations
                          1. Silent Mutations
                            1. Splice Site Mutations
                            2. Small Insertions and Deletions
                              1. Frameshift Mutations
                                1. In-frame Indels
                                  1. Microsatellite Instability
                                2. Structural Variations
                                  1. Large-Scale Rearrangements
                                    1. Deletions
                                      1. Duplications
                                        1. Inversions
                                          1. Translocations
                                          2. Complex Rearrangements
                                            1. Chromothripsis
                                              1. Chromoplexy
                                                1. Kataegis
                                                2. Gene Fusions
                                                  1. Formation Mechanisms
                                                    1. Functional Consequences
                                                      1. Oncogenic Fusions
                                                    2. Copy Number Alterations
                                                      1. Amplifications
                                                        1. Focal Amplifications
                                                          1. Broad Amplifications
                                                            1. Oncogene Amplification
                                                            2. Deletions
                                                              1. Homozygous Deletions
                                                                1. Hemizygous Deletions
                                                                  1. Tumor Suppressor Loss
                                                                  2. Aneuploidy
                                                                    1. Whole Chromosome Gains
                                                                      1. Whole Chromosome Losses
                                                                        1. Chromosomal Instability
                                                                      2. Epigenetic Alterations
                                                                        1. DNA Methylation Changes
                                                                          1. CpG Island Hypermethylation
                                                                            1. Global Hypomethylation
                                                                              1. Methylation Patterns
                                                                              2. Histone Modifications
                                                                                1. Acetylation Changes
                                                                                  1. Methylation Changes
                                                                                    1. Chromatin States
                                                                                    2. Chromatin Remodeling
                                                                                      1. Nucleosome Positioning
                                                                                        1. Chromatin Accessibility
                                                                                          1. Remodeling Complex Mutations
                                                                                        2. Transcriptomic Alterations
                                                                                          1. Expression Level Changes
                                                                                            1. Oncogene Overexpression
                                                                                              1. Tumor Suppressor Downregulation
                                                                                                1. Pathway Dysregulation
                                                                                                2. Splicing Alterations
                                                                                                  1. Alternative Splicing
                                                                                                    1. Splice Site Mutations
                                                                                                      1. Splicing Factor Mutations
                                                                                                      2. Non-coding RNA Dysregulation
                                                                                                        1. MicroRNA Alterations
                                                                                                          1. Long Non-coding RNA Changes
                                                                                                            1. Regulatory RNA Networks

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                                                                                                        1. Introduction to Cancer Genomics

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                                                                                                        3. Genomic Technologies and Methods