Cancer Genomics

  1. Genomic Technologies and Methods
    1. Sample Collection and Processing
      1. Sample Types
        1. Fresh Frozen Tissue
          1. Formalin-Fixed Paraffin-Embedded
            1. Blood Samples
              1. Bone Marrow
              2. Sample Quality Assessment
                1. Tumor Content Evaluation
                  1. Nucleic Acid Quality
                    1. Contamination Assessment
                    2. Sample Preparation
                      1. Microdissection Techniques
                        1. Nucleic Acid Extraction
                          1. Library Preparation
                        2. DNA Sequencing Technologies
                          1. Next-Generation Sequencing Platforms
                            1. Illumina Sequencing
                              1. Ion Torrent Sequencing
                                1. Platform Comparison
                                2. Long-Read Sequencing
                                  1. Pacific Biosciences
                                    1. Oxford Nanopore
                                      1. Applications and Advantages
                                      2. Sequencing Approaches
                                        1. Whole Genome Sequencing
                                          1. Whole Exome Sequencing
                                            1. Targeted Panel Sequencing
                                            2. Single-Cell DNA Sequencing
                                              1. Technical Challenges
                                                1. Applications in Cancer
                                                  1. Data Analysis Considerations
                                                2. RNA Sequencing Technologies
                                                  1. Bulk RNA Sequencing
                                                    1. Library Preparation Methods
                                                      1. Sequencing Depth Considerations
                                                        1. Applications in Cancer
                                                        2. Single-Cell RNA Sequencing
                                                          1. Technical Workflow
                                                            1. Computational Challenges
                                                              1. Cancer Applications
                                                              2. Specialized RNA-Seq
                                                                1. Small RNA Sequencing
                                                                  1. Long Non-coding RNA Sequencing
                                                                    1. Ribosome Profiling
                                                                  2. Other Genomic Technologies
                                                                    1. Array-Based Methods
                                                                      1. SNP Arrays
                                                                        1. Expression Arrays
                                                                          1. Methylation Arrays
                                                                          2. Targeted Detection Methods
                                                                            1. Digital PCR
                                                                              1. Quantitative PCR
                                                                                1. In Situ Hybridization
                                                                                2. Proteomics Technologies
                                                                                  1. Mass Spectrometry
                                                                                    1. Protein Arrays
                                                                                      1. Immunohistochemistry
                                                                                    2. Quality Control and Validation
                                                                                      1. Sequencing Quality Metrics
                                                                                        1. Read Quality Assessment
                                                                                          1. Coverage Analysis
                                                                                            1. Contamination Detection
                                                                                            2. Validation Methods
                                                                                              1. Orthogonal Technology Validation
                                                                                                1. Functional Validation
                                                                                                  1. Clinical Validation

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                                                                                              2. Types of Genomic Alterations in Cancer

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                                                                                              4. Bioinformatics and Data Analysis