Cancer Genomics

Cancer genomics is an interdisciplinary field that applies high-throughput sequencing and bioinformatics to characterize the complete set of DNA and RNA alterations present in cancer cells. By comparing the genome of a tumor to the normal genome of the same individual, researchers can identify the specific somatic mutations, copy number variations, and gene expression changes that drive the initiation and progression of the disease. This detailed molecular profiling provides critical insights into the biological mechanisms of cancer and is fundamental to the development of precision medicine, enabling the discovery of new diagnostic biomarkers and the creation of targeted therapies designed to exploit a tumor's unique genetic vulnerabilities.

1. Introduction to Cancer Genomics
   1. Overview of Cancer Genomics
      1. Definition and Scope
      2. Historical Development of the Field
      3. Importance in Modern Oncology
      4. Key Milestones in Cancer Genomics
   2. Fundamentals of Cancer Biology
      1. Normal Cell Biology
         1. Cell Cycle Regulation
         2. DNA Damage Response
         3. Apoptosis Mechanisms
         4. Cell Differentiation
      2. Cellular Transformation
         1. Mechanisms of Transformation
         2. Loss of Growth Control
         3. Acquisition of Invasive Properties
      3. The Hallmarks of Cancer
         1. Sustaining Proliferative Signaling
         2. Evading Growth Suppressors
         3. Resisting Cell Death
         4. Enabling Replicative Immortality
         5. Inducing Angiogenesis
         6. Activating Invasion and Metastasis
         7. Reprogramming Energy Metabolism
         8. Evading Immune Destruction
         9. Genome Instability and Mutation
         10. Tumor-Promoting Inflammation
      4. Cancer Classification
         1. Histological Classification
         2. Molecular Classification
         3. Staging Systems
   3. Fundamentals of Genomics
      1. Genome Organization
         1. Chromosome Structure
         2. Gene Structure and Organization
         3. Regulatory Elements
         4. Non-coding Regions
      2. Types of Genetic Variation
         1. Single Nucleotide Polymorphisms
         2. Structural Variations
         3. Copy Number Variations
         4. Epigenetic Modifications
      3. Germline vs Somatic Genetics
         1. Inherited Genetic Factors
         2. Acquired Genetic Changes
         3. Implications for Cancer Development
      4. The Human Genome Project
         1. Goals and Achievements
         2. Impact on Cancer Research
         3. Reference Genome Assembly
   4. Cancer Genetics Foundations
      1. Oncogenes
         1. Proto-oncogene Function
         2. Mechanisms of Oncogene Activation
         3. Key Oncogene Examples
      2. Tumor Suppressor Genes
         1. Normal Function
         2. Mechanisms of Inactivation
         3. Two-Hit Hypothesis
         4. Key Tumor Suppressor Examples
      3. DNA Repair Genes
         1. Types of DNA Repair
         2. Hereditary Cancer Syndromes
         3. Repair Deficiency in Cancer
      4. Somatic Mutation Theory
         1. Accumulation of Mutations
         2. Clonal Evolution
         3. Driver vs Passenger Mutations