depmap

# DepMap — Cancer Dependency Map ## Overview The Cancer Dependency Map (DepMap) project, run by the Broad Institute, systematically characterizes genetic dependencies across hundreds of cancer cell lines using genome-wide CRISPR knockout screens (DepMap CRISPR), RNA interference (RNAi), and compound sensitivity assays (PRISM). DepMap data is essential for: - Identifying which genes are essential for specific cancer types - Finding cancer-selective dependencies (therapeutic targets) - Validating oncology drug targets - Discovering synthetic lethal interactions **Key resources:** - DepMap Portal: https://depmap.org/portal/ - DepMap data downloads: https://depmap.org/portal/download/all/ - Python package: `depmap` (or access via API/downloads) - API: https://depmap.org/portal/api/ ## When to Use This Skill Use DepMap when: - **Target validation**: Is a gene essential for survival in cancer cell lines with a specific mutation (e.g., KRAS-mutant)? - **Biomarker discovery**: What genomic features predict sensitivity to knockout of a gene? - **Synthetic lethality**: Find genes that are selectively essential when another gene is mutated/deleted - **Drug sensitivity**: What cell line features predict response to a compound? - **Pan-cancer essentiality**: Is a gene broadly essential across all cancer types (bad target) or selectively essential? - **Correlation analysis**: Which pairs of genes have correlated dependency profiles (co-essentiality)? ## Core Concepts ### Dependency...