cancer-genomics-evidence

name	cancer-genomics-evidence
description	Synthesize public cancer genomic alterations across genes, cohorts, molecular profiles, clinical annotations, and literature. Use for somatic landscape, biomarker, resistance, or translational oncology research.
license	MIT

Cancer Genomics Evidence

1. Define cancer type/subtype, stage, cohort, sample/patient unit, gene/variant, alteration class, molecular profile, and clinical endpoint.
2. Resolve genes with cBioPortal/NCBI/Ensembl; retrieve cohort evidence from cBioPortal and curated clinical interpretation from CIViC/ClinVar only where applicable.
3. Preserve study version, assay coverage, tumor purity, sample count, denominator, alteration definition, co-occurrence method, and missing data.
4. Separate prevalence, prognosis, predictive association, functional mechanism, resistance, and clinical actionability.
5. Compare cohorts without pooling incompatible eligibility, ancestry, platform, treatment, or follow-up.

Return cohort-specific evidence, conflicts, bias/coverage limitations, and validation steps. Never present research output as patient-specific interpretation.

Record cohort queries and denominator decisions with $science-provenance; run $science-review before translational claims.