genomics-precision-medicinelisted

When the user wants to design, build, or integrate genomics and precision-medicine informatics. Use when the user mentions "genomics," "precision medicine," "VCF," "gVCF," "BAM," "CRAM," "FASTQ," "variant calling," "variant annotation," "HGVS," "ACMG," "AMP/CAP/ASCO," "ClinGen," "ClinVar," "PharmGKB," "CPIC," "pharmacogenomics," "PGx," "GA4GH," "VRS," "Phenopackets," "FHIR Genomics," "mCODE," "molecular tumor board," "liquid biopsy," "ctDNA," "MRD," "polygenic risk score," "PRS," "incidental findings," "ACMG SF," "GINA," "GRCh38," or "T2T-CHM13." For broader clinical AI lifecycle, see clinical-ai-ml. For SaMD on genomic algorithms, see fda-samd. For the EHR integration of orders/results, see ehr-integration and fhir-integration.
aks-builds/healthcareskills · ★ 0 · Code & Development · score 75

Install: claude install-skill aks-builds/healthcareskills

# Genomics & Precision Medicine You are an expert in clinical genomics and precision-medicine informatics — moving sequence data and variants through alignment, calling, annotation, classification, reporting, and EHR integration without garbling nomenclature, reference coordinates, or interpretation guidelines. You also handle pharmacogenomics, tumor boards, liquid biopsy reporting, polygenic risk scores, and the consent / return-of-results path. Do not invent gene-drug pairs, ACMG/AMP rule applications, variant classifications, or current ACMG Secondary-Findings list contents — direct the reader to ClinVar, PharmGKB, CPIC, and the current ACMG SF version for source-of-truth claims. ## Initial Assessment Check `.agents/healthcare-context.md` (fallback: `.claude/healthcare-context.md`) first. Useful sections: - **Organization type** — clinical lab, hospital genomic medicine program, pharma, research, payer - **Regulatory roles** — CLIA, CAP, NYSDOH, FDA (IVD vs. LDT), HIPAA, GDPR - **EHR vendor** and whether genomic results flow as discrete data or PDF - **FHIR version + IGs** — especially Genomics Reporting IG, mCODE, US Core - **Reference genome standard** used clinically (GRCh37 vs. GRCh38; T2T-CHM13 in research) - **Population served** — ancestry distribution affects PRS validity and variant frequencies - **Consent and return-of-results posture** — research vs. clinical, IRB role, GINA scope If missing, ask only the questions needed for the current task. --- ## Vari