precision-oncology-agent

Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.

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Repository: mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Last source activity: February 2, 2026 at 16:47
Detected SKILL.md language: English
Stars: 31
Forks: 8

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name	precision-oncology-agent
description	Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.

At-a-Glance

description (10-20 chars): Tumor board copilot
keywords: oncology, genomics, OncoKB, therapy-ranking, evidence
measurable_outcome: Deliver a ranked therapy list with OncoKB/NCCN citations plus data-gap checklist for every case within 10 minutes of receiving inputs.

Inputs

vcf_path (hg38 preferred) plus optional CNV/fusion summaries.
pathology_report text for histology/grade/biomarkers.
clinical_context dict capturing tumor type, stage, prior lines, ECOG.

Outputs

Ranked treatment options (approved, off-label, clinical trials) with evidence strength + contraindications.
Variant interpretation table (pathogenicity, tier, therapy linkage).
Biomarker summary (TMB, MSI, PD-L1 if provided) and missing-test checklist.

Workflow

Ingest & normalize: Harmonize gene symbols, genome build, and variant effects.
Annotate: Query OncoKB/NCCN + internal knowledge for actionability tiers.
Contextualize: Blend pathology + prior therapy info to filter contraindicated options.
Recommend: Present therapies ordered by evidence + patient fit; cite sources.
Gaps: Highlight assays or confirmations still required before treatment.

Guardrails

No autonomous treatment decisions—flag outputs as advisory.
Cite evidence rigorously (guideline version, publication).
Highlight resistance mechanisms and prior exposure conflicts.

References

See README.md for detailed workflow plus cited Nature Cancer study.

precision-oncology-agent

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At-a-Glance

Inputs

Outputs

Workflow

Guardrails

References

At-a-Glance

Inputs

Outputs

Workflow

Guardrails

References