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tooluniverse-precision-medicine-stratification

Stratifies patients into risk tiers and treatment groups using genomic, clinical, and pharmacogenomic data.

1.7k|254|Updated Mar 3, 2025
Search Tags:#clinical trials#pharmacogenomics#biomarkers#clinvar#risk score#precision medicine#patient stratification
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-precision-medicine-stratification
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-precision-medicine-stratification
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-precision-medicine-stratification
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-precision-medicine-stratification

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Clinicians and researchers need to integrate germline variants, somatic mutations, clinical biomarkers, and pharmacogenomic genotypes into a single actionable patient stratification, but this data lives across dozens of disconnected databases like ClinVar, PharmGKB, GWAS Catalog, and OpenTargets.

Core Features & Use Cases

  • Integrated Risk Scoring: Computes a 0-100 Precision Medicine Risk Score from genetic (0-35), clinical (0-30), molecular (0-25), and pharmacogenomic (0-10) components, mapped to LOW through VERY HIGH tiers.
  • Disease-Specific Pipelines: Routes analysis through dedicated paths for cancer, metabolic, cardiovascular, neurological, rare/monogenic, and autoimmune diseases.
  • Pharmacogenomic Profiling: Evaluates CYP2D6, CYP2C19, SLCO1B1, DPYD, HLA alleles and FDA PGx biomarkers to guide drug selection and dosing.
  • Use Case: Stratify an NSCLC patient with EGFR L858R, TMB 25 mut/Mb, and PD-L1 80% to receive a VERY HIGH risk score, osimertinib as first-line therapy, matched clinical trials, and a monitoring plan.

Quick Start

Ask the agent to stratify a breast cancer patient with a BRCA1 pathogenic variant, ER+/HER2- status, stage IIA, age 45, and request the risk tier and recommended treatment.

Frequently Asked Questions about tooluniverse-precision-medicine-stratification

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I stratify a cancer patient using genomic data?▼

Provide the disease name plus at least one data layer such as somatic mutations, germline variants, or biomarkers like TMB and PD-L1. The skill resolves the disease to an EFO ID, checks ClinVar and cBioPortal for actionable drivers, and outputs a risk score with treatment recommendations.

What inputs are required for precision medicine stratification?▼

A disease or condition name and at least one of: germline variants, somatic mutations, gene names, or clinical biomarkers. Optional inputs like age, stage, PGx genotypes, comorbidities, and medications improve scoring accuracy.

How is the precision medicine risk score calculated?▼

The score sums four components: genetic risk (0-35), clinical risk (0-30), molecular features (0-25), and pharmacogenomic risk (0-10). Totals map to tiers: LOW (0-24), INTERMEDIATE (25-49), HIGH (50-74), and VERY HIGH (75-100).

Which pharmacogenes does the stratification evaluate?▼

It evaluates CYP2D6, CYP2C19, CYP2C9, SLCO1B1, DPYD, VKORC1, UGT1A1, TPMT, and HLA alleles using PharmGKB clinical annotations, CPIC dosing guidelines, and FDA PGx biomarker labels.

When should I not use patient stratification and use a different analysis?▼

Use dedicated skills for single variant interpretation, immunotherapy response prediction, drug-drug interaction checks, polygenic risk score calculation, or clinical trial search alone. Stratification is for integrated multi-layer patient assessment.

Does the stratification report include clinical trial matches?▼

Yes, Phase 8 searches ClinicalTrials.gov for biomarker-driven and precision medicine trials matching the patient's molecular profile, including basket and umbrella trials, with eligibility criteria retrieval.

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