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Skillstooluniverse-clinical-trial-matching

tooluniverse-clinical-trial-matching

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Updated 10-15 16:45

About this skill

Source: https://github.com/aipoch/medical-research-skills

Clinical Trial Matching for Precision Medicine

Transform patient molecular profiles and clinical characteristics into prioritized clinical trial recommendations. Searches ClinicalTrials.gov and cross-references with molecular databases (CIViC, OpenTargets, ChEMBL, FDA) to produce evidence-graded, scored trial matches.

KEY PRINCIPLES:

  1. Report-first approach - Create report file FIRST, then populate progressively
  2. Patient-centric - Every recommendation considers the individual patient's profile
  3. Molecular-first matching - Prioritize trials targeting patient's specific biomarkers
  4. Evidence-graded - Every recommendation has an evidence tier (T1-T4)
  5. Quantitative scoring - Trial Match Score (0-100) for every trial
  6. Eligibility-aware - Parse and evaluate inclusion/exclusion criteria
  7. Actionable output - Clear next steps, contact info, enrollment status
  8. Source-referenced - Every statement cites the tool/database source
  9. Completeness checklist - Mandatory section showing analysis coverage
  10. English-first queries - Always use English terms in tool calls. Respond in user's language

When to Use

Apply when user asks:

  • "What clinical trials are available for my NSCLC with EGFR L858R?"
  • "Patient has BRAF V600E melanoma, failed ipilimumab - what trials?"
  • "Find basket trials for NTRK fusion"
  • "Breast cancer with HER2 amplification, post-CDK4/6 inhibitor trials"
  • "KRAS G12C colorectal cancer clinical trials"
  • "Immunotherapy trials for TMB-high solid tumors"
  • "Clinical trials near Boston for lung cancer"
  • "What are my options after failing osimertinib for EGFR+ NSCLC?"

NOT for (use other skills instead):

  • Single variant interpretation without trial focus -> Use tooluniverse-cancer-variant-interpretation
  • Drug safety profiling -> Use tooluniverse-adverse-event-detection
  • Target validation -> Use tooluniverse-drug-target-validation
  • General disease research -> Use tooluniverse-disease-research

Input Parsing

Required Input

  • Disease/cancer type: Free-text disease name (e.g., "non-small cell lung cancer", "melanoma")

Strongly Recommended

  • Molecular alterations: One or more biomarkers (e.g., "EGFR L858R", "KRAS G12C", "PD-L1 50%", "TMB-high")
  • Stage/grade: Disease stage (e.g., "Stage IV", "metastatic", "locally advanced")
  • Prior treatments: Previous therapies and outcomes (e.g., "failed platinum chemotherapy", "progressed on osimertinib")

Optional

  • Performance status: ECOG or Karnofsky score (e.g., "ECOG 0-1")
  • Geographic location: City/state for proximity filtering (e.g., "Boston, MA")
  • Trial phase preference: I, II, III, IV, or "any"
  • Intervention type: drug, biological, device, etc.
  • Recruiting status preference: recruiting, not yet recruiting, active

Biomarker Parsing Quick Reference

Input Format Parsed As Example
Gene + amino acid change Specific mutation EGFR L858R
Gene + exon notation Exon-level alteration EGFR exon 19 deletion
Gene + fusion partner Fusion EML4-ALK fusion
Gene + amplification Copy number gain HER2 amplification
Gene + expression level Expression biomarker PD-L1 50%
Gene + status Status biomarker MSI-high, TMB-high
Gene + resistance Resistance mutation EGFR T790M

Gene Symbol Normalization

Common Alias Official Symbol Notes
HER2 ERBB2 Search both in trials
PD-L1 CD274 Often searched as "PD-L1" in trials
ALK ALK EML4-ALK is a fusion
VEGF VEGFA Often searched as "VEGF"
PD-1 PDCD1 Search as "PD-1" in trials
BRCA BRCA1/BRCA2 Specify which BRCA gene

Detailed parsing rules and regex patterns: see references/parsing_and_validation.md

Workflow Overview

Phase Name Summary
0 Tool Parameter Reference Verify all tool parameters before calling. See references/phases_detail.md
1 Patient Profile Standardization Resolve disease→EFO ID, genes→Ensembl/Entrez IDs, classify biomarker actionability
2 Broad Trial Discovery Disease/biomarker/intervention searches on ClinicalTrials.gov, deduplicate results
3 Trial Characterization Batch-fetch eligibility, interventions, locations, status, descriptions for candidate NCT IDs
4 Molecular Eligibility Matching Parse eligibility text for biomarker requirements, score patient-trial molecular match (0-40)
5 Drug-Biomarker Alignment Identify trial drug mechanisms via OpenTargets/ChEMBL, verify target overlap with patient biomarkers
6 Evidence Assessment FDA approval, PubMed literature, CIViC evidence, evidence tier classification (T1-T4)
7 Geographic & Feasibility Trial site locations, enrollment status, proximity to patient location
8 Alternative Options Basket/tumor-agnostic trials, expanded access, compassionate use programs
9 Scoring & Ranking Calculate Trial Match Score (0-100), assign tier, rank trials
10 Report Synthesis Generate markdown report with executive summary, ranked trials, evidence grading, checklist

Detailed phase execution code and tool call examples: see references/phases_detail.md

Trial Match Score (0-100)

Score Components

Component Max Points Key Criteria
Molecular Match 40 Exact variant match=40, Gene-level=30, Pathway=20, No criteria=10, Excluded=0
Clinical Eligibility 25 All criteria met=25, Most=18, Some=10, Ineligible=0
Evidence Strength 20 FDA-approved (T1)=20, Phase III (T2)=15, Phase II (T3)=10, Phase I (T4)=5
Trial Phase 10 Phase III=10, Phase II=8, Phase I/II=6, Phase I=4
Geographic Feasibility 5 Patient's city=5, Same country=3, International=1, Unknown=0

Recommendation Tiers

Score Tier Label Action
80-100 Tier 1 Optimal Match Strongly recommend - contact site immediately
60-79 Tier 2 Good Match Recommend - discuss with care team
40-59 Tier 3 Possible Match Consider - needs further eligibility review
0-39 Tier 4 Exploratory Backup option - consider if Tier 1-3 unavailable

Detailed scoring rules, evidence tier definitions, and matching algorithms: see references/scoring_and_matching.md

Output Format

Report file: clinical_trial_matching_[DISEASE]_[BIOMARKER]_[DATE].md

Required Sections

  1. Executive Summary - Top 3 trial recommendations with scores
  2. Patient Profile Summary - Standardized disease/biomarker/stage table
  3. Ranked Trial Matches - Per-trial score breakdown, eligibility, evidence, locations
  4. Trials by Category - Targeted/Immuno/Combination/Basket groupings
  5. Additional Testing Recommendations - Biomarkers that unlock more trials
  6. Alternative Options - Expanded access, off-label options
  7. Evidence Grading Summary - T1-T4 counts
  8. Completeness Checklist - Analysis step status tracking
  9. Disclaimer - Research-only notice
  10. Sources - Data source list

Full report template with markdown structure: see references/phases_detail.md#phase-10-report-synthesis

Edge Cases & Common Pitfalls

  1. ClinicalTrials.gov query complexity - Overly specific queries often return zero results. Start simple, then combine.
  2. CIViC search limitations - civic_search_variants/civic_search_evidence_items do NOT filter by query. Use civic_get_variants_by_gene with gene ID instead.
  3. No matching trials - Broaden to gene-level → pathway-level → basket trials → suggest biomarker testing.
  4. Rare biomarkers - Search gene-level trials, check CIViC, note rarity, suggest molecular tumor board.
  5. Multiple biomarkers - Search independently + in combination, score by most actionable.
  6. Conflicting eligibility - Score partial match transparently, highlight met/unmet criteria.

Full edge case handling and use patterns: see references/parsing_and_validation.md

Known CIViC Gene IDs

Gene CIViC ID Gene CIViC ID
ALK 1 MET 52
ABL1 4 PIK3CA 37
BRAF 5 ROS1 118
EGFR 19 RET 122
ERBB2 20 NTRK1 197
KRAS 30 NTRK2 560
TP53 45 NTRK3 561

Input Validation

This skill accepts requests that match the documented purpose of tooluniverse-clinical-trial-matching and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

tooluniverse-clinical-trial-matching only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

References

File Content
references/phases_detail.md Phase 0-10 detailed execution code, tool call examples, parameter tables, report template
references/scoring_and_matching.md Scoring algorithm details, drug-biomarker alignment rules, evidence tier classification, matching logic
references/parsing_and_validation.md Biomarker parsing regex, eligibility text parsing, gene resolution code, edge case handling, common use patterns