| name | tooluniverse-clinical-trial-matching |
| description | AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks clinical trials from ClinicalTrials.gov using multi-dimensional matching across molecular eligibility... |
| license | MIT |
| author | AIPOCH |
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:
- Report-first approach - Create report file FIRST, then populate progressively
- Patient-centric - Every recommendation considers the individual patient's profile
- Molecular-first matching - Prioritize trials targeting patient's specific biomarkers
- Evidence-graded - Every recommendation has an evidence tier (T1-T4)
- Quantitative scoring - Trial Match Score (0-100) for every trial
- Eligibility-aware - Parse and evaluate inclusion/exclusion criteria
- Actionable output - Clear next steps, contact info, enrollment status
- Source-referenced - Every statement cites the tool/database source
- Completeness checklist - Mandatory section showing analysis coverage
- 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
- Executive Summary - Top 3 trial recommendations with scores
- Patient Profile Summary - Standardized disease/biomarker/stage table
- Ranked Trial Matches - Per-trial score breakdown, eligibility, evidence, locations
- Trials by Category - Targeted/Immuno/Combination/Basket groupings
- Additional Testing Recommendations - Biomarkers that unlock more trials
- Alternative Options - Expanded access, off-label options
- Evidence Grading Summary - T1-T4 counts
- Completeness Checklist - Analysis step status tracking
- Disclaimer - Research-only notice
- Sources - Data source list
Full report template with markdown structure: see references/phases_detail.md#phase-10-report-synthesis
Edge Cases & Common Pitfalls
- ClinicalTrials.gov query complexity - Overly specific queries often return zero results. Start simple, then combine.
- 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.
- No matching trials - Broaden to gene-level → pathway-level → basket trials → suggest biomarker testing.
- Rare biomarkers - Search gene-level trials, check CIViC, note rarity, suggest molecular tumor board.
- Multiple biomarkers - Search independently + in combination, score by most actionable.
- 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 |
