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Cancer Variant Interpretation for Precision Oncology · mims-harvard | DecimalAI

scienceby mims-harvard

Cancer Variant Interpretation for Precision Oncology

mims-harvard/tooluniverse-cancer-variant-interpretation

Source mims-harvard/ToolUniverse ↗License Apache-2.0

Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical evidence tier (CIViC, OncoKB), therapeutic options (FDA-approved + investigational), resistance mechanisms, prognosis, and matching clinical trials.

SkillScore64Maintained

On-demandOn-demand: invoked explicitly — never occupies your agent's context until called.

Clinical / Healthcare pack

Last verified 8/6/2026

What it changes

Passed 10 of 15 test cases with the skill, and 5 of 15 without it.

Without skill36%

With skill64%

Checks it passed that the model alone missed

Classifies preclinical model evidence as Tier 3.
Uses ESM_explain_variant_mechanism to analyze variant mechanisms.
Uses query as the search term parameter name for MyGene_query_genes.

and 6 more in the full report

9 fixed5 passed either way5 still failing3 broke

Pass-rate lift: +27 pp
Tokens: +156%
Agent turns: 0%
Response time: -31%

Model gemini-3.6-flashMeasured 8/6/2026v114 of 22 cases passed with skill · 15 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-cancer-variant-interpretation/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-cancer-variant-interpretation/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mims-harvard-tooluniverse-cancer-variant-interpretation, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mims-harvard-tooluniverse-cancer-variant-interpretation/ and pins it in .decimal/skills.lock

decimalai skills add mims-harvard-tooluniverse-cancer-variant-interpretation

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-cancer-variant-interpretation/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-cancer-variant-interpretation/SKILL.md

Raw file: /s/mims-harvard-tooluniverse-cancer-variant-interpretation/SKILL.md ↗ · machine-readable summary at /s/mims-harvard-tooluniverse-cancer-variant-interpretation.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 9 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 9

Prompt

When retrieving gene metadata via MyGene_query_genes, what parameter name carries the search term string?

What was checked, without and with the skill
Checked	Without skill	With skill
Uses query as the search term parameter name for MyGene_query_genes.	Missed	Passed

case-08 · gemini-3.6-flash · 8/6/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md204 linessingle file

Cancer Variant Interpretation for Precision Oncology

Comprehensive clinical interpretation of somatic mutations in cancer. Transforms a gene + variant input into an actionable precision oncology report covering clinical evidence, therapeutic options, resistance mechanisms, clinical trials, and prognostic implications.

KEY PRINCIPLES:

Report-first approach - Create report file FIRST, then populate progressively
Evidence-graded - Every recommendation has an evidence tier (T1-T4)
Actionable output - Prioritized treatment options, not data dumps
Clinical focus - Answer "what should we treat with?" not "what databases exist?"
Resistance-aware - Always check for known resistance mechanisms
Cancer-type specific - Tailor all recommendations to the patient's cancer type when provided
Source-referenced - Every statement must cite the tool/database source
English-first queries - Always use English terms in tool calls (gene names, drug names, cancer types), even if the user writes in another language. Respond in the user's language

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first (PubMed, UniProt, ChEMBL, ClinVar, etc.) rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

When to Use

Apply when user asks:

"What treatments exist for EGFR L858R in lung cancer?"
"Patient has BRAF V600E melanoma - what are the options?"
"Is KRAS G12C targetable?"
"Patient progressed on osimertinib - what's next?"
"What clinical trials are available for PIK3CA E545K?"
"Interpret this somatic mutation: TP53 R273H"

Input Parsing

Required: Gene symbol + variant notation (e.g., "EGFR L858R", "BRAF p.V600E", "EML4-ALK fusion", "HER2 amplification") Optional: Cancer type (improves specificity)

Track record

Benchmark

10 / 15

test cases passed, vs 5 / 15 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/2/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mims-harvard / ToolUniverse

skills/tooluniverse-cancer-variant-interpretation/SKILL.md

View on GitHub ↗

License Apache-2.0Imported 8/2/2026Version v1

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See it in action

What's inside

Cancer Variant Interpretation for Precision Oncology

LOOK UP, DON'T GUESS

COMPUTE, DON'T DESCRIBE

When to Use

Input Parsing

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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