Cancer Variant Interpretation (ToolUniverse Claude Skill)

A ToolUniverse agent skill that interprets a somatic cancer mutation — gene, variant, and cancer type — into an actionable precision-oncology report with clinical evidence tiers, therapeutic options, resistance mechanisms, prognosis, and matching clinical trials.


Type	Claude Skill (one of ToolUniverse’s pre-built agent skills)
Supplier	Zitnik Lab, Harvard Medical School
Availability	GA — part of the ToolUniverse skills collection (`skills/tooluniverse-cancer-variant-interpretation/`)
Pricing	Free / OSS (Apache-2.0); wraps public APIs (CIViC, OncoKB, cBioPortal, OpenTargets, ChEMBL, DrugBank, ClinicalTrials.gov)
Capabilities	Read-only — drives ToolUniverse tool calls; no data writes
Verified	works · 2026-07-20
Security	cleared · 2026-07-20 — provenance matches Zitnik Lab, Apache-2.0, skill dir confirmed, no OSV advisories

How to install

This skill calls ToolUniverse tools, so the ToolUniverse MCP server must be installed first (see the ToolUniverse page). Simplest registration:

claude mcp add --transport stdio tooluniverse -- uvx tooluniverse

Then add the skills:

Claude Code — install the whole skill collection (the skill resolves as tooluniverse-cancer-variant-interpretation):
```
npx skills add mims-harvard/ToolUniverse
```
Manual / other agents — copy just this skill directory into your skills folder:
```
git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-cancer-variant-interpretation ~/.claude/skills/
```
(replace ~/.claude/skills/ with your agent’s skills directory if you are not using Claude Code/Desktop.)

The skill sets disable-model-invocation: true upstream, so invoke it explicitly (e.g. ask Claude to “use the cancer-variant-interpretation skill”) rather than relying on automatic dispatch.

What it does

Runs an eight-phase somatic-mutation interpretation pipeline:

Gene disambiguation — resolve symbols to Ensembl/UniProt/Entrez IDs (MyGene_query_genes, UniProt_search, ensembl_lookup_gene).
Clinical variant evidence — query CIViC for curated evidence items and tiers.
Mutation prevalence — cBioPortal hotspot status and cancer-type distribution.
Therapeutic associations — FDA-approved and investigational drugs via OpenTargets, ChEMBL, DrugBank.
Resistance mechanisms — known on-target and bypass-pathway resistance variants.
Clinical trials — match to active trials via ClinicalTrials.gov.
Prognostic impact — survival and pathway context (Reactome, GTEx).
Report synthesis — prioritized, evidence-graded (T1–T4) treatment recommendations, each citing its database origin.

Primary use cases: precision-oncology variant reporting, therapy matching for a somatic mutation, resistance-mechanism review.

Notes

It is a reasoning layer over ToolUniverse; without the MCP server registered, the tool calls fail. Output is report-first (creates the output file before populating data) and cancer-type specific. It surfaces clinical evidence but is a research aid, not a clinical decision tool — recommendations should be reviewed against primary sources. ToolUniverse ships ~150 such skills; other drug-discovery and oncology workflows are catalogued separately.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.