Cancer Genomics TCGA (ToolUniverse Claude Skill)

A ToolUniverse agent skill that runs cancer-type-specific TCGA/GDC analyses from cohort selection through somatic mutation frequencies, copy-number changes, survival, and clinically actionable variant annotation.


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-genomics-tcga/`)
Pricing	Free / OSS (Apache-2.0); wraps public APIs (GDC/TCGA, Progenetix, OncoKB)
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-genomics-tcga):
```
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-genomics-tcga ~/.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-genomics-tcga skill”) rather than relying on automatic dispatch.

What it does

Runs a six-phase cancer-genomics workflow:

Study selection — identify and confirm TCGA projects (GDC_list_projects, GDC_search_cases).
Clinical data — patient demographics, diagnoses, treatments (GDC_get_clinical_data).
Somatic mutations — mutation frequencies and specific variants (GDC_get_ssm_by_gene, GDC_get_mutation_frequency).
CNV analysis — copy-number amplifications/deletions (Progenetix_cnv_search, Progenetix_search_biosamples).
Survival analysis — Kaplan-Meier curves and log-rank p-values split by mutation status (GDC_get_survival).
Variant interpretation — oncogenicity and FDA-approved therapies (OncoKB_annotate_variant).

The skill emphasizes cancer-type-specific cohorts and warns against uncontextualized pan-cancer queries.

Primary use cases: cohort-based somatic-mutation profiling, biomarker survival stratification, actionable-variant triage, and evidence for oncology target/repurposing hypotheses.

Notes

It is a reasoning layer over ToolUniverse; without the MCP server registered, the tool calls fail. Complements the Precision Oncology and Cancer Variant Interpretation skills — this one is the TCGA/GDC cohort-analysis workflow specifically. ToolUniverse ships ~68 such skills; other workflows are catalogued separately.

Sources

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