DeepDNA local MCP server

DeepDNA MCP server

A remote Model Context Protocol server that gives AI agents cited pharmacogenomic and gene-variant lookups, so answers can quote CPIC and DPWG guidance and its sources. This repository also holds a local package that reads a raw DNA file on the user's own computer; nothing from the file is sent to DeepDNA, but what the package reports becomes part of the conversation with the AI model.

https://deepdna.ai/mcp

Streamable HTTP, stateless, no API key, no account. Listed in the official MCP registry as ai.deepdna/knowledge.

Educational information only, not medical advice. The server reports what curated sources and guidelines say about a gene, a variant or a drug–gene pair. It does not diagnose, prescribe or recommend a dose.

Tools

All five tools are read-only.

Two prompts, medicationreview and explainvariant, package the common questions for clients that show MCP prompts.

Coverage today is 12 genes: CYP2C19, CYP2C9, CYP2D6, SLCO1B1, VKORC1, UGT1A1, G6PD, MTHFR, COMT, HFE, APOE and BRCA1, with 51 curated drug–gene pairs across 11 of them: 40 cite a CPIC or DPWG guideline, the rest a drug label or the primary literature; the basis field in check_medications says which (guideline is null, or "drug label", when no guideline exists). It is a small, reviewed set, not a mirror of PharmGKB/ClinPGx. Every record lists its sources. The level field (the guideline's evidence grade) is null for every pair today.

Connect

Claude Code

claude mcp add --transport http deepdna https://deepdna.ai/mcp

Cursor (~/.cursor/mcp.json) and other clients that use an mcpServers file:

{
  "mcpServers": {
    "deepdna": { "type": "http", "url": "https://deepdna.ai/mcp" }
  }
}

VS Code (.vscode/mcp.json):

{
  "servers": {
    "deepdna": { "type": "http", "url": "https://deepdna.ai/mcp" }
  }
}

Claude Desktop and claude.ai: add https://deepdna.ai/mcp as a custom connector.

Gemini CLI (installs the remote, read-only server https://deepdna.ai/mcp as an extension, not the local package; gemini-extension.json is in this repo):

gemini extensions install https://github.com/alfonsoguv/deepdna-mcp

Try it without a client

curl -s https://deepdna.ai/mcp \
  -H "Content-Type: application/json" \
  -H "Accept: application/json, text/event-stream" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"lookup_drug_gene","arguments":{"gene":"CYP2C19","drug":"clopidogrel"}}}'

The answer carries the CPIC recommendation for clopidogrel by CYP2C19 metabolizer group, the sources it was written from, and the disclaimer. The same data is available as plain REST, documented in the API docs and the OpenAPI spec:

GET https://deepdna.ai/api/v1/pgx/CYP2C19/clopidogrel
GET https://deepdna.ai/api/v1/variants/rs4244285

Read a raw DNA file on your own computer

Shortened. The full README is on GitHub.