pgx-mcp

An open-source MCP server that gives Claude real-time access to pharmacogenomics databases — turning genetic variant lookups and drug interaction checks from a 45-minute manual workflow into a single conversation.

Features

• ClinVar: Variant clinical significance and pathogenicity

• PharmGKB: Drug-gene interactions, clinical annotations, CPIC/DPWG dosing guidelines

• gnomAD: Population allele frequencies across ancestries

• Open Targets: Drug-target-disease associations, pharmacogenomics evidence

• ClinicalTrials.gov: Clinical trial search (US and international)

Related MCP server: gwas-mcp

Installation

pip install pgx-mcp

Or with uvx:

uvx pgx-mcp

Claude Desktop Configuration

Add to your Claude Desktop config (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "pgx-mcp": {
      "command": "uvx",
      "args": ["pgx-mcp"]
    }
  }
}

For local development:

{
  "mcpServers": {
    "pgx-mcp": {
      "command": "uv",
      "args": ["--directory", "/path/to/mcp-pharmacogenomics", "run", "pgx-mcp"]
    }
  }
}

Available Tools

Example Usage

Ask Claude:

"My patient is a CYP2D6 poor metabolizer (*4/*4) and needs pain management. What should I prescribe?"

"What are the CPIC guidelines for clopidogrel and CYP2C19?"

"Are there any recruiting pharmacogenomics clinical trials in Germany?"

Configuration

All settings are optional and configured via environment variables (or a .env file):

Development

git clone https://github.com/Julius-Schmidt/mcp-pharmacogenomics.git
cd mcp-pharmacogenomics
pip install -e ".[dev]"
pytest

Roadmap

• Demo video/GIF in README

• EU Clinical Trials Register integration (currently no public API — European trials are covered through ClinicalTrials.gov registrations)

• PharmVar star-allele nomenclature lookups

• FDA Pharmacogenomic Biomarkers table integration

License

MIT