Genomics Clinical

🧬 Genomics Clinical MCP Server

MCP 2026-07-28 · Clinical genomics & pharmacogenomics decision support for AI agents
Author: David Osher · Diagnostica

Node.js 20+ MCP Protocol License: CC BY-NC-SA 4.0

Model Context Protocol server for clinical genomics and pharmacogenomics decision support. Integrates ClinVar variant pathogenicity data with PharmGKB/ClinPGx drug-gene interaction guidelines.

Sibling project: Israel Drugs MCP Server — Israeli Ministry of Health pharmaceutical database

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✨ Why This Server?

Capability	Description
ClinVar Integration	Search variants, check pathogenicity, scan genomic regions
PharmGKB/ClinPGx	Drug-gene interactions, patient risk assessment, gene-drug pairs
Clinical Summary	Integrated variant + pharmacogenomic analysis
Reference Resources	8 static genomics references (pharmacogenes, pathogenicity guide, etc.)
Clinical Prompts	Variant interpretation, dosing review, summary templates
Modern MCP	SDK v2, OAuth 2.1, stateless HTTP, Cursor-ready

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🎯 Use Cases

• Variant interpretation — ACMG-style workflow with ClinVar lookup
• Pharmacogenomic dosing — CPIC/DPWG guidelines for warfarin, clopidogrel, etc.
• Patient medication review — Match genotypes to drug-gene interactions
• Research & education — Reference resources for gene-disease, metabolizer phenotypes

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🛠 Tools

Tool	Description
clinvar_get_variant_info	Search ClinVar by gene, rsID, HGVS, genomic location, ClinVar ID
clinvar_check_pathogenicity	Quick pathogenicity check for a variant
clinvar_find_variants_in_region	Scan genomic region for variants
pharmgkb_get_drug_gene_interactions	Comprehensive drug pharmacogenomics (CPIC, FDA labels)
pharmgkb_check_patient_drug_risk	Assess drug safety for patient genotypes
pharmgkb_get_gene_drug_pairs	Find drugs affected by a gene (ClinPGx API)
genomics_clinical_summary	Integrated clinical summary

All tools support concise (human-readable) and detailed (full metadata) response formats.

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📚 Resources

Resource	URI	Content
Gene-Disease Map	genomics://gene-disease-map	Key gene-disease associations
VIP Pharmacogenes	genomics://pharmacogenes	CYP2C9, CYP2D6, VKORC1, etc.
Genome Builds	genomics://genome-builds	GRCh37/GRCh38 reference
Pathogenicity Guide	genomics://pathogenicity-guide	ClinVar classification
Drug-Gene Pairs	genomics://drug-gene-pairs	High-priority interactions
Metabolizer Phenotypes	genomics://metabolizer-phenotypes	PM, IM, NM, RM definitions
Variant Nomenclature	genomics://variant-nomenclature	HGVS, rsID formats
Testing Indications	genomics://testing-indications	When to order PGx testing

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🚀 Quick Start

Prerequisites

• Node.js 20+
• npm
• Internet (ClinVar, ClinPGx APIs)

Installation

git clone https://github.com/DavidOsherdiagnostica/genomics-clinical-mcp-server.git
cd genomics-clinical-mcp-server
npm install
npm run build
cp .env.example .env   # optional

Cursor (stdio — recommended for local)

Create .cursor/mcp.json locally (not committed to the repo):

{
  "mcpServers": {
    "genomics-clinical": {
      "type": "stdio",
      "command": "node",
      "args": ["dist/index.js"],
      "cwd": "${workspaceFolder}",
      "envFile": "${workspaceFolder}/.env"
    }
  }
}

Enable in Cursor Settings → MCP, then restart Cursor.

Claude Desktop

{
  "mcpServers": {
    "genomics-clinical": {
      "command": "node",
      "args": ["/path/to/genomics-clinical-mcp-server/dist/index.js"]
    }
  }
}

HTTP (remote / Docker)

npm run start:http
# Server: http://127.0.0.1:3000/mcp
# Health:  http://127.0.0.1:3000/health

Docker

docker build -t genomics-clinical-mcp .
docker run -p 8080:8080 genomics-clinical-mcp

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⚙️ Configuration

See .env.example for all options. Key variables:

Variable	Default	Description
CLINVAR_BASE_URL	NCBI E-utilities	ClinVar API
PHARMGKB_BASE_URL	https://api.clinpgx.org/v1	ClinPGx (PharmGKB migrated)
NCBI_API_KEY	—	Optional, higher rate limits
OAUTH_ENABLED	false	Enable OAuth for HTTP
OAUTH_REQUIRED	false	Require Bearer token on /mcp
HOST	127.0.0.1	HTTP bind address
PORT	3000	HTTP port

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🔐 Security & OAuth

• stdio mode: No OAuth; credentials via env if needed
• HTTP mode: OAuth 2.1 optional; enable for production remote deployment
• RFC 9728: /.well-known/oauth-protected-resource when OAuth enabled
• Rate limiting: 60 req/min default on /mcp
• Origin validation: Configurable via CORS_ORIGINS, ALLOWED_HOSTS

For remote Cursor connection with OAuth:

{
  "mcpServers": {
    "genomics-clinical": {
      "url": "https://your-server.example.com/mcp",
      "auth": {
        "CLIENT_ID": "${env:MCP_CLIENT_ID}",
        "scopes": ["genomics:read", "genomics:tools"]
      }
    }
  }
}

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📋 Supported Formats

• Gene symbols: HGNC (BRCA1, CYP2C9)
• rsIDs: rs9923231
• HGVS: NM_007294.4:c.3101_3102del
• Genomic locations: chr, start, end, GRCh37/GRCh38
• ClinVar IDs: VCV/RCV
• Drugs: warfarin, clopidogrel
• Genotypes: *1/*3, TT

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🏗 Architecture

┌─────────────┐     stdio      ┌──────────────────────┐
│   Cursor    │◄──────────────►│  Genomics Clinical   │
│ Claude etc. │                │  MCP Server v2       │
└─────────────┘                └──────────┬───────────┘
                                          │
                    ┌─────────────────────┼─────────────────────┐
                    ▼                     ▼                     ▼
              ┌──────────┐         ┌──────────┐         ┌──────────┐
              │ ClinVar  │         │ ClinPGx  │         │ Resources│
              │ E-utils  │         │ InfoBtn  │         │ (static) │
              └──────────┘         └──────────┘         └──────────┘

• SDK: @modelcontextprotocol/server v2 (MCP 2026-07-28)
• Transports: stdio (local), Streamable HTTP (remote, stateless)
• Entry points: dist/index.js (stdio), dist/server.js --http (HTTP)

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⚠️ Medical Disclaimer

For research and clinical decision support only. Not a substitute for professional medical advice, diagnosis, or treatment. Always consult qualified healthcare providers and genetic counselors.

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🤝 Contributing

1. Fork the repository
2. Create a feature branch
3. Run npm run build && npm test
4. Submit a pull request

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📄 License

CC BY-NC-SA 4.0 — Attribution, NonCommercial, ShareAlike

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👤 Author

David Osher · GitHub · LinkedIn

Author of MCP connectors for Israel Gov open data and Israel MoH drug DB. Building reliable AI tooling for healthcare.

Related projects:

• Israel Drugs MCP
• data-gov-il-mcp