Genomics MCP Server

An MCP (Model Context Protocol) server that provides programmatic access to SNP (Single Nucleotide Polymorphism) data by trait. Enables LLM-powered applications to query curated genomics information through a standardized interface.

🌟 Features

• 🧬 Search SNPs by trait - Find genetic variants associated with specific traits (e.g., "alzheimer_risk", "athletic_performance")
• 🔍 Detailed SNP information - Get comprehensive data including genomic coordinates, genes, effects, and research sources
• 🧪 Genotype interpretation - Understand what a specific genotype (e.g., "AG", "TT") means for a given SNP
• 📋 Trait discovery - List all available traits with SNP counts, grouped by category, with optional pagination
• 📊 Dataset metadata - Query server version, SNP count, trait count, and last-updated date via get_metadata
• 📚 Evidence-based - All data includes source citations with URLs and study types
• ⚡ Fast lookups - In-memory indexing for sub-millisecond queries
• 🔄 Database-ready - Repository pattern enables easy migration from JSON to SQL/NoSQL
• 🌐 HTTP transport - Run as a standalone HTTP server (--transport http) in addition to the default stdio mode

📦 Installation

# Install dependencies
bun install

# Run the server (stdio transport — default)
bun start

# Run as HTTP server (port 3000 by default)
bun start -- --transport http

# HTTP on a custom port
bun start -- --transport http --port 8080

🚀 Quick Start

Testing with MCP Inspector

The MCP Inspector is the recommended way to test your server:

# Run the inspector (launches web UI)
bun run inspector

Then open the URL shown in your browser to interact with the tools.

Integration with an MCP Client

Add this server to your MCP client's configuration. For example, in a config.json:

{
  "mcpServers": {
    "genomics": {
      "command": "bun",
      "args": ["/absolute/path/to/genomics-mcp/src/index.ts"]
    }
  }
}

Note: Replace /absolute/path/to/genomics-mcp with the actual path to your installation. Consult your MCP client's documentation for the exact config file location and format.

🛠️ Available Tools

The server provides 5 MCP tools for querying genomics data:

Tool	Description
search_by_trait	Search for SNPs associated with one or more traits (supports "any"/"all" matching, pagination)
get_snp_details	Get comprehensive information about a specific SNP by rsID
interpret_genotype	Interpret what a specific genotype (e.g., "AG", "CT") means for a given SNP
list_traits	List all available traits with SNP counts, grouped by category (supports filtering and pagination)
get_metadata	Return dataset statistics (SNP count, trait count, last-updated) and server version

All tools support both markdown and json response formats.

👉 See Tool Reference for detailed documentation, parameters, and examples.

📊 Dataset

The dataset covers a broad range of well-studied SNPs across multiple trait categories, including:

• Neurological: Alzheimer's risk (APOE), memory (BDNF), cognitive function (COMT), dopamine signaling (DRD2)
• Behavioral: Social behavior (OXTR), addiction risk (DRD2), nicotine dependence (CHRNA3)
• Cardiovascular: Heart disease risk (9p21), hypertension (AGT), HDL cholesterol (CETP), beta-blocker response (ADRB1)
• Metabolic: Folate metabolism (MTHFR), obesity risk (FTO), triglyceride levels (APOA5)
• Pharmacogenomics: Drug metabolism (CYP2C9, CYP2C19), warfarin sensitivity (VKORC1), fluorouracil toxicity (DPYD), hepatitis C treatment (IFNL3), abacavir hypersensitivity (HCP5)
• Autoimmune & Immune: Celiac disease (HLA-DQA1), rheumatoid arthritis (STAT4), autoimmune risk (PTPN22)
• Inflammation: IL-1β (IL1B), IL-10 (IL10), CRP levels (CRP)
• Cancer & Developmental: Detoxification (NQO1), melanoma risk (TYR), lung cancer risk (CHRNA3)
• Eye & Vision: Age-related macular degeneration (CFH, ARMS2)
• Bone & Musculoskeletal: Bone density (COL1A1, ESR1), osteoporosis risk
• Iron & Liver: Hemochromatosis (HFE), Gilbert syndrome (UGT1A1)
• Physical Traits: Eye color (OCA2), skin pigmentation (TYR, MC1R)
• Athletic: Sprint/endurance performance (ACTN3)
• Nutrition & Metabolism: Lactose intolerance (MCM6), vitamin D levels (GC, VDR)
• Circadian & Sleep: Circadian rhythm (CLOCK), sleep duration (DEC2)
• Musculoskeletal & Uric Acid: Gout risk (ABCG2), uric acid levels (SLC2A9)

All SNPs include:

• Genomic coordinates (chromosome, position)
• Associated genes and traits
• Genotype-specific effects with risk levels
• Population frequencies
• Research source citations with URLs

🏗️ Architecture

The server uses a layered architecture: Tools → Use Cases → Repository → Data, with in-memory indexing for sub-millisecond queries and a repository interface that makes database migration trivial.

👉 See Architecture Guide for diagrams, design patterns, data model, and technical details.

🧪 Development

# Install dependencies
bun install

# Run in development mode (auto-reload)
bun run dev

# Run automated tests
bun test

# Type-check (optional — Bun runs TypeScript directly)
bun run build

# Format code
bun run format

# Lint code
bun run lint

# Lint + format in one pass (auto-fixes)
bun run check

A pre-commit hook runs bun run check on staged files and then bun test before every commit.

📝 Adding New SNPs

To add new SNPs to the dataset:

1. Edit src/repositories/data/snps.json
2. Follow the schema with required fields:
   • rsid, genes, traits, description, chromosome, position
   • reference_allele, effects_by_genotype, sources, last_updated
3. Restart the server — Zod validates on startup and will report any schema violations
4. If the SNP introduces a new trait slug, add it to both the TRAIT_CATEGORIES map (for category grouping) and the TRAIT_DISPLAY_NAMES map (for the display label) in src/types/trait-categories.ts. Unlisted slugs fall back to Other and auto-generated Title Case respectively.
5. Optionally run bun run build to type-check

The data is validated against Zod schemas on load, so any schema violations will be caught immediately.

📚 Resources

• Tool Reference — Complete tool documentation with examples
• Testing Guide — Automated test suite, manual MCP Inspector test cases, and HTTP transport testing
• Architecture Guide — Design patterns and technical details
• Project Status — Health metrics, resolved items, and pending features
• Model Context Protocol Documentation
• MCP TypeScript SDK

Data Sources

The curated SNP dataset draws on the following authoritative genomics databases:

• dbSNP — NCBI reference database for SNP identifiers, genomic coordinates, and allele frequencies
• ClinVar — NCBI archive of clinically relevant genomic variants and their interpretations
• SNPedia — Community-curated wiki of SNP associations and genotype effects
• PharmGKB — Pharmacogenomics knowledge base for drug–gene interactions
• CPIC — Clinical Pharmacogenetics Implementation Consortium guidelines
• GnomAD — Genome Aggregation Database for population allele frequencies

📄 License

MIT License - see LICENSE file for details

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Note: This server provides educational genomics information only. It is not intended for clinical use or medical diagnosis. Always consult healthcare professionals for medical decisions.