23andMe Genotype Lookup MCP Server

Overview

The 23andMe Raw Data MCP Server is a lightweight, proof‑of‑concept service that exposes raw genotype information from 23andMe TSV files to AI assistants via the Model Context Protocol. By converting a static genotype file into an interactive query endpoint, it removes the need for custom parsing logic in every application that wants to access individual SNP data. This is especially valuable for developers building AI‑powered tools—such as personalized health advisors, ancestry research assistants, or educational bots—that need to answer questions about specific genetic markers without hosting a full genomic database.

Problem Solved

Genomic data is typically stored in large, compressed files that are difficult to query directly. Developers often write bespoke parsers or import the data into relational databases, which adds complexity and latency. The MCP server abstracts this process: a single TSV file is parsed once at startup, then served through a standardized interface. This eliminates repetitive parsing code, ensures consistent data access patterns, and keeps the deployment footprint minimal.

Core Functionality

• RSID‑Based Lookup: The server exposes a single tool, , which accepts an RSID (e.g., ) and returns the genotype string (). If a marker is missing from the file, it gracefully returns .
• Real‑time Interaction: Once started with a data file, the server listens on for MCP messages, enabling instant responses to AI assistant requests.
• Minimal Dependencies: Built on Node.js v18+, the server requires only the raw TSV file and runs as a single command, making it easy to integrate into existing workflows or containerized environments.

Key Features & Advantages

• Zero‑Configuration Parsing: The server automatically interprets the 23andMe TSV format, handling header comments and column ordering without manual setup.
• Standard MCP Interface: By adhering to the MCP specification, any Claude or other MCP‑compatible assistant can discover and invoke the tool with minimal configuration.
• Scalable for Small Projects: Designed as a proof of concept, it is ideal for rapid prototyping, educational demonstrations, or lightweight services where full genomic infrastructure would be overkill.
• Extensible: While currently focused on RSID lookups, the architecture can be expanded to include additional tools (e.g., allele frequency queries or haplotype extraction) with negligible effort.

Real‑World Use Cases

1. Personalized Health Bots: An AI assistant can answer user questions like “What is my genotype at rs12345?” by delegating the lookup to this server, providing instant, accurate responses.
2. Ancestry Research Tools: Researchers building interactive maps or ancestry inference models can query specific markers on demand, reducing data transfer overhead.
3. Educational Platforms: Teachers can demonstrate how genetic variants influence traits by querying a sample dataset through the MCP interface, allowing students to experiment without handling raw files.
4. Compliance‑Aware Deployments: Because the server operates locally and does not transmit data over the network, it supports privacy‑conscious environments where genomic data must remain on-premises.

Integration with AI Workflows

Developers configure the MCP client (e.g., ) to launch the server as a child process, passing the path to the raw data file. Once registered, any AI assistant that supports MCP can automatically detect the tool and invoke it during a conversation. The assistant can then embed the returned genotype directly into responses, logs, or further downstream processing, enabling seamless, data‑driven interactions without manual file handling.

In summary, the 23andMe Raw Data MCP Server turns a static genotype file into an interactive, protocol‑compliant service. It simplifies genomic data access for AI assistants, reduces development overhead, and opens up a wide range of applications—from health advisory bots to educational tools—while maintaining privacy and performance.