GeneSnap

A web application that parses raw 23andMe genetic data, identifies clinically significant SNP variants, and provides annotated results linked to scientific literature and databases.

Disclaimer: This tool is for informational purposes only and is not medical advice. Clinically significant findings should be confirmed with clinical-grade testing and reviewed with a genetic counselor.

Tech Stack

• Backend: Python 3.12+, FastAPI, SQLite (aiosqlite), uv
• Frontend: React 19, TypeScript, Vite, Tailwind CSS

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Prerequisites

• uv (Python package manager)
• Node.js 18+
• Docker (optional, for containerized setup)

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Running Locally (Development)

1. Import the variant database

cd backend

# Install dependencies
uv sync

# Seed the schema
uv run python -m genesnap.db.seed

# Full import — downloads ClinVar and GWAS Catalog automatically, skips PharmGKB
uv run scripts/import_variants.py

# Optionally include PharmGKB (requires manual download from pharmgkb.org)
uv run scripts/import_variants.py --pharmgkb data/clinical_annotations.tsv

Source	Data	Filter applied
ClinVar	Pathogenic / likely pathogenic / drug response variants	≥ 2 ClinVar review stars, single rsID, no conflicting interpretations
GWAS Catalog	Genome-wide significant associations	p < 5×10⁻⁸, sample size ≥ 1,000, single rsID
PharmGKB	Drug–gene interactions	CPIC Level 1A / 1B only

Note: PharmGKB does not provide open FTP access. Download clinical_annotations.tsv manually from their downloads page or use the one under 'backend/data', and pass it via --pharmgkb.

2. Backend

cd backend

# Copy and configure environment variables
cp ../.env.example .env
# Edit .env and set NCBI_API_KEY (optional but recommended for higher API rate limits)

# Start the dev server
uv run uvicorn genesnap.main:app --reload --port 8000

The API will be available at http://localhost:8000. Interactive API docs (Swagger UI) are at http://localhost:8000/docs.

3. Frontend

cd frontend

# Install dependencies
npm install

# Start the dev server
npm run dev

The frontend will be available at http://localhost:5173.

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Running with Docker

# Copy and configure environment variables
cp .env.example .env
# Edit .env and set NCBI_API_KEY if desired

# Build and start both services
docker compose up --build

The app will be available at http://localhost:3000.

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Environment Variables

Copy .env.example to .env in the project root:

Variable	Required	Description
NCBI_API_KEY	Optional	Free NCBI API key for higher rate limits on ClinVar/PubMed. Get one at https://www.ncbi.nlm.nih.gov/account/settings/

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Development

Backend

cd backend

# Run tests
uv run pytest

# Lint and format
uv run ruff check .
uv run ruff format .

# Type checking
uv run mypy src/

Frontend

cd frontend

# Lint
npm run lint

# Build for production
npm run build

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API Endpoints

Method	Path	Description
POST	/api/upload	Upload a 23andMe .txt file and get analysis results
GET	/api/variants/{rsid}	Get curated variant details for an rsID
GET	/api/enrich/{rsid}	Fetch live enrichment data from ClinVar, PubMed, Ensembl
GET	/api/health	Health check