GWAS Target Finder

GWAS CatalogEnsemblOpen Targets

About GWAS Target Finder

Overview

The GWAS Target Finder is a tool designed to help researchers identify potential therapeutic targets from genome-wide association studies (GWAS) data. It integrates information from multiple bioinformatics resources to provide a seamless workflow for identifying druggable genes associated with specific traits or diseases.

This application is particularly useful for researchers in genomics, drug discovery, and personalized medicine who want to quickly move from genetic associations to potential therapeutic targets.

How It Works

  1. Input a trait or disease: Start by entering a trait name or EFO ID (e.g., "Type 2 diabetes" or "EFO_0001360"). You can also adjust the p-value threshold and genomic window size.
  2. Fetch significant SNPs: The system queries the GWAS Catalog to retrieve SNPs significantly associated with your trait of interest.
  3. Map to genomic coordinates: Each SNP is mapped to its precise genomic location using data from the Ensembl database.
  4. Identify nearby genes: Protein-coding genes within the specified window of each SNP are identified.
  5. Check drug target status: The Open Targets Platform is used to determine which of the identified genes are known drug targets.
  6. Analyze results: The results are presented in an interactive table and visualizations, allowing you to explore the findings and filter for genes of interest.

Data Sources

GWAS Catalog

The NHGRI-EBI GWAS Catalog is a database of SNP-trait associations extracted from published genome-wide association studies. It provides a comprehensive resource of associations between genetic variants and phenotypic traits.

Ensembl

Ensembl is a genome browser that provides annotations for the genomes of various species. We use Ensembl to map SNPs to genomic coordinates and identify nearby genes.

Open Targets Platform

The Open Targets Platform is a resource that integrates genetic and genomic data to help identify and prioritize drug targets. We use this platform to check if the identified genes are known drug targets.

Technical Architecture

The GWAS Target Finder consists of a Node.js/Express.js backend API and a Next.js frontend application:

  • Backend: RESTful API built with Node.js and Express.js that handles the data retrieval and processing from external databases.
  • Frontend: Modern web interface built with Next.js, React, TypeScript, and Tailwind CSS with shadcn UI components.
  • Data Flow: The frontend communicates with the backend API, which in turn queries the external databases (GWAS Catalog, Ensembl, Open Targets) and processes the results.