tooluniverse-gwas-trait-to-gene

Search GWAS Catalog associations for the trait using gwas_search_associations, filter by genome-wide significance (p < 5e-8), then aggregate mapped genes across studies. Enrich results with Open Targets L2G scores for fine-mapped causal gene predictions.

L2G (locus-to-gene) is an Open Targets score from 0 to 1 that integrates eQTL, chromatin interaction, and distance evidence to predict causal genes. A score above 0.5 is considered a strong prediction, outperforming nearest-gene positional mapping.

This tool returns errors for most queries and is documented as broken. Use gwas_search_associations with the trait as the query parameter instead, which returns data in a {data, metadata} response format.

No. GWAS identifies correlated variants, not confirmed causal genes, and linkage disequilibrium means the lead SNP may tag a nearby gene. Treat results as ranked candidates requiring replication across cohorts and orthogonal validation such as eQTL or knockout data.

Most GWAS use European populations, so effect sizes and implicated genes can differ across ancestries. Fine-mapping covers only a subset of studies, intergenic variants are hard to map, and small older studies may produce false negatives.