tooluniverse-gwas-trait-to-gene

Use Cases

Clinical Research

• "What genes are associated with type 2 diabetes?"
• "Find genetic risk factors for coronary artery disease"
• "Which genes contribute to Alzheimer's disease susceptibility?"

Drug Target Discovery

• Identify genes with strong genetic evidence for disease causation
• Prioritize targets based on L2G scores and replication across studies
• Find genes with genome-wide significant associations (p < 5e-8)

Functional Genomics

• Map disease-associated variants to candidate genes
• Analyze genetic architecture of complex traits
• Understand polygenic disease mechanisms

Key Concepts

Genome-wide Significance

• Standard threshold: p < 5×10⁻⁸
• Accounts for multiple testing burden across ~1M common variants
• Higher confidence: p < 5×10⁻¹⁰ or replicated across studies

Gene Mapping Methods

• Positional: Nearest gene to lead SNP
• Fine-mapping: Statistical refinement to credible variants
• Locus-to-Gene (L2G): Integrative score combining multiple evidence types

Evidence Confidence Levels

• High: L2G score > 0.5 OR multiple studies with p < 5e-10
• Medium: 2+ studies with p < 5e-8
• Low: Single study or marginal significance

GWAS Catalog (11 tools)

• gwas_get_associations_for_trait - Get all associations for a trait (sorted by p-value)
• gwas_search_snps - Search SNPs by gene mapping
• gwas_get_snp_by_id - Get SNP details (MAF, consequence, location)
• gwas_get_study_by_id - Get study metadata
• gwas_search_associations - Search associations with filters
• gwas_search_studies - Search studies by trait/cohort
• gwas_get_associations_for_snp - Get all associations for a SNP
• gwas_get_variants_for_trait - Get variants for a trait
• gwas_get_studies_for_trait - Get studies for a trait
• gwas_get_snps_for_gene - Get SNPs mapped to a gene
• gwas_get_associations_for_study - Get associations from a study