LDexpress

LDexpress maps population-specific linkage disequilibrium from the 1000 Genomes Project to tissue-specific gene expression from GTEx to connect GWAS-identified germline variants with nearby gene expression and nominate candidate genes.

Key Features:

• Integration of Diverse Data Sources: Combines population-specific LD data from the 1000 Genomes Project with tissue-specific expression profiles from GTEx to link germline variation to nearby gene expression.
• Population-specific LD Analysis: Uses population-specific LD patterns to account for genetic diversity across different 1000 Genomes populations when mapping variants to genes.
• Tissue-specific Expression Context: Incorporates GTEx tissue-specific expression data to provide context-dependent insights into gene regulation.
• Support for Multiple Query Variants: Enables analysis of multiple query variants simultaneously for large-scale variant interrogation.
• Candidate Gene Nomination: Maps regional germline variation to changes in nearby gene expression to nominate candidate genes for functional follow-up.

Scientific Applications:

• Cancer Research: Facilitates interpretation of GWAS loci in cancer by linking germline variants to tissue-specific gene expression.
• GWAS Follow-up and Interpretation: Supports post-GWAS analyses to identify candidate genes underlying association signals.
• Study of Genetic Architecture of Complex Traits: Enables investigation of how regional germline variation influences nearby gene expression across tissues and populations.

Methodology:

Mapping germline variations identified in GWAS to nearby gene expression; utilizing population-specific LD data from the 1000 Genomes Project; and incorporating tissue-specific expression data from GTEx.