ColocQuiaL

ColocQuiaL performs colocalization tests between single-tissue expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) from the Genotype-Tissue Expression (GTEx) version 8 database and genome-wide association study (GWAS) signals to identify shared causal variants.

Key Features:

• Scalable framework: Enables genome-wide colocalization analyses across loci at scale.
• Integration with GTEx v8 data: Uses single-tissue eQTLs and sQTLs from GTEx version 8 for colocalization comparisons.
• Statistical colocalization via COLOC: Applies the COLOC statistical method to evaluate sharing of causal variants between QTLs and GWAS signals.
• Comprehensive output: Produces summary files and locus visualization plots for reviewed colocalization results.
• R implementation: Implemented primarily in R for computational analyses.

Scientific Applications:

• Linking GWAS signals to genes: Supports identification of candidate causal genes by testing overlap between GWAS signals and eQTLs/sQTLs.
• Studying genetic architecture: Assists investigation of the genetic architecture of complex traits and diseases through colocalization of expression and splicing QTLs with GWAS loci.
• Applied case study: Has been applied to type 2 diabetes GWAS data in conjunction with GTEx v8 datasets to identify potential causal relationships.

Methodology:

ColocQuiaL employs the COLOC statistical method to assess the likelihood that eQTLs/sQTLs and GWAS signals share a common causal variant.