eQTLHap

eQTLHap performs haplotype-based eQTL analysis to detect gene expression associations driven by multi-SNP haplotype blocks using phased genotype data.

Key Features:

• Haplotype-Based Approach: Utilizes haplotype blocks for eQTL analysis to detect complex genetic associations involving multiple SNPs within a block that are often missed by single-SNP methods.
• Enhanced Detection Power: Demonstrates superior performance in simulation studies compared to typical SNP-based eQTL methodologies, especially when the causal architecture involves multiple SNPs.
• Robustness to Phasing Errors: Maintains high sensitivity with minimal influence from phasing errors (less than 4%).

Scientific Applications:

• GEUVADIS and GTEx analysis: Applied to GEUVADIS and GTEx datasets to identify 22 gene expression associations not detectable by single-SNP approaches, with replication in larger studies or across tissues.

Methodology:

Uses phased genotypes from haplotype phasing tools to construct haplotype blocks for association testing and evaluates performance via simulation studies.