Adaptive gene- and pathway-trait association testing with GWAS summary statistics

• DOI: 10.1093/bioinformatics/btv719
• Publication Date: 2015-12-12T01:49:22Z
• Authors: Il-Youp Kwak; Wei Pan
• Keywords: Genome-wide Association Study; Association (psychology); Trait; Genetic Association; Summary statistics

Abstract Background: Gene- and pathway-based analyses offer a useful alternative complement to the usual single SNP-based analysis for GWAS. On other hand, most existing gene- tests are not highly adaptive, and/or require availability of individual-level genotype phenotype data. It would be desirable have adaptive applicable summary statistics SNPs. This has become increasingly important given popularity large-scale meta-analyses multiple GWASs practical either GWAS or meta-analyzed Results: We extend two pathway-level association with univariate trait case without use WTCCC data evaluate compare proposed methods several methods. further illustrate their applications dataset identify genes pathways associated blood pressure, demonstrating potential usefulness The implemented in R package aSPU, freely publicly available. Availability implementation: https://cran.r-project.org/web/packages/aSPU/ Contact: [e-mail] Supplementary information: available at Bioinformatics online.