Gene- and pathway-based association tests for multiple traits with GWAS summary statistics

• DOI: 10.1093/bioinformatics/btw577
• Publication Date: 2016-09-05T00:07:40Z
• Authors: Il-Youp Kwak; Wei Pan
• Keywords: Genome-wide Association Study; Trait; Genetic Association; Summary statistics; SNP; Association test; Statistical power; Association (psychology)

To identify novel genetic variants associated with complex traits and to shed new insights on underlying biology, in addition the most popular single SNP-single trait association analysis, it would be useful explore multiple correlated (intermediate) at gene- or pathway-level by mining existing GWAS meta-analyzed data. For this purpose, we present an adaptive gene-based test a pathway-based for analysis of summary statistics. The proposed tests are both SNP- trait-levels; that is, they account possibly varying patterns (e.g. signal sparsity levels) across SNPs traits, thus maintaining high power wide range situations. Furthermore, methods general: can applied mixed types Z-statistics P-values as statistics obtained from either meta-analysis GWAS. Our numerical studies simulated real data demonstrated promising performance methods.The implemented R package aSPU, freely publicly available at: https://cran.r-project.org/web/packages/aSPU/ CONTACT: [e-mail] information: Supplementary Bioinformatics online.