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

By Il-Youp Kwak, Wei Pan

Posted 07 May 2016
bioRxiv DOI: 10.1101/052068 (published DOI: 10.1093/bioinformatics/btw577)

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

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