Published in

Frontiers Media, Frontiers in Genetics, (12), 2021

DOI: 10.3389/fgene.2021.644419

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An Omnibus Test for Detecting Multiple Phenotype Associations Based on GWAS Summary Level Data

Journal article published in 2021 by Wei Liu, Yunshan Guo, Zhonghua Liu ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

Abundant Genome-wide association study (GWAS) findings have reflected the sharing of genetic variants among multiple phenotypes. Exploring the association between genetic variants and multiple traits can provide novel insights into the biological mechanism of complex human traits. In this article, we proposed to apply the generalized Berk-Jones (GBJ) test and the generalized higher criticism (GHC) test to identify the genetic variants that affect multiple traits based on GWAS summary statistics. To be more robust to different gene-multiple traits association patterns across the whole genome, we proposed an omnibus test (OMNI) by using the aggregated Cauchy association test. We conducted extensive simulation studies to investigate the type one error rates and compare the powers of the proposed tests (i.e., the GBJ, GHC and OMNI tests) and the existing tests (i.e., the minimum of the p-values (MinP) and the cross-phenotype association test (CPASSOC) in a wide range of simulation settings. We found that all of these methods could control the type one error rates well and the proposed OMNI test has robust power. We applied those methods to the summary statistics dataset from Global Lipids Genetics Consortium and identified 19 new genetic variants that were missed by the original single trait association analysis.