A Bayesian hierarchically structured prior for gene-based association testing with multiple traits in genome-wide association studies

Yi Yang, Saonli Basu, Lin Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

Although genome-wide association studies (GWAS) often collect data on multiple correlated traits for complex diseases, conventional gene-based analysis is usually univariate, and therefore, treating traits as uncorrelated. Multivariate analysis of multiple correlated traits can potentially increase the power to detect genes that affect some or all of these traits. In this study, we propose the multivariate hierarchically structured variable selection (HSVS-M) model, a flexible Bayesian model that tests the association of a gene with multiple correlated traits. With only summary statistics, HSVS-M can account for the correlations among genetic variants and among traits simultaneously and can also estimate the various directions and magnitudes of associations between a gene and multiple traits. Simulation studies show that HSVS-M substantially outperforms competing methods in various scenarios, particularly when variants in a gene are associated with a trait in similar directions and magnitudes. We applied HSVS-M to the summary statistics of a meta-analysis GWAS on four lipid traits from the Global Lipids Genetics Consortium and identified 15 genes that have also been confirmed as risk factors in previous studies.

Original languageEnglish (US)
Pages (from-to)63-72
Number of pages10
JournalGenetic epidemiology
Volume46
Issue number1
DOIs
StatePublished - Feb 2022

Bibliographical note

Funding Information:
This study is supported in part by grants to S.B. from the National Institutes of Health/National Institute on Drug Abuse 5R01DA033958‐02 and 1R21DA046188‐01A1. This study makes use of data generated by the Global Lipids Genetics Consortium.

Publisher Copyright:
© 2021 Wiley Periodicals LLC

PubMed: MeSH publication types

  • Journal Article
  • Meta-Analysis
  • Research Support, N.I.H., Extramural

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