Genetic Epidemiology

A fast and powerful eQTL weighted method to detect genes associated with complex trait using GWAS summary data

Early View

Abstract Although genomewide association studies (GWASs) have identified many genetic variants underlying complex traits, a large fraction of heritability still remains unexplained. Integrative analysis that incorporates additional information, such as expression quantitativetrait locus (eQTL) data into sequencing studies (denoted as transcriptomewide association study [TWAS]), can aid the discovery of trait‐associated genetic variants. However, general TWAS methods only incorporate one eQTL‐derived weight (e.g., cis‐effect), and thus can suffer a substantial loss of power when the single estimated cis‐effect is not predictive for the effect size of a genetic variant or when there are estimation errors in the estimated cis‐effect, or if the data are not consistent with the model assumption. In this study, we propose an omnibus test (OT) which utilizes a Cauchy association test to integrate association evidence demonstrated by three different traditional tests (burden test, quadratic test, and adaptive test) using GWAS summary data with multiple eQTL‐derived weights. The p value of the proposed test can be calculated analytically, and thus it is fast and efficient. We applied our proposed test to two schizophrenia (SCZ) GWAS summary data sets and two lipids trait (HDL) GWAS summary data sets. Compared with the three traditional tests, our proposed OT can identify more trait‐associated genes.

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