A copula-based set-variant association test for bivariate continuous or mixed phenotypes

TL;DR

This paper introduces CBMAT, a novel copula-based method for detecting associations between genetic regions and bivariate traits, effectively handling non-normal and mixed phenotype distributions in GWAS.

Contribution

The paper develops a flexible copula-based multivariate association test that overcomes limitations of existing methods assuming normality, with a data-driven p-value approach.

Findings

CBMAT controls type I error well in simulations.

CBMAT shows higher power than existing methods for non-normal traits.

Application to lipid data identified significant gene-phenotype associations.

Abstract

In genome wide association studies (GWAS), researchers are often dealing with non-normally distributed traits or a mixture of discrete-continuous traits. However, most of the current region-based methods rely on multivariate linear mixed models (mvLMMs) and assume a multivariate normal distribution for the phenotypes of interest. Hence, these methods are not applicable to disease or non-normally distributed traits. Therefore, there is a need to develop unified and flexible methods to study association between a set of (possibly rare) genetic variants and non-normal multivariate phenotypes. Copulas are multivariate distribution functions with uniform margins on the $[0, 1]$ interval and they provide suitable models to deal with non-normality of errors in multivariate association studies. We propose a novel unified and flexible Copula-Based Multivariate Association Test (CBMAT) for discovering association between a genetic region and a bivariate continuous or mixed phenotype. We also derive a data-driven analytic p-value procedure of the proposed region-based score-type test. Through simulation studies, we demonstrate that CBMAT has well controlled type I error rates and higher power to detect associations compared with other existing methods, for discrete and non-normally distributed traits. At last, we apply CBMAT to detect the association between two genes located on chromosome 11 and several lipid levels measured on 1,477 subjects from the ASLPAC study.