CMAX3: A Robust Statistical Test for Genetic Association Accounting for Covariates

Abstract

The additive genetic model as implemented in logistic regression has been widely used in genome-wide association studies (GWASs) for binary outcomes. Unfortunately, for many complex diseases, the underlying genetic models are generally unknown and a mis-specification of the genetic model can result in a substantial loss of power. To address this issue, the MAX3 test (the maximum of three separate test statistics) has been proposed as a robust test that performs plausibly regardless of the underlying genetic model. However, the original implementation of MAX3 utilizes the trend test so it cannot adjust for any covariates such as age and gender. This drawback has significantly limited the application of the MAX3 in GWASs, as covariates account for a considerable amount of variability in these disorders. In this paper, we extended the MAX3 and proposed the CMAX3 (covariate-adjusted MAX3) based on logistic regression. The proposed test yielded a similar robust efficiency as the original MAX3 while easily adjusting for any covariate based on the likelihood framework. The asymptotic formula to calculate the p-value of the proposed test was also developed in this paper. The simulation results showed that the proposed test performed desirably under both the null and alternative hypotheses. For the purpose of illustration, we applied the proposed test to re-analyze a case-control GWAS dataset from the Collaborative Studies on Genetics of Alcoholism (COGA). The R code to implement the proposed test is also introduced in this paper and is available for free download.

Robust tests for combining p-values under arbitrary dependency structures

“…With recent advancements in biotechnologies, huge amount of data has been generated in genetics and genomics studies. For instance, in genomewide association studies (GWAS) to identify genetic risk factors associated with given disease, many gene-or set-based association tests have been developed which utilize the approaches for combining p-values [10][11][12][13][14] . How to combine these p-values is still a challenging topic in the area.…”