AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS

MOTIVATION: Pharmacogenomics (PGx) research holds the promise for detecting association between genetic variants and drug responses in randomized clinical trials, but it is limited by small populations and thus has low power to detect signals. It is critical to increase the power of PGx genome-wide association studies (GWAS) with small sample sizes so that variant–drug-response association discoveries are not limited to common variants with extremely large effect. RESULTS: In this article, we first discuss the challenges of PGx GWAS studies and then propose the adaptively weighted joint test (AWOT) and Cauchy Weighted jOint Test (CWOT), which are two flexible and robust joint tests of the single nucleotide polymorphism main effect and genotype-by-treatment interaction effect for continuous and binary endpoints. Two analytic procedures are proposed to accurately calculate the joint test P-value. We evaluate AWOT and CWOT through extensive simulations under various scenarios. The results show that the proposed AWOT and CWOT control type I error well and outperform existing methods in detecting the most interesting signal patterns in PGx settings (i.e. with strong genotype-by-treatment interaction effects, but weak genotype main effects). We demonstrate the value of AWOT and CWOT by applying them to the PGx GWAS from the Bezlotoxumab Clostridium difficile MODIFY I/II Phase 3 trials. AVAILABILITY AND IMPLEMENTATION: The R package COWT is publicly available on CRAN https://cran.r-project.org/web/packages/cwot/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.