Testing Hardy-Weinberg disequilibrium using the generalized linear model

Abstract

Current methods for detecting Hardy-Weinberg disequilibrium (HWD) only deal with one locus at a time. We developed a method that can jointly detect HWD for multiple loci. The method was developed under the generalized linear model (GLM) using the probit link function. When applied to a single locus, the new method is more powerful than the exact test. When applied to two or more loci, the method can reduce false positives caused by linkage disequilibrium (LD). We applied the method to 24 single nucleotide polymorphism (SNP) markers of a single human gene and eliminated several false positive HWDs due to LD. We developed an R package 'hwdglm' for joint HWD detection, which can be downloaded from our personal website (www.statgen.ucr.edu).