Abstract
Genome-wide scans for deviations from Hardy-Weinberg equilibrium (HWE) are commonly applied to detect genotyping errors. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations towards equilibrium. Several populations world-wide have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry and thus in allele frequencies. Sex-biased admixture makes testing for HWE difficult on X, because deviations are naturally expected, even under random mating post-admixture and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ2 test that detect deviations from HWE on X while allowing for natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations (e.g., as a quality control step), our tests reject fewer SNPs (among those showing frequency differences between the sexes) than other tests.
