Likelihood Ratio Test for Excess Homozygosity at Marker Loci on X Chromosome

The assumption of Hardy-Weinberg equilibrium (HWE) is generally required for association analysis using case-control design on autosomes; otherwise, the size may be inflated. There has been an increasing interest of exploring the association between diseases and markers on X chromosome and the effect of the departure from HWE on association analysis on X chromosome. Note that there are two hypotheses of interest regarding the X chromosome: (i) the frequencies of the same allele at a locus in males and females are equal and (ii) the inbreeding coefficient in females is zero (without excess homozygosity). Thus, excess homozygosity and significantly different minor allele frequencies between males and females are used to filter X-linked variants. There are two existing methods to test for (i) and (ii), respectively. However, their size and powers have not been studied yet. Further, there is no existing method to simultaneously detect both hypotheses till now. Therefore, in this article, we propose a novel likelihood ratio test for both (i) and (ii) on X chromosome. To further investigate the underlying reason why the null hypothesis is statistically rejected, we also develop two likelihood ratio tests for detecting (i) and (ii), respectively. Moreover, we explore the effect of population stratification on the proposed tests. From our simulation study, the size of the test for (i) is close to the nominal significance level. However, the size of the excess homozygosity test and the test for both (i) and (ii) is conservative. So, we propose parametric bootstrap techniques to evaluate their validity and performance. Simulation results show that the proposed methods with bootstrap techniques control the size well under the respective null hypothesis. Power comparison demonstrates that the methods with bootstrap techniques are more powerful than those without bootstrap procedure and the existing methods. The application of the proposed methods to a rheumatoid arthritis dataset indicates their utility.