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

ABSTRACT: 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)

SUBMITTER: You XP 

PROVIDER: S-EPMC4684405 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature