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Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data

Qiong Li, Hélène Massam and Xin Gao

Testing for Hardy-Weinberg equilibrium of genotype frequencies is a crucial first step in the study of population genetics. In this paper, we develop an Expectation-Maximization algorithm to estimate the genotype frequencies for sibship data with genotype uncertainty. We also develop a likelihood ratio test of Hardy-Weinberg equilibrium for sibships with no parental genotypes available and with possible genotyping errors. Simulations show that our likelihood ratio test maintains valid control of the type I error rate and good statistical power. Finally, the likelihood ratio test is extended across strata when a sample is stratified by multiple ethnic populations with different genotype frequencies.