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.
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