A heterozygote–homozygote test of Hardy–Weinberg equilibrium

The century-old Hardy–Weinberg law remains fundamental to population genetics. Typically Hardy–Weinberg equilibrium is tested in unrelated individuals using a χ2 goodness-of-fit test that compares expected and observed numbers of heterozygotes and homozygotes. In this report, we propose a likelihood ratio test for Hardy–Weinberg equilibrium that accommodates a mixture of pedigree and random sample data. The underlying statistical model depends on a parameter γ determining the ratio of heterozygous genotypes to homozygous genotypes among pedigree founders. As our heterozygous–homozygous test accommodates markers with dominant and recessive alleles, it can handle the phase ambiguities encountered in combining several linked single nucleotide polymorphisms into a single supermarker. No prior haplotyping is necessary. Our experience on real and simulated data suggests that the heterozygous–homozygous test has good type-one error and power.