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Eur J Hum Genet. 2009 Nov;17(11):1495-500. doi: 10.1038/ejhg.2009.57. Epub 2009 Apr 15.

A heterozygote-homozygote test of Hardy-Weinberg equilibrium.

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Department of Biomathematics, The University of California, Los Angeles, 90095, USA.


The century-old Hardy-Weinberg law remains fundamental to population genetics. Typically Hardy-Weinberg equilibrium is tested in unrelated individuals using a chi(2) 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 gamma 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.

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