A heterozygote-homozygote test of Hardy-Weinberg equilibrium

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

Abstract

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.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Female
  • Gene Frequency
  • Genetic Markers
  • Genetics, Population*
  • Heterozygote*
  • Homozygote*
  • Humans
  • Likelihood Functions
  • Male
  • Models, Genetic
  • Models, Statistical*
  • Polymorphism, Single Nucleotide*

Substances

  • Genetic Markers