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Originally published as Genetics Published Articles Ahead of Print on September 15, 2004.

Genetics, Vol. 168, 2349-2361, December 2004, Copyright © 2004
doi:10.1534/genetics.104.031617

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Testing for Hardy-Weinberg Equilibrium in Samples With Related Individuals

Catherine Bourgain*,1, Mark Abney{dagger}, Daniel Schneider{dagger}, Carole Ober{dagger} and Mary Sara McPeek{dagger},{ddagger}

* INSERM U535, 94817 Villejuif Cedex, France
{dagger} Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
{ddagger} Department of Statistics, University of Chicago, Chicago, Illinois 60637

1 Corresponding author: INSERM U535, Hopital Paul Brousse, Batiment Leriche, BP 100, 94817 Villejuif Cedex, France.
E-mail: bourgain{at}vjf.inserm.fr

When the classical {chi}2 goodness-of-fit test for Hardy-Weinberg (HW) equilibrium is used on samples with related individuals, the type I error can be greatly inflated. In particular the test is inappropriate in population isolates where the individuals are related through multiple lines of descent. In this article, we propose a new test for HW (the QL-HW test) suitable for any sample with related individuals, including large inbred pedigrees, provided that their genealogy is known. Performed conditional on the pedigree structure, the QL-HW test detects departures from HW that are not due to the genealogy. Because the computation of the QL-HW test becomes intractable for very polymorphic loci in large inbred pedigrees, a simpler alternative, the GCC-HW test, is also proposed. The statistical properties of the QL-HW and GCC-HW tests are studied through simulations considering a sample of independent nuclear families, a sample of extended outbred genealogies, and samples from the Hutterite population, a North American highly inbred isolate. Finally, the method is used to test a set of 143 biallelic markers spanning 82 genes in this latter population.




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