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doi:10.1534/genetics.104.031617
A more recent version of this article appeared on December 1, 2004.
Regular Research Papers |
Testing for Hardy-Weinberg equilibrium in samples with related individuals
Catherine Bourgain 1*, Mark Abney 2, Dan Schneider 2, Carole Ober 2 and Mary Sara Mc Peek 3
1 INSERM U535
2 Dpt Human Genetics, University of Chicago
3 Dpt Statistics, University of Chicago
* To whom correspondence should be addressed. E-mail: bourgain{at}vjf.inserm.fr.
Submitted on May 28, 2004
Revised on July 20, 2004
Accepted on 2 September 2004
When the classical 
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 paper, 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 bi-allelic markers spanning 82 genes in this latter population.
Key Words: Hardy-weinberg equilibrium, complex pedigrees, genotyping error, quasi-likelihood, score test
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