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Am. J. Hum. Genet. 76:887883, 2005 A Note on Exact Tests of Hardy-Weinberg Equilibrium

Summary: Am. J. Hum. Genet. 76:887­883, 2005
A Note on Exact Tests of Hardy-Weinberg Equilibrium
Janis E. Wigginton,1
David J. Cutler,2
and Gonc¸alo R. Abecasis1
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor; and 2
Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore
Deviations from Hardy-Weinberg equilibrium (HWE) can indicate inbreeding, population stratification, and even
problems in genotyping. In samples of affected individuals, these deviations can also provide evidence for association.
Tests of HWE are commonly performed using a simple x2
goodness-of-fit test. We show that this x2
test can have
inflated type I error rates, even in relatively large samples (e.g., samples of 1,000 individuals that include 100
copies of the minor allele). On the basis of previous work, we describe exact tests of HWE together with efficient
computational methods for their implementation. Our methods adequately control type I error in large and small
samples and are computationally efficient. They have been implemented in freely available code that will be useful


Source: Abecasis, Goncalo - Department of Biostatistics, University of Michigan


Collections: Biology and Medicine; Mathematics