Article

Performing the Exact Test of Hardy-Weinberg Proportion for Multiple Alleles

Department of Statistics, University of Washington Seattle, Seattle, Washington, United States
Biometrics (Impact Factor: 1.57). 07/1992; 48(2):361-72. DOI: 10.2307/2532296
Source: PubMed

ABSTRACT

The Hardy-Weinberg law plays an important role in the field of population genetics and often serves as a basis for genetic inference. Because of its importance, much attention has been devoted to tests of Hardy-Weinberg proportions (HWP) over the decades. It has long been recognized that large-sample goodness-of-fit tests can sometimes lead to spurious results when the sample size and/or some genotypic frequencies are small. Although a complete enumeration algorithm for the exact test has been proposed, it is not of practical use for loci with more than a few alleles due to the amount of computation required. We propose two algorithms to estimate the significance level for a test of HWP. The algorithms are easily applicable to loci with multiple alleles. Both are remarkably simple and computationally fast. Relative efficiency and merits of the two algorithms are compared. Guidelines regarding their usage are given. Numerical examples are given to illustrate the practicality of the algorithms.

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    • "The Fisher's exact test was used to check for genotypic linkage disequilibrium for all pairs of loci by employing the Markov chain method, as implemented in GENEPOP[6]. Deviations from Hardy–Weinberg (HW) proportions were evaluated through the Weir and Cockerham's[7]and Robertson and Hill's[8]estimates of F IS to test for heterozygote deficit with Levene's correction for small sample size, using the method described by Guo and Thompson[9]. "
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    • "equilibrium (HWE) was assessed using the procedure of Guo and Thompson (1992) "
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    • "Deviations from Hardy–Weinberg equilibrium (HWE) were tested with the exact test (Guo and Thompson, 1992), as implemented in GENEPOP 3.4 (Rousset, 2008) and Arlequin 3.5 (Excoffier and Lischer, 2010). Genetic differentiation between populations was measured with pairwise F ST estimates (Weir and Cockerham, 1984), using Arlequin 3.5 (Excoffier and Lischer, 2010). "
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