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


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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    DESCRIPTION: Populations of the European brown bear (Ursus arctos L.) differ substantially in size, degree of geographic isolation and level of genetic diversity. Present patterns result from phylogeographic processes and profound human intervention. We assessed the genetic variability of a subpopulation of brown bears near the periphery of their range in the Western Carpathian Mountains and compared their genetic properties with those of bears in the core of the same population and elsewhere. Samples were collected non-invasively in 2007-2008 and 2010 in Strážovské vrchy Protected Landscape Area (PLA) in Slovakia (included to the NATURA 2000 networking programme). Seven polymorphic microsatellite loci (UaMU26, UaMU64, G10B, G1D, G10L, UaMU50 and UaMU51) were amplified using a nested PCR in order to assess the following parameters: variability, allelic combinations, heterozygosity, number of alleles and inbreeding coefficient. Sufficient brown bear DNA for analysis was obtained from 57 out of 140 samples (41%), among which 45 different genotypes were identified. Loci had a mean of 2.71 ± 0.76 alleles. Average observed heterozygosity was 0.59. The inbreeding coefficient was negative for all but one of the analysed loci (2007-2008). In the year 2010 was negative three of seven loci. These results imply that gene flow with other parts of the population has been maintained in the reduced level and the isolation level of bears in the study area was not so low. Nevertheless, the genetic variability of bears in Strážovské vrchy PLA was lower than that reported from other localities in the Carpathian Mountains. The results are discussed in the context of behavioural ecology and conservation genetics.
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    • "equilibrium (HWE) was assessed using the procedure of Guo and Thompson (1992) "
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    Full-text · Article · Mar 2016
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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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