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: 1.52). 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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    • "Tests for pairwise linkage disequilibrium (LD) between all allelic pairs among loci from all sampling sites were calculated in ARLEQUIN. HWE significance was calculated using an exact test (Guo and Thompson, 1992) with a Markov chain of 10 6 steps and 10 5 dememorisation steps. Significance values for LD were calculated using a likelihood-ratio test (LRT) of 20,000 permutations (Slatkin and Excoffier, 1996). "
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