The approximate variance for the standardized measure of gametic linkage disequilibrium has been described. However, this approach assumes knowledge of the phase of double heterozygotes or Hardy-Weinberg equilibrium. Here we give the approximate variance for a composite measure of linkage disequilibrium which depends only on genotype frequencies. We show by simulation that this variance approxi...

Hardy-Weinberg equilibrium (HWE) holds when, in a closed population with random mating and without mutation and natural selection, genotype frequencies at any locus is a simple function of allele frequencies. Testing for HWE is now a common practice in population genetics and genetic association studies of non-communicable diseases; however, it is less-regarded, or sometimes miss-interpreted, i...

Testing for Hardy-Weinberg equilibrium is ubiquitous and has traditionally been carried out via frequentist approaches. However, the discreteness of the sample space means that uniformity of p-values under the null cannot be assumed, with enumeration of all possible counts, conditional on the minor allele count, offering a computationally expensive way of p-value calibration. In addition, the i...

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It is well established that test statistics and P-values derived from discrete data, such as genetic markers, are also discrete. In most genetic applications, the null distribution for a discrete test statistic is approximated with a continuous distribution, but this approximation may not be reasonable. In some cases using the continuous approximation for the expected null distribution may caus...

Hardy-Weinberg equilibrium (HWE) is the state of the genotypic frequency of two alleles of one autosomal gene locus after one discrete generation of random mating in an indefinitely large population: if the alleles are A and a with frequencies p and q(=1-p), then the equilibrium gene frequencies are simply p and q and the equilibrium genotypic frequencies for AA, Aa and aa are p2, 2pq and q2. I...