Distributions of Hardy-Weinberg equilibrium test statistics

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 cause truly null test statistics to appear nonnull. We explore the implications of using continuous distributions to approximate the discrete distributions of Hardy-Weinberg equilibrium test statistics and P-values. We derive exact P-value distributions under the null and alternative hypotheses, enabling a more accurate analysis than is possible with continuous approximations. We apply these methods to biological data and find that using continuous distribution theory with exact tests may underestimate the extent of Hardy-Weinberg disequilibrium in a sample. The implications may be most important for the widespread use of whole-genome case-control association studies and Hardy-Weinberg equilibrium (HWE) testing for data quality control.