– in other words, do the genotypes in your sample deviate from Hardy–Weinberg equilibrium (HWE)? In the simple case of a bi-allelic variant, like a SNP, the expected distribution of genotypes is easily derived via a Punnett square, and HWE can be tested using Pearson's Chi-square. In contrast, examining polymorphisms with more variants and/or in smaller samples might require use of Fisher's exact test. Moreover, departures from HWE can result from a variety of population level disturbances that are out of the researchers’ control (assortative mating, selection, mutation, and migration). It should be noted, however, that studies which oversample for specific traits or disorders (e.g., case–control designs) will also, to the extent that they examine genetic variants associated with those characteristics, yield deviations from HWE.
