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Abstract:
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Many statistical methods for analyzing genetic data assume Hardy Weinberg Equilibrium (HWE), such as those used in genome wide association studies. Therefore, to use such methods, one must check whether the HWE assumption is valid. For a case-control study, researchers have recognized that Hardy Weinberg proportions will be distorted if the marker being tested happens to be associated with the disease. To deal with this, it is typical that HWE tests are carried out only on controls. This raises the question of whether controls as a whole is a good representation of the population. One may justify this by further assuming that the disease is rare. However, many diseases being studied are in fact common, and even worse, the rare disease assumption is often conveniently forgotten. In this study, we attempt to answer a number of questions related to HWE testing. We consider whether the rare disease assumption is sufficient for the controls to be representative of the population. We additionally investigate whether it is justifiable to perform HWE testing on controls only even if the disease being studied is rare.
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