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Abstract:
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Hardy-Weinberg equilibrium (HWE), which specifies the relationships between allele frequencies under random mating, has been central to genetics for 100 years. One important application in modern times is in quality control for high-throughput genotyping, where departures from HWE are a valuable diagnostic. Some large cohort studies are conducting large-scale genotyping on a subsample of their participants, to reduce costs. HWE will typically not hold in the subsample, especially when participants experiencing medical events are oversampled. I will discuss HWE testing under subsampling. It is straightforward to develop a large-sample, design-based test, which I will present, but large-sample tests for HWE have notoriously poor performance at practical sample sizes and allele frequencies. I will also present a modification of Fisher's exact HWE test for unequal probability sampling.
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