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Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations

Wei Hao, John D. Storey
doi: https://doi.org/10.1101/240804
Wei Hao
*Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA. Email: .
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  • For correspondence: whao@princeton.edu
John D. Storey
†Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA. Email: .
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  • For correspondence: jstorey@princeton.edu
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Abstract

Testing for Hardy-Weinberg equilibrium (HWE) is an important component in almost all analyses of population genetic data. Genetic markers that violate HWE are often treated as special cases; for example, they may be flagged as possible genotyping errors or they may be investigated more closely for evolutionary signatures of interest. The presence of population structure is one reason why genetic markers may fail a test of HWE. This is problematic because almost all natural populations studied in the modern setting show some degree of structure. Therefore, it is important to be able to detect deviations from HWE for reasons other than structure. To this end, we extend statistical tests of HWE to allow for population structure, which we call a test of “structural HWE” (sHWE). Additionally, our new test allows one to automatically choose tuning parameters and identify accurate models of structure. We demonstrate our approach on several important studies, provide theoretical justification for the test, and present empirical evidence for its utility. We anticipate the proposed test will be useful in a broad range of analyses of genome-wide population genetic data.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted December 29, 2017.
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Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations
Wei Hao, John D. Storey
bioRxiv 240804; doi: https://doi.org/10.1101/240804
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Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations
Wei Hao, John D. Storey
bioRxiv 240804; doi: https://doi.org/10.1101/240804

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