ArticleGenetic epidemiology2011
Approximate and exact tests of Hardy-Weinberg equilibrium using uncertain genotypes.
Article in Genetic epidemiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Efficient test for deviation from Hardy-Weinberg equilibrium with known or ambiguous typing in highly polymorphic loci.Briefings in bioinformatics · 2024Article
- Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists.Frontiers in genetics · 2022Article
- A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Prospective cohort study of the risk factors for stress fractures in Chinese male infantry recruits.The Journal of international medical research · 2016Article
- Impact of Hardy-Weinberg disequilibrium on post-imputation quality control.Human genetics · 2013Article
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1 author.
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Abstract
Testing for Hardy-Weinberg equilibrium (HWE) is commonly used as a quality control filter in genome-wide scans for markers with experimentally determined genotypes. In contrast, for markers with imputed genotypes, there are post-imputation metrics of quality that can be used as screens but there are no formal tests of deviation from HWE. Similarly, there are no formal tests of deviation from HWE for probabilistic genotypes that are generated by sequencing projects. Here, I describe generalizations of the approximate χ(2) and exact tests of HWE for use with uncertain genotypes. The tests fully account for the probabilities of all possible genotypes at a marker for each individual. By computer simulation, the approximate and exact tests are shown to maintain valid control of the type I error rate. Calculations of the loss of power as the uncertainty in genotypes increases are illustrated. The tests are compatible with chip-based genotypes for single-nucleotide polymorphisms and copy number polymorphisms, imputed genotypes, and probabilistic assignments of genotype from variable-coverage sequence data.
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