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Exact inference for Hardy-Weinberg proportions with missing genotypes: single and multiple imputation

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10.1534/g3.115.022111
 
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Graffelman, JanMés informacióMés informacióMés informació
Nelson, S.
Gogarten, S.M.
Weir, B.S.
Document typeArticle
Defense date2015-09-15
Rights accessOpen Access
Attribution-NonCommercial-NoDerivs 3.0 Spain
Except where otherwise noted, content on this work is licensed under a Creative Commons license : Attribution-NonCommercial-NoDerivs 3.0 Spain
Abstract
This paper addresses the issue of exact-test based statistical inference for Hardy-Weinberg equilibrium in the presence of missing genotype data. Missing genotypes often are discarded when markers are tested for Hardy-Weinberg equilibrium, which can lead to bias in the statistical inference about equilibrium. Single and multiple imputation can improve inference on equilibrium. We develop tests for equilibrium in the presence of missingness by using both inbreeding coefficients (or, equivalently, ¿2 statistics) and exact p-values. The analysis of a set of markers with a high missing rate from the GENEVA project on prematurity shows that exact inference on equilibrium can be altered considerably when missingness is taken into account. For markers with a high missing rate (>5%), we found that both single and multiple imputation tend to diminish evidence for Hardy-Weinberg disequilibrium. Depending on the imputation method used, 6-13% of the test results changed qualitatively at the 5% leve
CitationGraffelman, J., Nelson, S., Gogarten, S., Weir, B. Exact inference for Hardy-Weinberg proportions with missing genotypes: single and multiple imputation. "G3-Genes Genomes Genetics", 15 Setembre 2015, vol. 5, núm. 11, p. 2365-2373. 
URIhttp://hdl.handle.net/2117/82666
DOI10.1534/g3.115.022111
ISSN2160-1836
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  • COSDA-UPC - COmpositional and Spatial Data Analysis - Articles de revista [88]
  • Departament d'Estadística i Investigació Operativa - Articles de revista [604]
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