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Statistical Inference for Hardy-Weinberg Proportions in the Presence of Missing Genotype Information

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  • Jan Graffelman
  • Milagros Sánchez
  • Samantha Cook
  • Victor Moreno

Abstract

In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking procedure. Missing genotypes are typically discarded prior to testing. In this paper we show that inference for Hardy-Weinberg proportions can be biased when missing values are discarded. We propose to use multiple imputation of missing values in order to improve inference for Hardy-Weinberg proportions. For imputation we employ a multinomial logit model that uses information from allele intensities and/or neighbouring markers. Analysis of an empirical data set of single nucleotide polymorphisms possibly related to colon cancer reveals that missing genotypes are not missing completely at random. Deviation from Hardy-Weinberg proportions is mostly due to a lack of heterozygotes. Inbreeding coefficients estimated by multiple imputation of the missings are typically lowered with respect to inbreeding coefficients estimated by discarding the missings. Accounting for missings by multiple imputation qualitatively changed the results of 10 to 17% of the statistical tests performed. Estimates of inbreeding coefficients obtained by multiple imputation showed high correlation with estimates obtained by single imputation using an external reference panel. Our conclusion is that imputation of missing data leads to improved statistical inference for Hardy-Weinberg proportions.

Suggested Citation

  • Jan Graffelman & Milagros Sánchez & Samantha Cook & Victor Moreno, 2013. "Statistical Inference for Hardy-Weinberg Proportions in the Presence of Missing Genotype Information," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-11, December.
  • Handle: RePEc:plo:pone00:0083316
    DOI: 10.1371/journal.pone.0083316
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    References listed on IDEAS

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    1. Attia John & Thakkinstian Ammarin & McElduff Patrick & Milne Elizabeth & Dawson Somer & Scott Rodney J & Klerk Nicholas de & Armstrong Bruce & Thompson John, 2010. "Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-17, January.
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    Cited by:

    1. Shuntaro Sato & Masao Ueki & Alzheimer’s Disease Neuroimaging Initiative, 2018. "Fast score test with global null estimation regardless of missing genotypes," PLOS ONE, Public Library of Science, vol. 13(7), pages 1-19, July.
    2. Graffelman, Jan, 2015. "Exploring Diallelic Genetic Markers: The HardyWeinberg Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 64(i03).

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