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Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium

Author

Listed:
  • Attia John

    (University of Newcastle)

  • Thakkinstian Ammarin

    (Mahidol University)

  • McElduff Patrick

    (University of Newcastle)

  • Milne Elizabeth

    (University of Western Australia)

  • Dawson Somer

    (University of Western Australia)

  • Scott Rodney J

    (University of Newcastle)

  • Klerk Nicholas de

    (University of Western Australia)

  • Armstrong Bruce

    (University of Sydney)

  • Thompson John

    (University of Leicester)

Abstract

Tests for Hardy-Weinberg equilibrium (HWE) have been used to detect genotyping error, but those tests have low power unless the sample size is very large. We assessed the performance of measures of departure from HWE as an alternative way of screening for genotyping error. Three measures of the degree of disequilibrium (?, ,D, and F) were tested for their ability to detect genotyping error of 5% or more using simulations and a real dataset of 184 children with leukemia genotyped at 28 single nucleotide polymorphisms. The simulations indicate that all three disequilibrium coefficients can usefully detect genotyping error as judged by the area under the Receiver Operator Characteristic (ROC) curve. Their discriminative ability increases as the error rate increases, and is greater if the genotyping error is in the direction of the minor allele. Optimal thresholds for detecting genotyping error vary for different allele frequencies and patterns of genotyping error but allele frequency-specific thresholds can be nominated. Applying these thresholds would have picked up about 90% of genotyping errors in our actual dataset. Measures of departure from HWE may be useful for detecting genotyping error, but this needs to be confirmed in other real datasets.

Suggested Citation

  • 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.
    • Handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:5
    DOI: 10.2202/1544-6115.1463
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    References listed on IDEAS

    as
    1. Ahn Kwangmi & Gordon Derek & Finch Stephen J, 2009. "Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-11, May.
    2. Tintle Nathan L & Gordon Derek & McMahon Francis J & Finch Stephen J, 2007. "Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 6(1), pages 1-29, February.
    3. Gordon Derek & Yang Yaning & Haynes Chad & Finch Stephen J & Mendell Nancy R & Brown Abraham M & Haroutunian Vahram, 2004. "Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-35, October.
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    Cited by:

    1. 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.
    2. Graffelman Jan & Moreno Victor, 2013. "The mid p-value in exact tests for Hardy-Weinberg equilibrium," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(4), pages 433-448, August.
    3. Brentani Helena & Nakano Eduardo Y & Martins Camila B & Izbicki Rafael & Pereira Carlos Alberto, 2011. "Disequilibrium Coefficient: A Bayesian Perspective," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, May.

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