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Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness

Author

Listed:
  • Borchers Bryce

    (Rose-Hulman Institute of Technology)

  • Brown Marshall

    (Seattle Pacific University)

  • McLellan Brian

    (Hope College)

  • Bekmetjev Airat

    (Hope College)

  • Tintle Nathan L

    (Hope College)

Abstract

The genome-wide association (GWA) study is an increasingly popular way to attempt to identify the causal variants in human disease. Duplicate genotyping (or re-genotyping) a portion of the samples in a GWA study is common, though it is typical for these data to be ignored in subsequent tests of genetic association. We demonstrate a method for including duplicate genotype data in linear trend tests of genetic association which yields increased power. We also consider the cost-effectiveness of collecting duplicate genotype data and find that when the relative cost of genotyping to phenotyping and sample acquisition costs is less than or equal to the genotyping error rate it is more powerful to duplicate genotype the entire sample instead of spending the same money to increase the sample size. Duplicate genotyping is particularly cost-effective when SNP minor allele frequencies are low. Practical advice for the implementation of duplicate genotyping is provided. Free software is provided to compute asymptotic and permutation based tests of association using duplicate genotype data as well as to aid in the duplicate genotyping design decision.

Suggested Citation

  • Borchers Bryce & Brown Marshall & McLellan Brian & Bekmetjev Airat & Tintle Nathan L, 2009. "Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-22, May.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:24
    DOI: 10.2202/1544-6115.1433
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    References listed on IDEAS

    as
    1. 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.
    2. Fridley, Brooke L. & Turner, Stephen T. & Chapman, Arlene B. & Rodin, Andrei S. & Boerwinkle, Eric & Bailey, Kent R., 2008. "Reproducibility of genotypes as measured by the affymetrix GeneChip® 100K Human Mapping Array set," Computational Statistics & Data Analysis, Elsevier, vol. 52(12), pages 5367-5374, August.
    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. Airat Bekmetjev & Dirk VanBruggen & Brian McLellan & Benjamin DeWinkle & Eric Lunderberg & Nathan Tintle, 2012. "The Cost-Effectiveness of Reclassification Sampling for Prevalence Estimation," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-6, February.

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