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A Review of Family-Based Tests for Linkage Disequilibrium between a Quantitative Trait and a Genetic Marker

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  • Warren J Ewens
  • Mingyao Li
  • Richard S Spielman

Abstract

Quantitative trait transmission/disequilibrium tests (quantitative TDTs) are commonly used in family-based genetic association studies of quantitative traits. Despite the availability of various quantitative TDTs, some users are not aware of the properties of these tests and the relationships between them. This review aims at outlining the broad features of the various quantitative TDT procedures carried out in the frequently used QTDT and FBAT packages. Specifically, we discuss the “Rabinowitz” and the “Monks-Kaplan” procedures, as well as the various “Abecasis” and “Allison” regression-based procedures. We focus on the models assumed in these tests and the relationships between them. Moreover, we discuss what hypotheses are tested by the various quantitative TDTs, what testing procedures are best suited to various forms of data, and whether the regression-based tests overcome population stratification problems. Finally, we comment on power considerations in the choice of the test to be used. We hope this brief review will shed light on the similarities and differences of the various quantitative TDTs.

Suggested Citation

  • Warren J Ewens & Mingyao Li & Richard S Spielman, 2008. "A Review of Family-Based Tests for Linkage Disequilibrium between a Quantitative Trait and a Genetic Marker," PLOS Genetics, Public Library of Science, vol. 4(9), pages 1-6, September.
    • Handle: RePEc:plo:pgen00:1000180
    DOI: 10.1371/journal.pgen.1000180
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    Cited by:

    1. Chabris, C. F. & Lee, J. J. & Cesarini, D. & Benjamin, D. J. & Laibson, David I., 2015. "The Fourth Law of Behavior Genetics," Scholarly Articles 30780203, Harvard University Department of Economics.
    2. John Beshears & James J. Choi & David Laibson & Brigitte C. Madrian & Katherine L. Milkman, 2015. "The Effect of Providing Peer Information on Retirement Savings Decisions," Journal of Finance, American Finance Association, vol. 70(3), pages 1161-1201, June.
    3. Boitard Simon & Mangin Brigitte & Azaïs Jean-Marc, 2010. "Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-25, January.

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