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Family-Based Bivariate Association Tests for Quantitative Traits

Author

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  • Lei Zhang
  • Aaron J Bonham
  • Jian Li
  • Yu-Fang Pei
  • Jie Chen
  • Christopher J Papasian
  • Hong-Wen Deng

Abstract

The availability of a large number of dense SNPs, high-throughput genotyping and computation methods promotes the application of family-based association tests. While most of the current family-based analyses focus only on individual traits, joint analyses of correlated traits can extract more information and potentially improve the statistical power. However, current TDT-based methods are low-powered. Here, we develop a method for tests of association for bivariate quantitative traits in families. In particular, we correct for population stratification by the use of an integration of principal component analysis and TDT. A score test statistic in the variance-components model is proposed. Extensive simulation studies indicate that the proposed method not only outperforms approaches limited to individual traits when pleiotropic effect is present, but also surpasses the power of two popular bivariate association tests termed FBAT-GEE and FBAT-PC, respectively, while correcting for population stratification. When applied to the GAW16 datasets, the proposed method successfully identifies at the genome-wide level the two SNPs that present pleiotropic effects to HDL and TG traits.

Suggested Citation

  • Lei Zhang & Aaron J Bonham & Jian Li & Yu-Fang Pei & Jie Chen & Christopher J Papasian & Hong-Wen Deng, 2009. "Family-Based Bivariate Association Tests for Quantitative Traits," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-9, December.
    • Handle: RePEc:plo:pone00:0008133
    DOI: 10.1371/journal.pone.0008133
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    References listed on IDEAS

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    1. Lange Christoph & van Steen Kristel & Andrew Toby & Lyon Helen & DeMeo Dawn L & Raby Benjamin & Murphy Amy & Silverman Edwin K & MacGregor Alex & Weiss Scott T & Laird Nan M, 2004. "A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-29, August.
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    1. Ding Xiao & Weiss Scott & Raby Benjamin & Lange Christoph & Laird Nan M, 2009. "Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-17, February.
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