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A Genomic Background Based Method for Association Analysis in Related Individuals

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  • Najaf Amin
  • Cornelia M van Duijn
  • Yurii S Aulchenko

Abstract

Background: Feasibility of genotyping of hundreds and thousands of single nucleotide polymorphisms (SNPs) in thousands of study subjects have triggered the need for fast, powerful, and reliable methods for genome-wide association analysis. Here we consider a situation when study participants are genetically related (e.g. due to systematic sampling of families or because a study was performed in a genetically isolated population). Of the available methods that account for relatedness, the Measured Genotype (MG) approach is considered the ‘gold standard’. However, MG is not efficient with respect to time taken for the analysis of genome-wide data. In this context we proposed a fast two-step method called Genome-wide Association using Mixed Model and Regression (GRAMMAR) for the analysis of pedigree-based quantitative traits. This method certainly overcomes the drawback of time limitation of the measured genotype (MG) approach, but pays in power. One of the major drawbacks of both MG and GRAMMAR, is that they crucially depend on the availability of complete and correct pedigree data, which is rarely available. Methodology: In this study we first explore type 1 error and relative power of MG, GRAMMAR, and Genomic Control (GC) approaches for genetic association analysis. Secondly, we propose an extension to GRAMMAR i.e. GRAMMAR-GC. Finally, we propose application of GRAMMAR-GC using the kinship matrix estimated through genomic marker data, instead of (possibly missing and/or incorrect) genealogy. Conclusion: Through simulations we show that MG approach maintains high power across a range of heritabilities and possible pedigree structures, and always outperforms other contemporary methods. We also show that the power of our proposed GRAMMAR-GC approaches to that of the ‘gold standard’ MG for all models and pedigrees studied. We show that this method is both feasible and powerful and has correct type 1 error in the context of genome-wide association analysis in related individuals.

Suggested Citation

  • Najaf Amin & Cornelia M van Duijn & Yurii S Aulchenko, 2007. "A Genomic Background Based Method for Association Analysis in Related Individuals," PLOS ONE, Public Library of Science, vol. 2(12), pages 1-7, December.
  • Handle: RePEc:plo:pone00:0001274
    DOI: 10.1371/journal.pone.0001274
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    Cited by:

    1. Jakris Eu-ahsunthornwattana & E Nancy Miller & Michaela Fakiola & Wellcome Trust Case Control Consortium 2 & Selma M B Jeronimo & Jenefer M Blackwell & Heather J Cordell, 2014. "Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data," PLOS Genetics, Public Library of Science, vol. 10(7), pages 1-20, July.
    2. Anirene G. T. Pereira & Yuri T Utsunomiya & Marco Milanesi & Rafaela B P Torrecilha & Adriana S Carmo & Haroldo H R Neves & Roberto Carvalheiro & Paolo Ajmone-Marsan & Tad S Sonstegard & Johann Sölkne, 2016. "Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth," PLOS ONE, Public Library of Science, vol. 11(7), pages 1-13, July.
    3. Leonieke M E van Koolwijk & Wishal D Ramdas & M Kamran Ikram & Nomdo M Jansonius & Francesca Pasutto & Pirro G Hysi & Stuart Macgregor & Sarah F Janssen & Alex W Hewitt & Ananth C Viswanathan & Jacoli, 2012. "Common Genetic Determinants of Intraocular Pressure and Primary Open-Angle Glaucoma," PLOS Genetics, Public Library of Science, vol. 8(5), pages 1-14, May.
    4. Duarte Nubia E. & Giolo Suely R. & Pereira Alexandre C. & de Andrade Mariza & Soler Júlia P., 2014. "Using the theory of added-variable plot for linear mixed models to decompose genetic effects in family data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(3), pages 359-378, June.
    5. Md. Moksedul Momin & Jisu Shin & Soohyun Lee & Buu Truong & Beben Benyamin & S. Hong Lee, 2023. "A method for an unbiased estimate of cross-ancestry genetic correlation using individual-level data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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