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Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families

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  • Glazner Chris

    (University of Washington)

  • Thompson Elizabeth Alison

    (University of Washington)

Abstract

We present a method for improving the power of linkage analysis by detecting chromosome segments shared identical by descent (IBD) by individuals not known to be related. Existing Markov chain Monte Carlo methods sample descent patterns on pedigrees conditional on observed marker data. These patterns can be stored as IBD graphs, which express shared ancestry only, rather than specific family relationships. A model for IBD between unrelated individuals allows the estimation of coancestry between individuals in different pedigrees. IBD graphs on separate pedigrees can then be combined using these estimates. We report results from analyses of three sets of simulated marker data on two different pedigrees. We show that when families share a gene for a trait due to shared ancestry on the order of tens of generations, our method can detect a linkage signal when independent analyses of the families do not.

Suggested Citation

  • Glazner Chris & Thompson Elizabeth Alison, 2012. "Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(2), pages 1-18, January.
    • Handle: RePEc:bpj:sagmbi:v:11:y:2012:i:2:n:11
    DOI: 10.2202/1544-6115.1718
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    References listed on IDEAS

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    1. Thompson, E.A., 2008. "The IBD process along four chromosomes," Theoretical Population Biology, Elsevier, vol. 73(3), pages 369-373.
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    Cited by:

    1. Sun, M. & Jobling, M.A. & Taliun, D. & Pramstaller, P.P. & Egeland, T. & Sheehan, N.A., 2016. "On the use of dense SNP marker data for the identification of distant relative pairs," Theoretical Population Biology, Elsevier, vol. 107(C), pages 14-25.
    2. Sheehan, Nuala A. & Bartlett, Mark & Cussens, James, 2014. "Improved maximum likelihood reconstruction of complex multi-generational pedigrees," Theoretical Population Biology, Elsevier, vol. 97(C), pages 11-19.

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