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Use of Ancestral Haplotypes in Genome-Wide Association Studies

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Genome-Wide Association Studies and Genomic Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1019))

Abstract

We herein present a haplotype-based method to perform genome-wide association studies. The method relies on hidden Markov models to describe haplotypes from a population as a mosaic of a set of ancestral haplotypes. For a given position in the genome, haplotypes deriving from the same ancestral haplotype are also likely to carry the same risk alleles. Therefore, the model can be used in several applications such as haplotype reconstruction, imputation, association studies or genomic predictions. We illustrate then the model with two applications: the fine-mapping of a QTL affecting live weight in cattle and association studies in a stratified cattle population. Both applications show the potential of the method and the high linkage disequilibrium between ancestral haplotypes and causative variants.

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Author information

Authors and Affiliations

  1. Fonds National de la Recherche Scientifique, Brussels, Belgium

    Tom Druet

  2. Unit of Animal Genomics, Faculty of Veterinary Medicine and Centre for Biomedical Integrative Genoproteomics, University of Liège, Liège, Belgium

    Tom Druet

  3. Department of Animal Productions, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium

    Frédéric Farnir

Authors
  1. Tom Druet
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  2. Frédéric Farnir
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Editor information

Editors and Affiliations

  1. , Ctr. Genetic Analysis and Applications, University of New England, Homestead Building 18, Armidale, 2351, New South Wales, Australia

    Cedric Gondro

  2. School of Environmental and Rural Scienc, Div. Animal Science, University of New England, Homestead Building 36, Armidale, 2351, New South Wales, Australia

    Julius van der Werf

  3. , Biosciences Research Division, Department of Primary Industries, Ring Road 5, Bundoora, 3083, Victoria, Australia

    Ben Hayes

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Druet, T., Farnir, F. (2013). Use of Ancestral Haplotypes in Genome-Wide Association Studies. In: Gondro, C., van der Werf, J., Hayes, B. (eds) Genome-Wide Association Studies and Genomic Prediction. Methods in Molecular Biology, vol 1019. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-447-0_15

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  • DOI: https://doi.org/10.1007/978-1-62703-447-0_15

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-446-3

  • Online ISBN: 978-1-62703-447-0

  • eBook Packages: Springer Protocols

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