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Genome-Wide Association Studies and Genomic Prediction pp 395–410Cite as

Genotype Imputation to Increase Sample Size in Pedigreed Populations

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

Abstract

Genotype imputation is a cost-effective way to increase the power of genomic selection or genome-wide association studies. While several genotype imputation algorithms are available, this chapter focuses on a heuristic algorithm, as implemented in the AlphaImpute software. This algorithm combines long-range phasing, haplotype library imputation, and segregation analysis and it is specifically designed to work with pedigreed populations.

The chapter is organized in different sections. First the challenges related to genotype imputation in pedigreed populations are described, along with the specifics of the imputation algorithm used in AlphaImpute. In the second section, factors affecting the accuracy of genotype imputation using this algorithm are discussed. The different parameters that control AlphaImpute are detailed and examples of how to apply AlphaImpute are given.

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Author information

Authors and Affiliations

  1. School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia

    John M. Hickey

  2. Biometrics and Statistics Unit, International Maize and Wheat Improvement Centre (CIMMYT), México, D.F., Mexico

    John M. Hickey

  3. Genus plc, Hendersonville, TN, USA

    Matthew A. Cleveland

  4. Department of Animal Science, North Carolina State University, Raleigh, NC, USA

    Christian Maltecca

  5. Department of Animal Science, University of Ljubljana, Domžale, Slovenia

    Gregor Gorjanc

  6. Qualitas AG, Zug, Switzerland

    Birgit Gredler

  7. Aviagen, Edinburgh, UK

    Andreas Kranis

Authors
  1. John M. Hickey
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  2. Matthew A. Cleveland
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  3. Christian Maltecca
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  4. Gregor Gorjanc
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  5. Birgit Gredler
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  6. Andreas Kranis
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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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Hickey, J.M., Cleveland, M.A., Maltecca, C., Gorjanc, G., Gredler, B., Kranis, A. (2013). Genotype Imputation to Increase Sample Size in Pedigreed Populations. 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_17

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  • DOI: https://doi.org/10.1007/978-1-62703-447-0_17

  • 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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