Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities

Andrew Whalen, Gregor Gorjanc, John Hickey

Research output: Contribution to journalArticlepeer-review

Abstract

In this paper, we evaluate the performance of using family-specific low-density genotype arrays to increase the accuracy of pedigree-based imputation. Genotype imputation is a widely used tool that decreases the costs of genotyping a population by genotyping the majority of individuals on a low-density array and using statistical regularities between the low-density and high-density individuals to fill in the missing genotypes. Previous work on population-based imputation has found that it is possible to increase the accuracy of imputation by maximizing the number of informative markers on an array. In the context of pedigree-based imputation, where the informativeness of a marker depends only on the genotypes of an individual’s parents, it may be beneficial to select the markers on each low-density array on a family-by-family basis.
Original languageEnglish
JournalGenetics Selection Evolution
DOIs
Publication statusPublished - 26 Jun 2019

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  • Chancellor's Fellowship - Gregor Gorjanc

    Gorjanc, G. (Principal Investigator)

    1/01/1931/12/23

    Project: Research

  • ISP 2017/22-Hickey John

    Hickey, J. (Principal Investigator)

    BBSRC

    1/04/1731/03/22

    Project: Research

  • ISP 2017/22-Gregor Gorjanc

    Gorjanc, G. (Principal Investigator)

    BBSRC

    1/04/1731/03/22

    Project: Research

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