IBDfinder and SNPsetter: Tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease

Authors

  • Ian M. Carr,

    Corresponding author
    1. Centre for Autozygosity Mapping and Section of Genetics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
    • Leeds Institute for Molecular Medicine, Level 9, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
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  • Eamonn Sheridan,

    1. Centre for Autozygosity Mapping and Section of Genetics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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  • Bruce E. Hayward,

    1. Centre for Autozygosity Mapping and Section of Genetics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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  • Alexander F. Markham,

    1. Centre for Autozygosity Mapping and Section of Genetics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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  • David T. Bonthron

    1. Centre for Autozygosity Mapping and Section of Genetics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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  • Communicated by A. Jamie Cuticchia

Abstract

Autozygosity mapping of recessive genes can be performed on a small number of affected individuals from consanguineous pedigrees. With the advent of microarray SNP analysis, acquiring genotype data has become extremely simple and quick, in comparison to gene mapping with microsatellite markers. However, the subsequent data analysis required to identify autozygous regions can still be a significant obstacle. For rapid gene identification, it may be desirable to integrate information from heterogeneous groups of affected individuals, both familial and isolated, under various assumptions of ancestry and locus heterogeneity, that are not amenable to formal linkage analysis. Unfortunately, there are few computer programs aimed specifically at facilitating this type of data sifting. Here, we demonstrate two new programs that facilitate the identification of autozygous regions within a heterogeneous SNP dataset derived from familial and sporadic affected individuals. Hum Mutat 30:1–8, 2009. © 2009 Wiley-Liss, Inc.

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