Genetic Variation and Population Substructure in Outbred CD-1 Mice: Implications for Genome-Wide Association Studies

Kimberly A Aldinger; Greta Sokoloff; David M Rosenberg; Abraham A Palmer; Kathleen J Millen

doi:10.1371/journal.pone.0004729

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Genetic Variation and Population Substructure in Outbred CD-1 Mice: Implications for Genome-Wide Association Studies

Journal article

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Genetic Variation and Population Substructure in Outbred CD-1 Mice: Implications for Genome-Wide Association Studies

Kimberly A Aldinger, Greta Sokoloff, David M Rosenberg, Abraham A Palmer and Kathleen J Millen

PloS one, Vol.4(3), pp.e4729-e4729

03/06/2009

DOI: 10.1371/journal.pone.0004729

PMCID: PMC2649211

PMID: 19266100

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Abstract

Outbred laboratory mouse populations are widely used in biomedical research. Since little is known about the degree of genetic variation present in these populations, they are not widely used for genetic studies. Commercially available outbred CD-1 mice are drawn from an extremely large breeding population that has accumulated many recombination events, which is desirable for genome-wide association studies. We therefore examined the degree of genome-wide variation within CD-1 mice to investigate their suitability for genetic studies. The CD-1 mouse genome displays patterns of linkage disequilibrium and heterogeneity similar to wild-caught mice. Population substructure and phenotypic differences were observed among CD-1 mice obtained from different breeding facilities. Differences in genetic variation among CD-1 mice from distinct facilities were similar to genetic differences detected between closely related human populations, consistent with a founder effect. This first large-scale genetic analysis of the outbred CD-1 mouse strain provides important considerations for the design and analysis of genetic studies in CD-1 mice.

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Title: Subtitle: Genetic Variation and Population Substructure in Outbred CD-1 Mice: Implications for Genome-Wide Association Studies
Creators: Kimberly A Aldinger - University of Chicago
Greta Sokoloff - University of Chicago
David M Rosenberg - University of Chicago
Abraham A Palmer - University of Chicago
Kathleen J Millen - University of Chicago
Resource Type: Journal article
Publication Details: PloS one, Vol.4(3), pp.e4729-e4729
DOI: 10.1371/journal.pone.0004729
PMID: 19266100
PMCID: PMC2649211
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: PUBLIC LIBRARY SCIENCE
Number of pages: 10
Grant note: HD053703; DA021336; MH70933; MH79103; DA024845 / National Institutes of Health Pre-doctoral Fellowship / Autism Speaks
Language: English
Date published: 03/06/2009
Academic Unit: Psychological and Brain Sciences
Record Identifier: 9984256844102771

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