Mammalian Genome

, Volume 19, Issue 3, pp 199–208

An imputed genotype resource for the laboratory mouse

  • Jin P. Szatkiewicz
  • Glen L. Beane
  • Yueming Ding
  • Lucie Hutchins
  • Fernando Pardo-Manuel de Villena
  • Gary A. Churchill
Article

DOI: 10.1007/s00335-008-9098-9

Cite this article as:
Szatkiewicz, J.P., Beane, G.L., Ding, Y. et al. Mamm Genome (2008) 19: 199. doi:10.1007/s00335-008-9098-9

Abstract

We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 49 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrated that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high-density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org/.

Supplementary material

335_2008_9098_MOESM1_ESM.doc (90 kb)
(DOC 89 kb)

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Jin P. Szatkiewicz
    • 1
  • Glen L. Beane
    • 1
  • Yueming Ding
    • 1
  • Lucie Hutchins
    • 1
  • Fernando Pardo-Manuel de Villena
    • 2
  • Gary A. Churchill
    • 1
  1. 1.The Jackson LaboratoryBar HarborUSA
  2. 2.Department of Genetics, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer CenterUniversity of North CarolinaChapel HillUSA

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