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/.
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Acknowledgments
This work was supported by the U.S. National Institutes of General Medical Sciences as part of the Center of Excellence in Systems Biology (1P50 GM076468). The authors thank Tim Wiltshire for sharing genotyping data prior to its publication and Jesse Hammer and Susan Moxley for graphics assistance.
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Szatkiewicz, J.P., Beane, G.L., Ding, Y. et al. An imputed genotype resource for the laboratory mouse. Mamm Genome 19, 199–208 (2008). https://doi.org/10.1007/s00335-008-9098-9
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DOI: https://doi.org/10.1007/s00335-008-9098-9