A customized and versatile high-density genotyping array for the mouse


We designed a high-density mouse genotyping array containing 623,124 single-nucleotide polymorphisms that captures the known genetic variation present in the laboratory mouse. The array also contains 916,269 invariant genomic probes targeted to functional elements and regions known to harbor segmental duplications. The array opens the door to the characterization of genetic diversity, copy-number variation, allele-specific gene expression and DNA methylation, and will extend the successes of human genome-wide association studies to the mouse.

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Figure 1: Spatial distribution of SNP and invariant genomic probes.
Figure 2: Detection of CNV using the mouse diversity array.


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This work was supported by the National Institute of General Medical Sciences National Centers of Systems Biology program grant GM-076468. We thank the Array Design and Bioinformatics teams at Affymetrix for their advice and assistance in the design and implementation of the mouse diversity array.

Author information




F.P.-M.V., G.A.C. and H.Y. conceived the study design and wrote the paper. H.Y., Y.D., L.N.H., J.S., B.J.P. and J.H.G. carried out bioinformatics analysis, and T.A.B. provided sequencing and molecular biology support.

Corresponding authors

Correspondence to Fernando Pardo-Manuel de Villena or Gary A Churchill.

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Yang, H., Ding, Y., Hutchins, L. et al. A customized and versatile high-density genotyping array for the mouse. Nat Methods 6, 663–666 (2009). https://doi.org/10.1038/nmeth.1359

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