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

Abstract

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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

References

  1. 1

    Kennedy, G.C. et al. Nat. Biotechnol. 21, 1233–1237 (2003).

    CAS  Article  Google Scholar 

  2. 2

    Shifman, S. et al. PLoS Biol. 4, e395 (2006).

    Article  Google Scholar 

  3. 3

    Lindblad-Toh, K. et al. Nat. Genet. 24, 381–386 (2000).

    CAS  Article  Google Scholar 

  4. 4

    Wade, C.M. et al. Nature 420, 574–578 (2002).

    CAS  Article  Google Scholar 

  5. 5

    Yang, H., Bell, T.A., Churchill, G.A. & Pardo-Manuel de Villena, F Nat. Genet. 39, 1100–1107 (2007).

    CAS  Article  Google Scholar 

  6. 6

    Clark, A.G., Hubisz, M.J., Bustamante, C.D., Williamson, S.H. & Nielsen, R. Genome Res. 15, 1496–1502 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Frazer, K.A. et al. Nature 448, 1050–1053 (2007).

    CAS  Article  Google Scholar 

  8. 8

    Chesler, E.J. et al. Mamm. Genome 19, 382–389 (2008).

    Article  Google Scholar 

  9. 9

    Williams, R., IV et al. PLoS One 4, e4649 (2009).

    Article  Google Scholar 

  10. 10

    Graubert, T.A. et al. PLoS Genet. 3, e3 (2007).

    Article  Google Scholar 

  11. 11

    Szatkiewicz, J.P. et al. Mamm. Genome 19, 199–208 (2008).

    Article  Google Scholar 

  12. 12

    Gimelbrant, A., Hutchinson, J.N., Thompson, B.R. & Chess, A. Science 318, 1136–1140 (2007).

    CAS  Article  Google Scholar 

  13. 13

    Bemmo, A. et al. BMC Genomics 9, 529 (2008).

    Article  Google Scholar 

  14. 14

    Kerkel, K. et al. Nat. Genet. 40, 904–908 (2008).

    CAS  Article  Google Scholar 

  15. 15

    She, X., Cheng, Z., Zöllner, S., Church, D.M. & Eichler, E.E. Nat. Genet. 40, 909–914 (2008).

    CAS  Article  Google Scholar 

  16. 16

    Bejerano, G. et al. Science 304, 1321–1325 (2004).

    CAS  Article  Google Scholar 

  17. 17

    Lovmar, L., Ahlford, A., Jonsson, M. & Syvanen, A.C. BMC Genomics 6, 35 (2005).

    Article  Google Scholar 

Download references

Acknowledgements

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

Affiliations

Authors

Contributions

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.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Tables 1–2 (PDF 4519 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing