A sequence-based variation map of 8.27 million SNPs in inbred mouse strains (original) (raw)

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Acknowledgements

Work was supported by funding from the NIEHS. H.M.K. and E.E. are partially supported by the NSF. H.M.K. is partially supported by a Samsung Scholarship. E.E. is partially supported by the NIH. At Perlegen Sciences, we thank A. Kloek for assistance with manuscript preparation; B. Nguyen, X. Chen, P. Chu, R. Patel, P.-E. Jiao, R. Irikat and J. Kwon for assistance with DNA sample preparation and hybridization of the high-density oligonucleotide arrays; R, Vergara for primer handling; H. Huang and W. Barrett for designing the high-density arrays; T. Genschoreck and J. Sheehan for data quality control; and S. Osborn for assistance with website development and data delivery. At NIEHS, we thank D. A. Schwartz, K. Olden, S. Wilson, L. Birnbaumer, J. Bucher, W. T. Schrader and D. M. Klotz for constructive scientific discussions, and J. A. Lewis and T. Hardee for administrative support. At The Jackson Laboratory, we thank S. Deveau and JAX DNA Resources for DNA sample preparation.

Author Contributions L.L.S., J.M., C.L.P. and K.A.F. supervised the experiments. K.A.F., D.R.C., M.J.D., F.M.J., E.J.B. and M.A.B designed the study. H.M.K., E.E, C.M.W., D.A.H., G.B.N., R.V.G. and M.M.M. performed data analysis. K.A.F., with help from E.J.B., D.A.H., E.E. and C.M.W., wrote the manuscript.

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Authors and Affiliations

  1. Perlegen Sciences, 2021 Stierlin Court, Mountain View, California 94043, USA,
    Kelly A. Frazer, David A. Hinds, Erica J. Beilharz, Robert V. Gupta, Julie Montgomery, Matt M. Morenzoni, Geoffrey B. Nilsen, Charit L. Pethiyagoda, Laura L. Stuve & David R. Cox
  2. Department of Computer Science and Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA,
    Eleazar Eskin
  3. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA,
    Hyun Min Kang
  4. The Jackson Laboratory, Bar Harbor, Maine 04609, USA,
    Molly A. Bogue
  5. Toxicology Operations Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA,
    Frank M. Johnson
  6. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA,
    Mark J. Daly & Claire M. Wade
  7. Center for Human Genetic Research, Massachussets General Hospital, 185 Cambridge St, Boston, Massachusetts 02114, USA,
    Mark J. Daly & Claire M. Wade

Authors

  1. Kelly A. Frazer
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  2. Eleazar Eskin
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  3. Hyun Min Kang
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  4. Molly A. Bogue
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  5. David A. Hinds
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  6. Erica J. Beilharz
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  7. Robert V. Gupta
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  8. Julie Montgomery
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  9. Matt M. Morenzoni
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  10. Geoffrey B. Nilsen
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  11. Charit L. Pethiyagoda
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  12. Laura L. Stuve
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  13. Frank M. Johnson
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  14. Mark J. Daly
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  15. Claire M. Wade
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  16. David R. Cox
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Corresponding author

Correspondence toKelly A. Frazer.

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Competing interests

D.A.H., R.V.G., J.M., M.M.M., G.B.N., C.L.P., L.L.S. and D.R.C. are employed by Perlegen Sciences. K.A.F. is a former employee of Perlegen Sciences

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-7, Supplementary Tables S2-S16 and S21, Supplementary Discussion and additional references. (PDF 515 kb)

Supplementary Table S1

This file contains Supplementary Table S1 indicating sequences tiled on the arrays that were lightly-masked or unmasked. (XLS 1082 kb)

Supplementary Table S17

This file contains Supplementary Table S17 listing SNPs that produce nonsense mutations. (XLS 175 kb)

Supplementary Table S18

This file contains Supplementary Table S18 listing SNPs that produce altered translation start sites. (XLS 70 kb)

Supplementary Table S19

This file contains Supplementary Table S19 listing SNPs that produce altered translation stop sites. (XLS 61 kb)

Supplementary Table S20

This file contains Supplementary Table S20 listing SNPs that produce altered splice sites. (XLS 139 kb)

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Frazer, K., Eskin, E., Kang, H. et al. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.Nature 448, 1050–1053 (2007). https://doi.org/10.1038/nature06067

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