Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs (original) (raw)
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Acknowledgements
We wish to thank G. Getz for discussions on algorithms and comments regarding the supplemental methods. We also thank E. Lander and J. Hirschhorn for their readings and feedback. Finally, we are indebted to the testing labs that provided us with many replicates of HapMap samples run on the Affymetrix SNP 6.0 array. S.A.M. was supported by a Lilly Life Sciences Research Fellowship.
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Author notes
- Joshua M Korn and Finny G Kuruvilla: These authors contributed equally to this work.
Authors and Affiliations
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, 02142, Massachusetts, USA
Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll, Alec Wysoker, James Nemesh, Marcia M Nizzari, Stacey B Gabriel, Shaun Purcell, Mark J Daly & David Altshuler - Harvard-MIT Division of Health Sciences and Technology, Cambridge, 02139, Massachusetts, USA
Joshua M Korn - Graduate Program in Biophysics, Harvard University, Cambridge, 02138, Massachusetts, USA
Joshua M Korn - Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll & David Altshuler - Center for Human Genetic Research, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll, Shaun Purcell, Mark J Daly & David Altshuler - Department of Pathology, Brigham & Women's Hospital, Boston, 02115, Massachusetts, USA
Finny G Kuruvilla - Affymetrix, Inc., Santa Clara, 95051, California, USA
Simon Cawley, Earl Hubbell, Jim Veitch & Patrick J Collins - Department of Pathology, Harvard Medical School, Boston, 02115, Massachusetts, USA
Katayoon Darvishi & Charles Lee - Department of Medicine, Harvard Medical School, Boston, 02115, Massachusetts, USA
Mark J Daly & David Altshuler
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Contributions
J.M.K., F.G.K., S.A.M., M.J.D. and D.A. conceived of and refined the four-stage structure of Birdsuite. S.A.M., F.G.K. and J.N. developed and implemented Canary. J.N., S.A.M. and J.M.K. validated Canary calls, using data provided by P.J.C., J.V. and S.C. J.M.K., F.G.K., A.W., S.C. and E.H. developed, implemented, tested and validated Birdseed. J.M.K. developed, implemented and validated Birdseye. A.W. implemented Fawkes, which J.N., A.W. and J.M.K. validated. J.N., A.W., M.M.N. and S.B.G. were responsible for integration of the components and supporting software. K.D., C.L., J.M.K. and S.A.M. compared Birdsuite to Nexus and Partek. S.P. implemented the association tools. J.M.K., F.G.K., S.A.M., S.P., M.J.D. and D.A. wrote the manuscript. Discussion among all authors led to improvements in the algorithms and their implementations.
Corresponding authors
Correspondence toJoshua M Korn or David Altshuler.
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Competing interests
S.C., E.H., J.V. and P.J.C. are employees of Affymetrix. The remaining authors (J.M.K., F.G.K., S.A.M., A.W., J.N., K.D., C.L., M.M.N., S.B.G., S.P., M.J.D. and D.A.) neither personally nor institutionally receive financial support from Affymetrix, and neither the authors nor their employers receive compensation or royalties from the work described in this article.
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Korn, J., Kuruvilla, F., McCarroll, S. et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.Nat Genet 40, 1253–1260 (2008). https://doi.org/10.1038/ng.237
- Received: 20 February 2008
- Accepted: 18 August 2008
- Published: 07 September 2008
- Issue Date: October 2008
- DOI: https://doi.org/10.1038/ng.237