Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs (original) (raw)

References

  1. Rabbee, N. & Speed, T.P. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22, 7–12 (2006).
    Article CAS Google Scholar
  2. Nicolae, D.L., Wu, X., Miyake, K. & Cox, N.J. GEL: a novel genotype calling algorithm using empirical likelihood. Bioinformatics 22, 1942–1947 (2006).
    Article CAS Google Scholar
  3. McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86–92 (2006).
    Article CAS Google Scholar
  4. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75–81 (2006).
    Article CAS Google Scholar
  5. McCarroll, S.A. & Altshuler, D.M. Copy-number variation and association studies of human disease. Nat. Genet. 39 (Suppl.), S37–S42 (2007).
    Article CAS Google Scholar
  6. McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy-number variation. Nat. Genet. advance online publication, 10.1038/ng.238 (7 September 2008).
  7. Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 16, 1575–1584 (2006).
    Article CAS Google Scholar
  8. Fiegler, H. et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res. 16, 1566–1574 (2006).
    Article CAS Google Scholar
  9. Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).
    Article Google Scholar
  10. Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665–1674 (2007).
    Article CAS Google Scholar
  11. Bengtsson, H., Irizarry, R., Carvalho, B. & Speed, T.P. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics 24, 759–767 (2008); published online 19 January 2008.
    Article CAS Google Scholar
  12. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005).
  13. Macconaill, L.E., Aldred, M.A., Lu, X. & Laframboise, T. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics 8, 211 (2007).
    Article Google Scholar
  14. Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Statist. Soc. B 39, 1–38 (1977).
    Google Scholar
  15. Viterbi, A.J. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans Info Theory IT-13, 260–269 (1967).
    Article Google Scholar
  16. Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007).
    Article CAS Google Scholar
  17. Laframboise, T., Harrington, D. & Weir, B.A. PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics 8, 323–336 (2007).
    Article Google Scholar
  18. Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008).
    Article CAS Google Scholar
  19. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
    Article CAS Google Scholar
  20. Clayton, D.G. et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37, 1243–1246 (2005).
    Article CAS Google Scholar
  21. Weiss, L.A. et al. Association between microdeletion and microduplication at 16p11.2 and autism. N. Engl. J. Med. 358, 667–675 (2008); published online 9 January 2008.
    Article CAS Google Scholar
  22. The International Schizophrenia Consortium. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature advance online publication, doi:10.1038/nature07239 (30 July 2008).

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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

  1. Joshua M Korn and Finny G Kuruvilla: These authors contributed equally to this work.

Authors and Affiliations

  1. 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
  2. Harvard-MIT Division of Health Sciences and Technology, Cambridge, 02139, Massachusetts, USA
    Joshua M Korn
  3. Graduate Program in Biophysics, Harvard University, Cambridge, 02138, Massachusetts, USA
    Joshua M Korn
  4. Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
    Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll & David Altshuler
  5. 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
  6. Department of Pathology, Brigham & Women's Hospital, Boston, 02115, Massachusetts, USA
    Finny G Kuruvilla
  7. Affymetrix, Inc., Santa Clara, 95051, California, USA
    Simon Cawley, Earl Hubbell, Jim Veitch & Patrick J Collins
  8. Department of Pathology, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Katayoon Darvishi & Charles Lee
  9. Department of Medicine, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Mark J Daly & David Altshuler

Authors

  1. Joshua M Korn
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  2. Finny G Kuruvilla
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  3. Steven A McCarroll
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  4. Alec Wysoker
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  5. James Nemesh
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  6. Simon Cawley
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  7. Earl Hubbell
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  8. Jim Veitch
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  9. Patrick J Collins
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  10. Katayoon Darvishi
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  11. Charles Lee
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  12. Marcia M Nizzari
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  13. Stacey B Gabriel
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  14. Shaun Purcell
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  15. Mark J Daly
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  16. 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

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