Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection (original) (raw)

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References

  1. Maron, B.J. et al. Circulation 92, 785–789 (1995).
    Article CAS Google Scholar
  2. Alcalai, R., Seidman, J.G. & Seidman, C.E. J. Cardiovasc. Electrophysiol. 19, 104–110 (2008).
    PubMed Google Scholar
  3. Hovingh, G.K. et al. Curr. Opin. Lipidol. 16, 139–145 (2005).
    Article CAS Google Scholar
  4. Willer, C.J. et al. Nat. Genet. 40, 161–169 (2008).
    Article CAS Google Scholar
  5. Kim, J.B. et al. Science 316, 1481–1484 (2007).
    Article CAS Google Scholar
  6. Hillier, L.W. et al. Nat. Methods 5, 183–188 (2008).
    Article CAS Google Scholar
  7. Chiang, D.Y. et al. Nat. Methods 6, 99–103 (2009).
    Article CAS Google Scholar
  8. Goossens, D. et al. Hum. Mutat. 30, 472–476 (2009).
    Article Google Scholar
  9. Lovett, M. Curr. Protoc. Hum. Genet. 6.3 (2001).
  10. Bashiardes, S. et al. Nat. Methods 2, 63–69 (2005).
    Article CAS Google Scholar
  11. Albert, T.J. et al. Nat. Methods 4, 903–905 (2007).
    Article CAS Google Scholar
  12. Gnirke, A. et al. Nat. Biotechnol. 27, 182–189 (2009).
    Article CAS Google Scholar
  13. Porreca, G.J. et al. Nat. Methods 4, 931–936 (2007).
    Article CAS Google Scholar
  14. Bentley, D.R. et al. Nature 456, 53–59 (2008).
    Article CAS Google Scholar
  15. Moore, D. & Dowhan, D. Curr. Protoc. Mol. Biol. 2.1A (2002).
  16. Parnes, J.R. et al. Proc. Natl. Acad. Sci. USA 78, 2253–2257 (1981).
    Article CAS Google Scholar
  17. Brown, T. Curr. Protoc. Mol. Biol. 2.9B (2001).
  18. Rees, W.A., Yager, T.D., Korte, J. & von Hippel, P.H. Biochemistry 32, 137–144 (1993).
    Article CAS Google Scholar
  19. Li, H., Ruan, J. & Durbin, R. Genome Res. 18, 1851–1858 (2008).
    Article CAS Google Scholar
  20. Kharchenko, P.V., Tolstorukov, M.Y. & Park, P.J. Nat. Biotechnol. 26, 1351–1359 (2008).
    Article CAS Google Scholar

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Acknowledgements

We thank J. Aach, J. Gorham, J. Kim, J.B. Li and L. Wang for helpful discussions and advice; J. Kastelein and J.A. Kuivenhoven for HDL subject genomic DNA and for assistance in selecting HDL target genes; S. Depalma for analysis of Affymetrix custom sequencing array data; L. Merrill and D. Sonkin at Partners Center for Personalized Genetic Medicine of Harvard Medical School for Illumina sequencing and support; B. Richter, D. Gurgul, S. Roylance, J. Xu and A. Zschau at Partners Healthcare for access to high-performance computing cluster and data storage; T. Levi and B. McDonough for subject recruitment and genomic DNA isolation; S. Cox and M. Iaculli for generating HCM amplimers; and members of the Drosophila RNAi Screening Center for access to their Molecular Devices Analyst GT plate reader. G.K.H. was supported by grants from the Dutch Heart Association (NHS 2007R001) and Saal van Zwanenbergstichting. This work was supported by grants from the National Cancer Institute, the National Heart, Lung and Blood Institute, the Howard Hughes Medical Institute, and the Leducq Foundation.

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Author notes

  1. J G Seidman and Christine E Seidman: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Daniel S Herman, G Kees Hovingh, Raju Kucherlapati, J G Seidman & Christine E Seidman
  2. Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    G Kees Hovingh
  3. Partners Healthcare Center for Personalized Genetic Medicine, Harvard Medical School, Boston, Massachusetts, USA
    Oleg Iartchouk, Heidi L Rehm, Raju Kucherlapati, J G Seidman & Christine E Seidman
  4. Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Heidi L Rehm
  5. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
    Christine E Seidman

Authors

  1. Daniel S Herman
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  2. G Kees Hovingh
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  3. Oleg Iartchouk
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  4. Heidi L Rehm
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  5. Raju Kucherlapati
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  6. J G Seidman
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  7. Christine E Seidman
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Contributions

D.S.H., G.K.H., J.G.S. and C.E.S. conceived and designed the study; D.S.H. and G.K.H. constructed libraries and target concatemers; D.S.H. analyzed sequence data; O.I. and R.K. sequenced the libraries; H.L.R., D.S.H. and R.K. designed and amplified HCM sequences; D.S.H., J.G.S. and C.E.S. wrote the manuscript.

Corresponding author

Correspondence toChristine E Seidman.

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Herman, D., Hovingh, G., Iartchouk, O. et al. Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection.Nat Methods 6, 507–510 (2009). https://doi.org/10.1038/nmeth.1343

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