Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine (original) (raw)

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Acknowledgements

We thank the patients and clinicians for their participation in this project. We thank the Broad Genomics Platform (specifically K. Anderka, A. Cheney, E. Wheeler, T. Mason and C. Crawford). We thank C. Sougnez for facilitating data deposition. We also thank A. Lane and A. Yoda (Dana-Farber Cancer Institute), for their contributions to the JAK3 experimental work: A. Lane provided Ba/F3 cells, and A. Yoda provided murine stem cell virus–puromycin vector. G.G. is partially funded by a Paul C. Zamecnik, MD, Chair in Oncology at Massachusetts General Hospital. This work was supported by the Starr Cancer Foundation (L.A.G.), the Prostate Cancer Foundation (E.M.V.A. and L.A.G.), US National Institutes of Health (NIH) NHGRI Clinical Sequencing Exploratory Research grant 1U01HG006492 (L.A.G.), the NIH National Cancer Institute grant 1U24CA126546 (L.A.G. and E.S.L.), the US Department of Defense (L.A.G.), NIH U24CA143845 grant (G.G.) and the Dana-Farber Leadership Council (E.M.V.A.).

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Author notes

1. Stacey Gabriel, Gad Getz and Levi A Garraway: These authors contributed equally to this work.
2. Stacey Gabriel, Gad Getz and Levi A Garraway: These authors jointly supervised this work.

Authors and Affiliations

1. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,
   Eliezer M Van Allen, Nikhil Wagle, Petar Stojanov, Sara Marlow, Judit Jane-Valbuena, Franklin W Huang, David Barbie, Leena Gandhi, Stacy W Gray, Steven Joffe, Pasi Janne, Judy Garber, Laura MacConaill, Neal Lindeman, Barrett Rollins, Philip Kantoff & Levi A Garraway
2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,
   Eliezer M Van Allen, Nikhil Wagle, Petar Stojanov, Danielle L Perrin, Kristian Cibulskis, Sara Marlow, Judit Jane-Valbuena, Dennis C Friedrich, Gregory Kryukov, Scott L Carter, Aaron McKenna, Andrey Sivachenko, Mara Rosenberg, Adam Kiezun, Douglas Voet, Michael Lawrence, Lee T Lichtenstein, Jeff G Gentry, Franklin W Huang, Jennifer Fostel, Deborah Farlow, Eric S Lander, Sheila A Fisher, Stacey Gabriel, Gad Getz & Levi A Garraway
3. Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,
   Aaron McKenna
4. Children's Hospital Boston, Boston, Massachusetts, USA
   Steven Joffe
5. Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
   Laura MacConaill & Neal Lindeman
6. Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA.,
   Gad Getz
7. Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,
   Gad Getz

Authors

1. Eliezer M Van Allen
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2. Nikhil Wagle
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3. Petar Stojanov
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4. Danielle L Perrin
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5. Kristian Cibulskis
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6. Sara Marlow
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7. Judit Jane-Valbuena
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8. Dennis C Friedrich
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9. Gregory Kryukov
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10. Scott L Carter
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11. Aaron McKenna
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12. Andrey Sivachenko
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13. Mara Rosenberg
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14. Adam Kiezun
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15. Douglas Voet
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16. Michael Lawrence
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17. Lee T Lichtenstein
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18. Jeff G Gentry
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19. Franklin W Huang
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20. Jennifer Fostel
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21. Deborah Farlow
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22. David Barbie
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23. Leena Gandhi
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24. Eric S Lander
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25. Stacy W Gray
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26. Steven Joffe
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27. Pasi Janne
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28. Judy Garber
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29. Laura MacConaill
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30. Neal Lindeman
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31. Barrett Rollins
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32. Philip Kantoff
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33. Sheila A Fisher
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34. Stacey Gabriel
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35. Gad Getz
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36. Levi A Garraway
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Contributions

All authors contributed extensively to the work presented in this paper. E.M.V.A. and N.W. contributed equally to this work. S.G., G.G. and L.A.G. contributed equally to this work. D.L.P., D.C.F., J.F., E.S.L., S.A.F., E.M.V.A. and S.G. contributed to FFPE sample sequencing protocols and analysis of sequencing metrics. E.M.V.A., P.S., D.F., K.C., G.K., S.L.C., A.M., A.S., A.K., D.V., M.L., L.T.L., J.G.G., M.R. and G.G. contributed to computational analyses for FFPE versus frozen sample comparisons and analysis of WES data generally. E.M.V.A., N.W., G.K., F.W.H., S.W.G., S.J., P.J., J.G., L.M., N.L., B.R., P.K. and L.A.G. contributed to clinical analysis and interpretation methods and application. N.W., S.M., J.J.-V. and L.A.G. contributed to experimental follow-up of the JAK3 mutation. D.B. and L.G. contributed clinical input for the patient case. All authors discussed the results and implications and commented on the manuscript at all stages.

Corresponding authors

Correspondence toGad Getz or Levi A Garraway.

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Competing interests

L.A.G. and N.W. are equity holders and consultants in Foundation Medicine. L.A.G. is a consultant to Novartis, Millenium/Takeda and Boehringer Ingelheim and a recipient of a grant from Novartis. G.G. is a consultant to The Kew Group. D.B. is a consultant to N-of-1.

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Van Allen, E., Wagle, N., Stojanov, P. et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.Nat Med 20, 682–688 (2014). https://doi.org/10.1038/nm.3559

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• Received: 19 April 2013
• Accepted: 14 October 2013
• Published: 18 May 2014
• Issue Date: June 2014
• DOI: https://doi.org/10.1038/nm.3559