The clonal and mutational evolution spectrum of primary triple-negative breast cancers (original) (raw)

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Aligned exome/genome sequence data, RNA-seq data and Affymetrix SNP6.0 data sets are available at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/) under study accession number EGAS00001000132. Normal reference RNA-seq datasets are available at the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces) under study accession number SRP000930.

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Acknowledgements

The support of the BC Cancer Agency Tumour Bank, CBCF Breast Tumour Bank Alberta and the Addenbrookes Tumour bank (supported by NIHR and ECMC) is acknowledged. Technical support is acknowledged from the Centre for Translational Genomics, the Michael Smith Genome Sciences Centre technical group, the BCCA Flow Cytometry Core Facility in the Terry Fox Laboratory and the Cancer Research UK Cambridge Research Institute. Supported by the BC Cancer Foundation, US Department of Defense CDMRP program, Canadian Breast Cancer Foundation (BC Yukon) (to S.A. and S.S.), Michael Smith Foundation for Health Research (to S.S.), US National Institutes of Health (NIH) Roadmap Epigenomics Program, NIH grant 5U01ES017154-02 (to M.H., M.A.M., J.C. and T.T.), Cancer Research UK (to C. Caldas and P.D.P.) and the National Institute of General Medical Sciences (R01GM084875 to W.W.W.), the Canadian Breast Cancer Research Alliance and the Canadian Cancer Society (to S.A. and C.E.). We thank B. Reva, Y. Antipin and C. Sander (Memorial Sloan Kettering Cancer Center) for assistance with MutationAssessor, and G. Wu (Ontario Institute for Cancer Research) for assistance with Reactome.

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Author notes

1. Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari and Ali Bashashati: These authors contributed equally to this work.

Authors and Affiliations

1. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada,
   Sohrab P. Shah, Andrew Roth, Arusha Oloumi, Gavin Ha, Gulisa Turashvili, Jiarui Ding, Gholamreza Haffari, Ali Bashashati, Leah M. Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Andrew McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza Heravi-Moussavi, Jamie Rosner, Daniel Lai, Peter Watson, David Huntsman & Samuel Aparicio
2. Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada ,
   Sohrab P. Shah, Andrew Roth, Arusha Oloumi, Gavin Ha, Gulisa Turashvili, Jiarui Ding, Gholamreza Haffari, Ali Bashashati, Leah M. Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Andrew McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza Heravi-Moussavi, Jamie Rosner, Daniel Lai, David Huntsman & Samuel Aparicio
3. Canada’s Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada ,
   Rodrigo Goya, Yongjun Zhao, Kane Tse, Inanc Birol, Richard Varhol, Angela Tam, Noreen Dhalla, Thomas Zeng, Kevin Ma, Simon K. Chan, Malachi Griffith, Annie Moradian, S.-W. Grace Cheng, Gregg B. Morin, Steven Jones, Martin Hirst & Marco A. Marra
4. Centre for Molecular Medicine and Therapeutics, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, Canada ,
   Virginie Bernard & Wyeth W. Wasserman
5. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
   Gregg B. Morin, Irmtraud M. Meyer, Wyeth W. Wasserman, Steven Jones & Marco A. Marra
6. British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada ,
   Peter Watson, Karen Gelmon & Stephen Chia
7. Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK ,
   Suet-Feung Chin, Christina Curtis, Oscar M. Rueda, Paul D. Pharoah & Carlos Caldas
8. Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK,
   Suet-Feung Chin, Christina Curtis, Oscar M. Rueda & Carlos Caldas
9. Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, California, USA
   Christina Curtis
10. Departments of Oncology and Laboratory Medicine and Pathology, University of Alberta, 11560 University Avenue, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada,
    Sambasivarao Damaraju & John Mackey
11. Life Technologies, 101 Lincoln Centre Dr., Foster City, 94404, California, USA
    Kelly Hoon, Timothy Harkins & Vasisht Tadigotla
12. Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 94143, California, USA
    Mahvash Sigaroudinia, Philippe Gascard & Thea Tlsty
13. Department of Neurosurgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, 94143, California, USA
    Joseph F. Costello
14. Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada,
    Irmtraud M. Meyer
15. Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada ,
    Irmtraud M. Meyer & Martin Hirst
16. Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada ,
    Connie J. Eaves
17. Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Dr., Burnaby, British Columbia V5A1S6, Canada,
    Steven Jones
18. Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Ave, Vancouver, British Columbia V5Z 4E6, Canada ,
    David Huntsman
19. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
    Martin Hirst
20. Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK ,
    Carlos Caldas
21. Cambridge Experimental Cancer Medicine Centre (ECMC), Cambridge CB2 0RE, UK ,
    Carlos Caldas

Authors

1. Sohrab P. Shah
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2. Andrew Roth
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3. Rodrigo Goya
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4. Arusha Oloumi
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5. Gavin Ha
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6. Yongjun Zhao
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7. Gulisa Turashvili
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8. Jiarui Ding
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9. Kane Tse
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10. Gholamreza Haffari
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11. Ali Bashashati
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12. Leah M. Prentice
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13. Jaswinder Khattra
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14. Angela Burleigh
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15. Damian Yap
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16. Virginie Bernard
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17. Andrew McPherson
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18. Karey Shumansky
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19. Anamaria Crisan
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20. Ryan Giuliany
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21. Alireza Heravi-Moussavi
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22. Jamie Rosner
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23. Daniel Lai
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24. Inanc Birol
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25. Richard Varhol
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26. Angela Tam
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27. Noreen Dhalla
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28. Thomas Zeng
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29. Kevin Ma
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30. Simon K. Chan
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31. Malachi Griffith
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32. Annie Moradian
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33. S.-W. Grace Cheng
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34. Gregg B. Morin
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35. Peter Watson
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36. Karen Gelmon
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37. Stephen Chia
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38. Suet-Feung Chin
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39. Christina Curtis
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40. Oscar M. Rueda
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41. Paul D. Pharoah
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42. Sambasivarao Damaraju
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43. John Mackey
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44. Kelly Hoon
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45. Timothy Harkins
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46. Vasisht Tadigotla
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47. Mahvash Sigaroudinia
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48. Philippe Gascard
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49. Thea Tlsty
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50. Joseph F. Costello
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51. Irmtraud M. Meyer
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52. Connie J. Eaves
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53. Wyeth W. Wasserman
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54. Steven Jones
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55. David Huntsman
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56. Martin Hirst
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57. Carlos Caldas
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58. Marco A. Marra
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59. Samuel Aparicio
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Contributions

S.A., S.P.S., C. Caldas and M.A.M. designed and implemented the research plan and wrote the manuscript. S.P.S., A.R., R. Goya, G. Ha, J.D., G. Haffari, A. Bashashati, A. McPherson, K.S., A.C., R. Giuliany, A.H.-M., J.R., D.L., I.B., R.V., S.W.C., M.G., I.M.M., S.J., C. Curtis, O.M.R., P.D.P., V.B. and W.W.W. conducted bioinformatic analyses of the data and/or gave advice on analytic methodology. G.T. conducted histopathological review and immunohistohemistry. A.O., Y.Z., G.T., K.T., L.M.P., J.K., A.B., D.Y., A.T., N.D., T.Z., S.-F.C., K.M. and M.H. conducted sequencing or experimental validation of somatic aberrations. D.Y., A. Moradian, S.-W.G.C. and G.B.M. conducted proteome validation of splicing. P.W., K.G., S.C., S.-F.C., G.T., J.M., C. Caldas, P.D.P. and D.H. collected and interpreted clinical data. S.D., J.F.C., T.T., M.S., P.G. and C.J.E. contributed materials or reagents. K.H., V.T., T.H., M.H. and M.A.M. generated sequence data.

Corresponding authors

Correspondence toSohrab P. Shah, Carlos Caldas, Marco A. Marra or Samuel Aparicio.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains legends for Supplementary Figures 1-12 (see pages 2-5), Supplementary Figures 1-12 (see pages 6-127), Supplementary Methods with additional references (see pages 128-140) and legends for Supplementary Tables 1-17 with additional references (see pages 142-145). (PDF 22432 kb)

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This file contains Supplementary Tables 1-17. (ZIP 5091 kb)

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Shah, S., Roth, A., Goya, R. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers.Nature 486, 395–399 (2012). https://doi.org/10.1038/nature10933

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• Received: 16 June 2011
• Accepted: 15 February 2012
• Published: 04 April 2012
• Issue Date: 21 June 2012
• DOI: https://doi.org/10.1038/nature10933