Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma (original) (raw)

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Gene Expression Omnibus

Data deposits

Exome sequence data have been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/) hosted by the European Bioinformatics Institute under accession EGAS00001000006 and expression data has been deposited with Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession GSE22316.

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Acknowledgements

P.A.F. and M.R.S. would like to acknowledge the Wellcome Trust for support under grant reference 077012/Z/05/Z and A. Coffey, D. Turner and L. Mamanova for assistance with the exon capture. K.F., K.D. and B.T.T. acknowledge the support of the Van Andel Research Institute. B.T.T. would like to acknowledge support from the Lee Foundation. I.V. is supported by a fellowship from The International Human Frontier Science Program Organization. D.J.A. acknowledges the support of Cancer Research UK. D.A.T. and P.A.P.-M. acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampo and thank W. Howatt, A. Hazelhurst and colleagues in the CRI core facilities for their support. B.T.T. would like to dedicate this work to Tat Hock Teh.

Author information

Authors and Affiliations

1. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
   Ignacio Varela, Patrick Tarpey, Keiran Raine, Philip Stephens, Helen Davies, David Jones, Meng-Lay Lin, Jon Teague, Graham Bignell, Adam Butler, Juok Cho, Gillian L. Dalgliesh, Danushka Galappaththige, Chris Greenman, Claire Hardy, Mingming Jia, Calli Latimer, King Wai Lau, John Marshall, Stuart McLaren, Andrew Menzies, Laura Mudie, Lucy Stebbings, Peter J. Campbell, Michael R. Stratton & P. Andrew Futreal
2. NCCS-VARI Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
   Dachuan Huang, Choon Kiat Ong, Waraporn Chan-on, Chutima Subimerb & Bin Tean Teh
3. Masonic Cancer Center, University of Minnesota, Minneapolis, 55455, Minnesota, USA
   David A. Largaespada
4. Department of Molecular Biology, Bioinformatics and Statistics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands,
   L. F. A. Wessels
5. Génétique Oncologique EPHE-INSERM U753, Faculté de Médecine Paris-Sud and Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France ,
   Stephane Richard
6. Centre Expert National Cancer Rares INCa “PREDIR”, Service d’Urologie, Hôpital de Bicêtre, AP-HP, 94276 Le Kremlin-Bicêtre, France ,
   Stephane Richard
7. Department of Urology, Spectrum Health Hospital, Grand Rapids, 49503, Michigan, USA
   Richard J. Kahnoski & John Anema
8. Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Robinson Way, Cambridge CB2 0RE, UK ,
   David A.Tuveson & Pedro A. Perez-Mancera
9. Bioinformatics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK ,
   Ville Mustonen & Andrej Fischer
10. Institut für Theoretische Physik, Universität zu Köln, Zülpicherstrasse 77, 50937 Köln, Germany ,
    Andrej Fischer
11. Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK ,
    David J. Adams & Alistair Rust
12. Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, 49503, Michigan, USA
    Karl Dykema & Kyle Furge
13. Laboratory of Cancer Therapeutics, DUKE-NUS Graduate Medical School, Singapore
    Bin Tean Teh
14. Laboratory of Cancer Genetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA ,
    Bin Tean Teh
15. Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK ,
    Michael R. Stratton

Authors

1. Ignacio Varela
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2. Patrick Tarpey
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3. Keiran Raine
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4. Dachuan Huang
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5. Choon Kiat Ong
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6. Philip Stephens
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7. Helen Davies
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8. David Jones
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9. Meng-Lay Lin
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10. Jon Teague
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11. Graham Bignell
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12. Adam Butler
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13. Juok Cho
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14. Gillian L. Dalgliesh
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15. Danushka Galappaththige
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16. Chris Greenman
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17. Claire Hardy
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18. Mingming Jia
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19. Calli Latimer
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20. King Wai Lau
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21. John Marshall
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22. Stuart McLaren
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23. Andrew Menzies
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24. Laura Mudie
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25. Lucy Stebbings
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26. David A. Largaespada
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27. L. F. A. Wessels
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28. Stephane Richard
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29. Richard J. Kahnoski
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30. John Anema
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31. David A.Tuveson
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32. Pedro A. Perez-Mancera
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33. Ville Mustonen
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34. Andrej Fischer
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35. David J. Adams
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36. Alistair Rust
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37. Waraporn Chan-on
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38. Chutima Subimerb
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39. Karl Dykema
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40. Kyle Furge
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41. Peter J. Campbell
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42. Bin Tean Teh
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43. Michael R. Stratton
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44. P. Andrew Futreal
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Contributions

I.V. and P.T. performed the main analytical aspects of the study. P.S., H.D., G.L.D., M.-L.L., G.B., C.H., L.M., S.M. performed the follow-up sequencing and analyses. K.R., D.J., J.T., A.B., C.G., D.G., M.J., C.L., J.M., A.M., L.S. contributed to the data processing, mapping and variant calling informatics. C.G. and K.W.L. performed statistical analyses. S.R., R.J.K., J.A. contributed samples and data for the clinical series. D.J.A., A.R., D.A.L., L.F.A.W., D.A.T., P.A.P.-M. performed the transposon screening and analyses. D.H., C.K.O., W.C., C.S. performed the siRNA and functional work. V.M., A.F. performed the missense mutation analysis. K.D., K.F. and J.C. performed the expression analyses. P.J.C., B.T.T., M.R.S., P.A.F. directed the study and wrote the manuscript, which all authors have approved.

Corresponding authors

Correspondence toBin Tean Teh, Michael R. Stratton or P. Andrew Futreal.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods and Data, additional references and Supplementary Tables 1-8. (PDF 2531 kb)

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Varela, I., Tarpey, P., Raine, K. et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.Nature 469, 539–542 (2011). https://doi.org/10.1038/nature09639

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• Received: 28 July 2010
• Accepted: 02 November 2010
• Published: 19 January 2011
• Issue Date: 27 January 2011
• DOI: https://doi.org/10.1038/nature09639