Discovery and saturation analysis of cancer genes across 21 tumour types (original) (raw)

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Data deposits

The data analysed in this manuscript have been deposited in Synapse (http://www.synapse.org), accession number syn1729383, and in dbGaP (http://www.ncbi.nlm.nih.gov/gap), accession numbers phs000330.v1.p1, phs000348.v1.p1, phs000369.v1.p1, phs000370.v1.p1, phs000374.v1.p1, phs000435.v2.p1, phs000447.v1.p1, phs000450.v1.p1, phs000452.v1.p1, phs000467.v6.p1, phs000488.v1.p1, phs000504.v1.p1, phs000508.v1.p1, phs000579.v1.p1, phs000598.v1.p1.

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Acknowledgements

This work was conducted as part of TCGA, a project of the National Cancer Institute and the National Human Genome Research Institute. We are grateful to T. I. Zack, S. E. Schumacher, and R. Beroukhim for sharing their copy-number analyses before publication.

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Author notes

  1. Eric S. Lander and Gad Getz: These authors contributed equally to this work.

Authors and Affiliations

  1. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachusetts, USA
    Michael S. Lawrence, Petar Stojanov, Craig H. Mermel, James T. Robinson, Levi A. Garraway, Todd R. Golub, Matthew Meyerson, Stacey B. Gabriel, Eric S. Lander & Gad Getz
  2. Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, Massachusetts, USA
    Petar Stojanov, Levi A. Garraway, Todd R. Golub & Matthew Meyerson
  3. Cancer Center and Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA,
    Craig H. Mermel & Gad Getz
  4. Harvard Medical School, 25 Shattuck Street, Boston, 02115, Massachusetts, USA
    Levi A. Garraway, Todd R. Golub, Matthew Meyerson, Eric S. Lander & Gad Getz
  5. Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, 20815, Maryland, USA
    Todd R. Golub
  6. Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA
    Eric S. Lander

Authors

  1. Michael S. Lawrence
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  2. Petar Stojanov
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  3. Craig H. Mermel
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  4. James T. Robinson
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  5. Levi A. Garraway
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  6. Todd R. Golub
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  7. Matthew Meyerson
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  8. Stacey B. Gabriel
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  9. Eric S. Lander
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  10. Gad Getz
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Contributions

G.G., E.S.L., T.R.G., M.M., L.A.G. and S.B.G. conceived the project and provided leadership. M.S.L., G.G., E.S.L., P.S. and C.H.M. analysed the data and contributed to scientific discussions. M.S.L., E.S.L. and G.G. wrote the paper. J.T.R., M.S.L., E.S.L. and G.G. created the website for visualizing this data set.

Corresponding authors

Correspondence toEric S. Lander or Gad Getz.

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Competing interests

A patent related to this work has been filed.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-9 and legends for Supplementary Tables 1-6 (see separate files for tables). (PDF 1511 kb)

Supplementary Table 1

This file contains a list of source datasets analyzed in this work, and references to the corresponding publications. (XLS 28 kb)

Supplementary Table 2

This file contains the 260 significantly mutated cancer genes found by analysis with the MutSig suite (see Supplementary Information file for full legend). (XLSX 709 kb)

Supplementary Table 3

This file contains a list of the 21 tumor types studied, and the significantly mutated genes found by the MutSig suite in each tumor type (see Supplementary Information file for full legend). (XLSX 16 kb)

Supplementary Table 4

The file contains a list of references reporting the identification of candidate cancer genes (see Supplementary Information file for full legend). (XLSX 58 kb)

Supplementary Table 5

This file contains a list of references to biological literature supporting the 33 novel candidate cancer genes with clear and compelling connections to cancer biology. (XLSX 21 kb)

Supplementary Table 6

This file contains a summary of the analysis comparing the performance of each of the three MutSig metrics separately, in pairwise combinations, and all three combined as in the main analysis (see Supplementary Information file for full legend). (XLS 24 kb)

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Lawrence, M., Stojanov, P., Mermel, C. et al. Discovery and saturation analysis of cancer genes across 21 tumour types.Nature 505, 495–501 (2014). https://doi.org/10.1038/nature12912

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