Subscribe to Journal
Get full journal access for 1 year
only $17.42 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
This study used data generated by the The Cancer Genome Atlas (TCGA, a collection of publicly available data from human tissues; http://cancergenome.nih.gov/). We ran dN/dS analyses on the data from TCGA, using published CaVeMan19,20 single-nucleotide variant calls, and ASCAT21 copy number calls, as described in Martincorena et al.13. Simulation data can be reproduced by using the R and Java scripts provided.
Greaves, M. & Maley, C. C. Nature 481, 306–313 (2012).
Yates, L. R. & Campbell, P. J. Nat. Rev. Genet. 13, 795–806 (2012).
Andor, N. et al. Nat. Med. 22, 105–113 (2016).
Nowell, P. C. Science 194, 23–28 (1976).
Nik-Zainal, S. et al. Cell 149, 994–1007 (2012).
Dentro, S. C., Wedge, D. C. & Van Loo, P. Cold Spring Harb. Perspect. Med. 7, a026625 (2017).
Williams, M. J., Werner, B., Barnes, C. P., Graham, T. A. & Sottoriva, A. Nat. Genet. 48, 238–244 (2016).
Johnson, D. C. et al. Blood 130, 1639–1643 (2017).
Zack, T. I. et al. Nat. Genet. 45, 1134–1140 (2013).
Bozic, I., Gerold, J. M. & Nowak, M. A. PLoS Comput. Biol. 12, e1004731 (2016).
Nei, M. & Gojobori, T. Mol. Biol. Evol. 3, 418–426 (1986).
Goldman, N. & Yang, Z. Mol. Biol. Evol. 11, 725–736 (1994).
Martincorena, I. et al. Cell 171, 1029–1041.e21 (2017).
Forbes, S. A. et al. Nucleic Acids Res. 45, D777–D783 (2017).
Williams, M. J. et al. Nat. Genet. 50, 895–903 (2018).
Al Hammal, O., Alonso, D., Etienne, R. S. & Cornell, S. J. PLoS Comput. Biol. 11, e1004134 (2015).
Herzog, H. A., Bentley, R. A. & Hahn, M. W. Proc. R. Soc. Lond. B 271, S353–S356 (2004).
Leigh, E. G. Jr. J. Evol. Biol. 20, 2075–2091 (2007).
Varela, I. et al. Nature 469, 539–542 (2011).
Jones, et al. Curr. Protoc. Bioinforma. 56, 15.10.1–15.10.18 (2016).
Van Loo, et al. Proc. Natl Acad. Sci. 107, 16910–16915 (2010).
This work was supported by The Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001202), the UK Medical Research Council (FC001202) and the Wellcome Trust (FC001202) (M.T. and P.V.L.). M.T. is supported as a postdoctoral fellow by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie Grant agreement no. 747852-SIOMICS). P.V.L. is a Winton Group Leader in recognition of the Winton Charitable Foundation’s support toward the establishment of The Francis Crick Institute. I.M. is funded by a Cancer Research UK Career Development Fellowship (C57387/A21777). D.C.W. is funded by the Li Ka Shing Foundation. This work was supported by grant 1U24CA210957 to P.T.S.. F.M. acknowledges support from the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited. Parts of this work were funded by Cancer Research UK core grant C14303/A17197 (F.M.). This project was enabled through access to the MRC eMedLab Medical Bioinformatics infrastructure, supported by the UK Medical Research Council (grant no. MR/L016311/1) (M.T. and P.V.L.). Parts of the results published here are based on data generated by the TCGA Research Network (http://cancergenome.nih.gov/).
About this article
Cite this article
Tarabichi, M., Martincorena, I., Gerstung, M. et al. Neutral tumor evolution?. Nat Genet 50, 1630–1633 (2018). https://doi.org/10.1038/s41588-018-0258-x
Cancer and Metastasis Reviews (2021)
Nature Methods (2021)
Nature Reviews Cancer (2020)