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Neutral tumor evolution?

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Fig. 1: M(f) ~ 1/f is an uninformative test for identifying (non-)neutrality in simulated and real data.

Data availability

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.

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Acknowledgements

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/).

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M.T., I.M., M.G., A.M.L., F.M., P.T.S., Q.D.M., O.C.L., D.C.W. and P.V.L. participated in argumentation. M.T., O.C.L., D.C.W. and P.V.L. derived the deterministic equations. M.T. wrote the code and generated the figures, with input from I.M., M.G., O.C.L., D.C.W. and P.V.L.; M.T., O.C.L., D.C.W. and P.V.L. drafted the manuscript, which was revised by I.M., M.G., A.M.L., F.M., P.T.S. and Q.D.M. All authors read and approved the manuscript.

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Correspondence to Peter Van Loo.

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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

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