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Reply to ‘Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data’

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Fig. 1: Signatures of neutral evolution are robust to confounding factors in the data.

Data availability

Gastric cancers from ref. 3 and colorectal cancers from ref. 4 were analyzed with our framework in our original manuscript2. The new TCGA pan-cancer analysis is based on publicly available GDC calls that can be downloaded from https://portal.gdc.cancer.gov/ (Supplementary Table 1).

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Acknowledgements

A.S. is supported by the Chris Rokos Fellowship in Evolution and Cancer and by Cancer Research UK (A22909). T.A.G. is supported by Cancer Research UK (A19771). C.P.B. is supported by the Wellcome Trust (097319/Z/11/Z). B.W. is supported by a Geoffrey W. Lewis Post-Doctoral Training fellowship. A.S. and T.A.G. are jointly supported by the Wellcome Trust (202778/B/16/Z and 202778/Z/16/Z, respectively). This work was also supported by Wellcome Trust funding to the Centre for Evolution and Cancer (105104/Z/14/Z).

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M.J.W. performed beta-binomial noise analysis. T.H. performed TCGA classification. All authors participated in the discussion and addressed the critiques. M.J.W., B.W., C.P.B., T.A.G., and A.S. wrote the manuscript.

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Correspondence to Trevor A. Graham or Andrea Sottoriva.

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The authors declare no competing interests.

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Williams, M.J., Werner, B., Heide, T. et al. Reply to ‘Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data’. Nat Genet 50, 1628–1630 (2018). https://doi.org/10.1038/s41588-018-0210-0

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