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. 2017 Oct 18;7:13467. doi: 10.1038/s41598-017-13338-8

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Experiment 2 (aneuploid cell lines DAH55 and DAH56). Effect of using incorrect copy numbers. (a) PyClone predicted cluster prevalences assuming diploid loci. The solid lines show the PyClone predicted cluster prevalences. The red solid line corresponds to a cluster of 21 DAH55 specific SNVs, the blue solid line to 27 DAH56 specific SNVs, the green solid line to a cluster of mainly shared SNVs and the purple solid lines to two other clusters, one of size 17 and the other of size 8 (see Supplementary Table S13). The other plot components are as in Fig. 1e. (b) PyClone predicted cluster prevalences adding random noise to copy number information. The solid lines show the PyClone predicted cluster prevalences. The red solid line corresponds to a cluster of 29 DAH55 specific SNVs, the blue solid line to 27 DAH56 specific SNVs, the green solid line to a cluster of 34 mainly shared SNVs and the purple solid line to a cluster of 9 mainly shared SNVs (see Supplementary Table S14). The other plot components are as in Fig. 1e. (c) Clomial predicted clonal prevalences. The red, blue, and purple solid lines correspond to the predicted clonal prevalences for the three estimated clones and the green solid line corresponds to the normal clone (see Tables S15 and S16 of the Supplementary Information).