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. 2020 Aug 25;6:27. doi: 10.1038/s41540-020-00147-5

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© The Author(s) 2020

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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Fig. 4 — a, b Lin et al. profiled five regions of each of nine HBV-positive HCCs. We profiled 6–8 regions of each of three Wilms’ tumors and ten regions of a castrate-resistant prostate cancer (CRPC). For each tumor, we exhaustively selected all region subsets size-2 and up, and compared the number of predicted tumor subclones across subsets to those obtained using all available region profiles using a Chimæra and b SCHISM. Chimæra analysis of any 4-tumor regions resulted in a similar number of subclones as analysis of five regions, however, profiling two regions produced fewer predicted subclones. SCHISM performed better on stable genomes (CG118) than on unstable genomes (CG163 and CRPC). c Chimæra analyses (top) of HCC6046 profiles suggested convergence of subclone predictions using three profiled regions, while SCHISM analyses (bottom) produced a higher prediction variability across profiling subsets. d Similarly, Chimæra analyses of four regions of CG565 produced a similar number of clones as profiles of eight regions. e Chimæra analyses of seven regions of our CRPC tumor produced a similar number of clones as analysis of ten regions; however, analyses based on five or fewer tumor areas produced significantly more predicted tumor subclones due to reduced aggregating power. SCHISM analyses based on six or more regions produced consistent counts of predicted subclones, but this number was considerably greater than the number of subclones predicted by Chimæra.