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. 2019 Nov;29(11):1860–1877. doi: 10.1101/gr.234435.118

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© 2019 Malikic et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 9. — Inferred tumor phylogeny for Patient 2 from Gawad et al. (2014) through the joint use of bulk and SCS data while allowing ISA violations. The topology of the tree and the mutational placements are similar to that of B-SCITE in Figure 8 with the key difference that three mutations are now eliminated by PhISCS: RRP8 and CMTM8 are eliminated due to inconsistent VAF and SCS data; CMTM8 has a similar SCS profile to INHA but has a significantly higher VAF. It also has a higher VAF than RRP8 but appears in 20 fewer cells. In addition, the mutation in RIMS2 is eliminated by PhISCS as per the figure. Evidence for ISA violations in this gene has been reported earlier (Kuipers et al. 2017).