Figure 1

Results for Experiment 1 and 2. (a) Experiment 1 (diploid cell lines HCT116 and 184-hTERT-L2). PyClone predicted cluster prevalences for each mixture. The vertical axis indicates the range of cluster prevalence. The horizontal axis indicates the true mixing proportions used to generate each sample, where x;y corresponds to proportion of 184-hTERT-L2 and HCT116, respectively. The dashed red and blue lines represent the true simulated tumour longitudinal growth for 184-hTERT-L2 and HCT116, respectively, and the solid lines show the predicted longitudinal growth given by the estimated cluster prevalences. The red solid line corresponds to a cluster containing 41 184-hTERT-L2 specific SNVs, the blue solid line to a cluster of 48 HCT116 specific SNVs, the green solid line to a cluster of 33 shared SNVs and the purple solid line to small cluster containing three shared SNVs. (b) Experiment 1 (diploid cell lines HCT116 and 184-hTERT-L2). Clomial predicted clonal prevalences for each mixture. The red, blue and green solid lines correspond to the predicted clonal prevalences for 184-hTERT-L2, HCT116 and normal clones, respectively. The other plot components are as in (a). (c) Experiment 1 (diploid cell lines HCT116 and 184-hTERT-L2). PhyloWGS predicted cluster prevalences for each mixture. The red, blue and green solid lines correspond to the predicted cluster prevalences for 184-hTERT-L2, HCT116 and shared cluster, respectively. The other plot components are as in (a). (d) Experiment 1 (diploid cell lines HCT116 and 184-hTERT-L2). Box plots of the absolute difference between estimated and true SNV cellular prevalences across all samples for PyClone, PhyloWGS and Clomial. (e) Experiment 2 (aneuploid cell lines DAH55 and DAH56). PyClone predicted cluster prevalences. The horizontal and vertical axes are as in (a). The dashed red and blue lines represent the true simulated tumour longitudinal growth for DAH55 and DAH56, respectively. The solid lines show the PyClone predicted cluster prevalences. The red solid line corresponds to a cluster containing 25 DAH55 specific SNVs, the blue solid line to a cluster of 24 DAH56 specific SNVs, the green solid line to a cluster of mainly shared SNVs and the purple solid lines to four other small clusters. (f) Experiment 2 (aneuploid cell lines DAH55 and DAH56). Box plots of the absolute difference between estimated and true SNV cellular prevalences across all samples for PyClone using the correct copy number information, PyClone assuming diploid loci, Clomial and PyClone with noisy copy numbers.