Fig. 1

ITH example with and without CNAs. a Visualization of a tree, where each node represents a subclone within a tumor sample. N denotes the normal cells, and A, B, C, and D denote the descending subclones. To simplify notation, we also use A, B, C, and D to denote the mutations that arise from the corresponding four subclones. We simulated a tumor purity of 0.762 with 1000 variants under the following scenarios: (1) no somatic copy number alterations (SCNAs) and (2) SCNAs in which mutations are equally distributed across clonal copy number states (0,1), (1,1), and (1,2). A copy number state denotes the number of copies of the two alleles. For example, copy number state (0,1) denotes deletion in one allele. b The second column corresponds to the cellular proportions of each subclone after accounting for tumor purity. The third and fourth columns correspond to the cellular prevalence and mean VAF (without SCNAs), respectively, of the mutations arising from each subclone. In (c) and (d), the black curve is the overall VAF density, and the colored curves are the subclone-specific VAF densities. Multiple subclone-specific VAF peaks with SCNA are due to combinations of multiplicity and subclone allocation