Figure 2:

a. Distribution of mutations across the metastatic NSCLC cases from the TRACERx cohort. Top panel: a mutation is either in a gene with a “putative role in cancer” (i.e., is a oncogene or tumor suppressor - colored orange) or with “no putative role in cancer” (colored gray). Orthogonally, the placement of the mutation is either concordant (i.e., is preserved in the omlta of the trees inferred by CONIPHER and PairTree for the case - solid color) or discordant (i.e., is deleted in the omlta - shaded color). The proportion of discordant mutations are higher among those in genes with a role in cancer. Bottom panel: the proportion of concordantly placed mutations among tumor suppressor genes are similar to that among oncogenes. b. For any given case, the “imbalance” of a clonal tree, measured as the mean node depth (distance from the root), is typically higher if inferred by CONIPHER. E.g., for case CRUK0337, the imbalance of the tree inferred by CONIPHER is 3, but the imbalance of the tree inferred by PairTree is 1.625. (Blue nodes in the trees represent the mutational clusters preserved in their omlta.) c. The inferred timing of metastatic branching (6) differs between the CONIPHER and PairTree trees for case CRUK0733. Left panel: In the CONIPHER inferred tree, the metastatic branching is characterized as “late” whereas in the PairTree tree for the same case, it is characterized as “early”. Middle panel: The timing of metastatic branching differs significantly between CONIPHER and PairTree trees: PairTree typically places the metastatic branching closer to the root. Right panel: The number of cases for which CONIPHER and PairTree agree/disagree with respect to the timing of metastatic branching; additionally, the timing of the metastatic branching based on omlta trees (given in parentheses) agree with CONIPHER more often.