Figure 3:

a. Metastatic tumors from the TRACERx NSCLC cohort, consists of 56 LUAD cases and 36 LUSC cases; the cohort also includes an additional 24 cases of other subtypes and 10 cases with no subtype annotation. b. For each case, omlta between the trees inferred by CONIPHER and PairTree was obtained and their concordance was measured as the proportion of robust mutational placements, i.e., 1 - omltd/number of mutations. The panel depicts all cases with a subtype annotation (only a subset of cases are labeled explicitly due to limited space) sorted based on the concordance values: LUSC cases tend to have higher concordance values and thus are more robust. c-d. A comparison between the distribution of LUAD and LUSC cases with respect to c concordance values, and d mean CCF of the mutations harbored: both distributions reveal a significant difference between the two subtypes. e. Pearson correlation between the mean CCF and tree concordance values among LUAD and LUSC cases: higher mean CCF values among LUSC cases may explain why their inferred trees tend to have higher concordance. f-g. For the two NSCLC subtypes, f LUAD and g LUSC, scatterplots show the number of cases in which a gene is mutated (y-axis) against the number of cases in which a mutation within that gene has discordant placement between CONIPHER and PairTree trees (x-axis). Genes with known “role in cancer” (in orange) are shown separately from genes with no putative role (in gray). The points for outlier genes are labeled to the extent that labels could be added without overlaps.