Extended Data Fig. 3: Cancer cell fractions and mutational spectra analysis.
(a) Circos representation of copy number gains harboring BRAF in multiple metastases from eight RAM cases. For each Circos plot (RAM case), the outermost layer represents chromosome 7 regions, and the inner heatmaps indicate copy number status (spanning region and depth ratio) of tumors with BRAF amplification. Arrow indicates the location of BRAF. (b) Schema of sub-clonal analysis of multi-organ metastases to identify organ-specific enrichment of mutations. Each mutation’s cancer cell fraction (CCF) is estimated using PyClone-VI. The ∆CCF of each mutation was calculated between tumors of organ A versus tumors of other organs in each RAM case. Enriched mutations in organ A are defined as those with a ∆CCF difference > 0.2. The recurrence of genes harboring organ A-enriched mutations is computed by combining the enriched mutations of tumors from organ A across all applicable RAM cases. (c) Intratumoral heterogeneity (ITH) levels (fraction of sub-clonal mutations per tumor) of RAM tumors by treatment histories. P values, Kruskal–Wallis test. ICB, n = 33; MAPKi, n = 14; ICB + MAPKi, n = 27. (d) Distribution of mutant allele frequencies (MAF) of early, intermediate, and late mutations. (e) Mutational spectra of early, intermediate, and late mutations. (f) Unsupervised clustering of mutational spectra among early, intermediate, and late mutations across treatment histories, RAM cases/patients, and organ sites.
