Extended Data Fig. 2: Genetic dynamics in EAC.
(a) Tumor cellularity of samples from different timepoints. Tumor cellularity was estimated from whole-exome sequencing data using Sequenza. (b) Violin plots showing the distribution of mutational burden stratified by treatment type (c). Mutations of each sample were classified as clonal or subclonal based on the copy number and cellularity adjusted cancer cell fraction. P values in panels A-C are calculated by the two-sided Wilcoxon test. (d) Selected phylogenetic trees with clade length indicating the number of shared mutations between samples from the same patient. Timepoint of samples are annotated at the tip of the clades with the letters A-C. Numbers at the nodes indicate bootstrap values. EAC drivers harboring mutations (without brackets) or indels (in squared brackets) and number of neoantigenic SNVs are annotated on the clades of the trees. REP: Responder, NRP: NonResponder, HI: homoplasy index, NeoSNVs: Neoantigenic single-nuceleotide variant. (e) Plot shows COSMIC signature weights of individual samples from NRP (left) and REP (right).
