Tumor heterogeneity and intratumoral immune landscapes in hypermutated and non-hypermutated tumors. (A) Violin plots (that is, box plots with a rotated probability density plot) of intratumoral heterogeneity represented by the calculated cancer cell fractions in MSI-H and MSS patients. MSS tumors (colored plots) were grouped in four clusters based on their cancer cell fraction distributions. The Kolmogorov-Smirnov D statistic was used as a similarity measure to cluster the tumors into the four groups (Figure S7 in Additional file 1). (B) Number of mutations and neo-antigen frequencies in the hypermutated tumors (MSI-H and MSS^) and in the four clusters of non-hypermutated tumors (MSS) colored as in panel (A). * P > 0.01, ** P < 0.01. Error bars represent standard error of the mean. (C) Survival analysis of the homogeneous (cluster1 and cluster2) and heterogeneous (cluster3 and cluster4) MSS tumors in late stages. (D) Volcano plots for enriched (red) and depleted (blue) TIL subpopulations in the distinct patient groups compared with normal samples (n = 50). (E) Log2 fold change of the expression (RNA sequencing data) of selected genes relative to normal tissue for the MSI-H and MSS patients colored as in (A).