Fig. 4

Multiregion analysis of CNAs. a Multiregion CNA profiles of PCRCs. Chromosomal arm-level CNAs were called from the WES data of the ten PCRCs. Heat maps represent the presence of chromosomal arm-level CNAs (red, gain; blue, loss) for each case, and the shades of color are proportional to log₂-scaled ratios between normalized tumor and normal read depths (log₂R). PCRC10, in which no CNAs were detected, was omitted. Samples in each case are sorted in the same order as in Fig. 1. b, c Bar plots showing the number of ubiquitous and heterogeneous CNAs in each case of the PCRCs (b) and ACRCs (c). Effects of different number of samples between cases were corrected by downsampling (Methods). d Violin plots showing the distribution of the number of ubiquitous and heterogeneous CNAs based on b and c. ACRCs harbored a significantly larger number of ubiquitous CNAs than PCRCs (P = 0.047; Wilcoxon rank-sum test), while the number of heterogeneous CNAs in ACRCs is comparable to that in PCRCs (P = 0.16; Wilcoxon rank-sum test). e Bar plots showing the frequencies of ubiquitous (orange) and heterogeneous (green) CNAs for PCRCs and ACRCs. For ACRCs, CNAs were called from our previously published WES data of the eight non-hypermutated ACRCs