Enrichment of CBS mutations was highest in CIN tumors, which are characterized by increased chromosomal aneuploidy. This prompted us to examine if mutations at CBSs in CIN tumors were correlated with somatic copy number alteration (SCNA) breakpoints. Strikingly, the distance between a CBS hotspot and its nearest SCNA breakpoint was significantly shorter in mutated than non-mutated tumors (P = 0.0018, two-sided Wilcoxon rank-sum test; Fig. 7a). In contrast, non-CBS mutation hotspots showed no such association (P = 0.53). The median distance between CBS hotspot mutations and its nearest SCNA breakpoint in the same sample was ~1 Mbp, notably shorter than the ~2 Mbp distance for non-CBS hotspots (Fig. 7a). To study whether this correlation between CBS mutations and SCNA breakpoints was specific to the CBS hotspots, we extended the analysis to all CBSs. Interestingly, we found that CBS mutations were correlated with occurrence of nearby SCNA breakpoints in the same samples, especially for mutations affecting CBSs at loop boundaries (Wilcoxon P = 5.7 × 10−16; Fig. 7b). Conversely, when we grouped 1 Mb windows of the genome according to SCNA breakpoint density, we found that the normalized CBS mutation rate was positively associated with SCNA breakpoint density (Fig. 7c–d). Overall, these results highlight a link between regional chromosomal instability and mutations at both CBS hotspots and boundary CBSs in general.Fig. 7Association between CBS mutations and genomic instability. a Distance to the nearest CNV breakpoint from CBS hotspots and other non-CBS mutation hotspots. b Distance to the nearest CNV breakpoint from CBSs at loop boundary and non-boundary CBSs. Wilcoxon rank-sum test P-values are shown. c Correlation of mutation rates with SCNA breakpoint density. d Correlation of normalized mutation rates with SCNA breakpoint density, correcting for the background mutation rate in each bin. Error bars represent the s.e.m. e The violin plots show the VAF distributions of somatic mutations in diploid regions of individual tumors. VAFs of the mutations at CBS hotspots are marked by red vertical lines. f Comparison between VAFs of the CBS hotspot mutations and VAFs of non-silent coding mutation on GC driver genes. The red points represent the median VAFs in each group. The dashed lines match mutations from the same samples. P-value is calculated by paired Wilcoxon rank-sum test