We found that gastric tumors of the genomic instable subtype (CIN) exhibited the highest mutation rate at CBSs compared to tumors of the other GC subtypes. Furthermore, CBS mutations were associated with the occurrence of nearby chromosomal breakpoints, suggesting a general link between CBS mutations and genomic instability. A previous study has suggested a model where genome higher-order interactions are directly poised for chromosomal breaks59. One important open question is whether these processes are coupled, and if so, what is the temporal order of CBS mutations and chromosomal breaks. Interestingly, somatic variant allele frequencies (VAFs) of the CBS hotspot mutations supported that these were generally clonal and likely early events in tumor evolution (Fig. 7e). Furthermore, we found that the VAFs of CBS hotspot mutations were comparable to non-silent coding mutations of known GC driver genes from the same sample (paired Wilcoxon P-value = 0.49; Fig. 7f).