In all three cases, we confirmed that the expression changes of these genes were significant after correcting for variation in DNA copy numbers and tumor purity between samples (Supplementary Fig. 12). We would expect mutations at these hotspots to be associated with expression change of the altered allele. However, allele-specific expression analysis is challenging to evaluate across distant sites. Indeed, for all three candidate CBS hotspots, we could not unambiguously resolve the two alleles because the maximum inter-SNP distance between hotspot and candidate target gene were >5 kb. As CBSs are essential in maintaining the chromosomal architecture, it is likely that these CBS hotspot mutations cause altered expression of nearby cancer driver genes by disrupting the local chromosomal organization. Indeed, using the set of constitutive CTCF-CTCF loops, we observed chromatin contacts between the KCNQ5 and SPG20 loci and their corresponding CBS hotspots (Supplementary Figs. 9, 10). Interestingly, the three genes were also differentially expressed in GC tumors compared to normal gastric tissue. CENPQ expression was upregulated in tumors (Wilcoxon P = 0.0028; Fig. 5c), while both KCNQ5 and SPG20 expression was downregulated in tumors compared to normal gastric samples (Wilcoxon P = 3.2 × 10−7 and 0.00082 respectively; Fig. 5f, i). Therefore, it is plausible that the expression of these three genes could be altered in GC through additional mechanisms. Indeed, KCNQ5 and SPG20 were found to be downregulated in colorectal cancer compared to the normal mucosa due to promoter hypermethylation49–51. These results further support the contributions of these genes to GC tumorigenesis.