Fig. 1: Overviews of structural variants in 170 gastric cancer (GC) genomes.

a The upper panels show the size distribution of structural variants (SVs). The middle panels show SV size and SV allele frequency (SVAF). The color of each dot represents the number of SVs. In the right panel, the copy number change at the breakpoints of tandem duplications is represented by the bubble size. b Genome-wide frequencies of tandem duplications (green) and inversions (cyan). The histograms depict a sliding window of 500 kb (50 kb overlap), and the Y-axis shows the frequency of the cases. The black histograms indicate the number of SVs with SVAF > 0.4. See Supplementary Fig. 5 for all four SV types. c Example of a singular-type SV hotspot on chromosome 16. The upper panel indicates the distribution of super-enhancers (pink) defined by the ROSE algorithm⁵⁰ from H3K27Ac peaks of gastric cancer cell lines (n = 5)⁴⁹, and tandem duplications (green) and inversions (cyan) at the chromosome 16 locus detected in these cases. The sample identifiers with underline indicate that they have transcriptional data (RNA-seq). The bottom panel shows copy numbers and expression (RPKM) of ZC3H7A and BCAR4. Each dot represents a case, and blue (copy number plot) and red (RPKM plot) indicate hotspot-positive SV cases. d Example of a multiple-type SV hotspot on chromosome 20. As shown in c, the upper panel indicates the distribution of super-enhancers and SVs in each case. The bottom panel presents the copy number and expression (RPKM) of four genes, including CEBPB, located within the hotspot. a–d, Source data are provided as a Source Data file.