Extended Data Fig. 4: Landscape of gene fusions and SMGs in CPGEA.

a, The circle represents gene fusions in Chinese and Western cohorts. Recurrent fusions (more than two samples) are displayed as connected gene pairs, in which the width of the connecting arc represents the number of samples that contained the fusion. Red indicates novel gene fusions not present in public databases (FusionHub). b, Fusion was validated by Sanger sequencing and RNA-seq data. Red cells indicate validated fusion events, and green cells indicate PCR failure. c, Circos plot displaying ETS family fusions. Expression levels are shown as a function of copy number. d, The SCHLAP1-UBE2E3 gene fusion. e, AMACR fusions. f, A heterozygous SND1-BRAF fusion found in CPGEA. g, In total, 83 SMGs were detected by MuSiC, including 7 genes called by both MuSiC and MutSigCV. h, Fraction of primary, metastatic, and other cancer types investigated by each study. i, Venn diagrams of SMGs defined in different studies. j, Genes significantly mutated in CPGEA, Western primary, and Western metastatic cohorts. Purple cells indicate that the gene was defined as an SMG in the study. h–j, The Western cohorts are from CPCG⁹, SU2C¹¹, T/C/B (Trento/Cornell/Broad, neuroendocrine prostate cancer)⁸, B/C (Broad/Cornell)⁷, CRC¹³, M/DFCI³, TCGA², Michigan¹¹, MSKCC¹⁵, Organoid¹⁰, CNA-PNAS¹² and MSK¹⁷.