Breakpoints of novel fusions in SK-BR-3. (a) The novel tumor allele supporting PREX1>CPNE1 consists of the first three exons of PREX1 (green), an intronic segment of PHF20 (orange) and the last three exons of CPNE1 (blue). The RNA PREX1>CPNE1 breakpoint between exons A and B was nominated by deFuse, while the genomic breakpoints SV1 and SV2 were detected by CREST. (b) Six genomic breakpoints from three gene fusions were selected for PCR validation (Additional file 8). SV1 and SV2 are from PREX1>CPNE1, SV3 and SV4 from MTBP-SAMD12, and SV5 and SV6 from WDR67-ZNF704. Clean PCR bands were observed at SV1, SV2, SV3 and SV6.