Common fusion transcripts identified in colorectal cancer cell lines by high throughput RNA sequencing

From altogether 220 million paired-end sequence reads from seven CRC cell lines we identified 3391 candidate fused transcripts, each with at least five-fold coverage across the fusion partners and at least three sequence-reads spanning the actual chimeric breakpoint. Stringent requirements left a set of eleven candidate fusion transcripts nominated for further experimental validation, of which ten were positive by RT-PCR and Sanger sequencing. Six of the fusions were intra-chromosomal transcripts and, interestingly, three of these, AKAP13-PDE8A, COMMD10-AP3S1, and CTB-35F21.1-PSD2, were present in respectively 18, 18 and 20 of 21 analyzed cell lines, and in respectively 18, 61 and 48 (17 to 58 percent) of 106 primary cancer tissues. These three fusion transcripts were also detected in two to four of 14 normal colonic mucosa samples (14 to 28 percent).