Table 1.
Recurrent TMPRSS2-ERG breakpoints in the cohort.
| Breakpoint | Count | 5’ breakpoint | 3’ breakpoint | Neoepitope Expected? | IAR | Count |
|---|---|---|---|---|---|---|
| 21:41508081–21:38445621 | 122 | 5′ UTR | Exon 2 | No | NA | |
| 21:41498119–21:38445621 | 48 | Exon 2 | Exon 2 | Yes | DNSKMALNS EALSVVSED | 37 |
| 21:41507950–21:38445621 | 35 | Exon 1 | Exon 2 | Yes*** | SGCEERGAA GSLISCE | 22 |
| 21:41508081–21:38474121 | 18 | 5′ UTR | Intron 1 | No | NA | |
| 21:41506445–21:38445621 | 18 | Intron 1 | Exon 2 | Yes* | NA | |
| 21:41508081–21:38584945 | 11 | 5′ UTR | 5’UTR | No | NA | |
| 21:41498119–21:38474121 | 7 | Exon 2 | Intron 1 | Yes** | DNSKMALNS LNSIDDAQL | 7 |
| 21:41508081–21:38423561 | 7 | 5′ UTR | Exon 3 | No | NA | |
| 21:41498119–21:38423561 | 4 | Exon 2 | Exon 3 | Yes*** | DNSKMALNS ELS | 1 |
| 21:41494356–21:38445621 | 3 | Exon 3 | Exon 2 | Yes*** | SPSGTVCTS RSLISCE | 3 |
IARs from 21:41498119 to 21:38445621 and 21:41507950 to 21:38445621 are recurrent suggesting the viability of universal peptide vaccine candidates. We do not expect to see an IAR from fusions with 5′ UTR breakpoints. *TransGene cannot handle de novo splice acceptors. **An epitope will exist where the TMPRSS2 reads into the intron of ERG. ***A frameshift is seen on the ERG side of the fusion.