Table 3.
Number of samples that have fusion neoantigens
| Fusion genes | # samples with fusion genes | # samples with in-frame fusion genes | # samples with neoantigen interacting with HLA-Is | # cancer types with neoantigen interacting with HLA-Is | # samples with neoantigen interacting with HLA-IIs | # cancer types with neoantigen interacting with HLA-IIs | PMIDs of previous studies | |
|---|---|---|---|---|---|---|---|---|
| BCR | ABL1 | 194 | 16 | 9 | 3 | 8 | 3 | 32117272, 27181332, 32301049, 11697642, 8289483, 22912393, 28153834 |
| EML4 | ALK | 78 | 21 | 8 | 5 | 7 | 5 | 32013991, 29732013 |
| RPS6KB1 | VMP1 | 98 | 14 | 7 | 5 | 6 | 4 | |
| CCDC6 | ANK3 | 27 | 11 | 6 | 3 | 5 | 2 | |
| CBFB | MYH11 | 57 | 10 | 6 | 3 | 1 | 1 | 32831296 |
| ARL8B | ITPR1 | 9 | 6 | 5 | 4 | 3 | 3 | |
| RUNX1 | RUNX1T1 | 99 | 8 | 5 | 2 | 2 | 1 | |
| EWSR1 | FLI1 | 90 | 4 | 5 | 3 | 2 | 2 | 34385178, 36900411 |
| REPS2 | TXLNG | 13 | 7 | 5 | 4 | 2 | 2 | |
| NCOR2 | SCARB1 | 28 | 10 | 4 | 4 | 4 | 4 | |
| FLNB | SLMAP | 14 | 6 | 4 | 4 | 4 | 4 | |
| PUM1 | NKAIN1 | 13 | 13 | 4 | 4 | 4 | 4 | |
| KIF5B | RET | 24 | 4 | 4 | 2 | 3 | 1 | |
| MPP5 | GPHN | 20 | 5 | 4 | 3 | 3 | 2 | |
| EWSR1 | ATF1 | 16 | 3 | 4 | 3 | 3 | 3 | |
| SMARCA4 | DNM2 | 11 | 6 | 4 | 4 | 3 | 3 | |
| ERC1 | RET | 10 | 5 | 4 | 3 | 3 | 2 | |
| SND1 | BRAF | 10 | 3 | 4 | 3 | 3 | 3 | |
| ASCC1 | MICU1 | 11 | 8 | 4 | 2 | 2 | 2 | |
| PLG | LPA | 16 | 4 | 4 | 1 | 1 | 1 | |
| WNK2 | CENPP | 5 | 4 | 4 | 3 | 1 | 1 | |
| LAPTM4B | MTDH | 8 | 5 | 3 | 3 | 4 | 4 | |
| ETV6 | NTRK3 | 36 | 7 | 3 | 3 | 3 | 3 | 36753024 |
| CAMKK2 | KDM2B | 15 | 8 | 3 | 1 | 3 | 1 | |
| PRRC2B | NUP214 | 14 | 7 | 3 | 3 | 3 | 3 | |
| LTBP1 | BIRC6 | 13 | 6 | 3 | 3 | 3 | 3 | |
| TRIM27 | RET | 7 | 3 | 3 | 3 | 3 | 3 | |
| AP2A2 | TALDO1 | 6 | 5 | 3 | 3 | 3 | 3 | |
| CABLES1 | RBBP8 | 6 | 3 | 3 | 1 | 3 | 1 | |
| IKBKB | ANK1 | 6 | 4 | 3 | 3 | 3 | 3 | |
| TMPRSS2 | ERG | 975 | 18 | 3 | 1 | 2 | 1 | 34891161, 34527198, 33244314 |
| EWSR1 | ERG | 16 | 5 | 3 | 2 | 2 | 2 | 36900411 |
| KAT6A | ADAM2 | 14 | 6 | 3 | 1 | 2 | 1 | |
| BCAS3 | VMP1 | 13 | 7 | 3 | 3 | 2 | 2 | |
| CD44 | PDHX | 12 | 8 | 3 | 3 | 2 | 2 | |
| RFTN1 | DAZL | 5 | 4 | 3 | 2 | 2 | 2 | |
| WWOX | VAT1L | 4 | 3 | 3 | 3 | 2 | 2 | |
| ZC3H7A | GSPT1 | 3 | 3 | 3 | 3 | 2 | 2 | |
| AFF1 | KMT2A | 45 | 3 | 3 | 2 | 1 | 1 | |
| PPP1CB | PLB1 | 20 | 7 | 3 | 2 | 1 | 1 | |
| ERG | TMPRSS2 | 18 | 10 | 3 | 1 | 1 | 1 | 34891161, 34527198, 33244314 |
| BPTF | PITPNC1 | 13 | 5 | 3 | 2 | 1 | 1 | |
| COMMD10 | AP3S1 | 10 | 4 | 3 | 3 | 1 | 1 | |
| KDM5A | NINJ2 | 9 | 9 | 3 | 3 | 1 | 1 | |
| LMBR1 | PTPRN2 | 7 | 4 | 3 | 3 | 1 | 1 | |
| ZMYND8 | EYA2 | 7 | 5 | 3 | 2 | 1 | 1 | |
| DLG1 | BDH1 | 6 | 4 | 3 | 3 | 1 | 1 | |
| ZMYND8 | SULF2 | 5 | 5 | 3 | 2 | 1 | 1 | |
| LTBP1 | TTC27 | 4 | 3 | 3 | 2 | 1 | 1 | |
| SNTB2 | TANGO6 | 4 | 3 | 3 | 3 | 1 | 1 | |
| BAZ2A | PRIM1 | 3 | 3 | 3 | 3 | 1 | 1 | |
| PML | RARA | 102 | 13 | 2 | 2 | 2 | 1 | 32117272 |
| TMPRSS2 | ETV4 | 49 | 7 | 2 | 1 | 2 | 1 | |
| KMT2A | MLLT3 | 32 | 3 | 2 | 2 | 2 | 2 | |
| MYB | NFIB | 18 | 4 | 2 | 2 | 2 | 2 | 31011208 |
| KDM2A | RHOD | 16 | 3 | 2 | 2 | 2 | 2 | |
| TPX2 | HM13 | 16 | 2 | 2 | 2 | 2 | 2 | |
| PPP6R3 | LRP5 | 15 | 5 | 2 | 2 | 2 | 2 | |
| KDM2A | C11orf80 | 14 | 4 | 2 | 2 | 2 | 2 | |
| QKI | PACRG | 14 | 5 | 2 | 2 | 2 | 2 | |
| PRCC | TFE3 | 13 | 3 | 2 | 2 | 2 | 2 | |
| VTI1A | TCF7L2 | 13 | 2 | 2 | 2 | 2 | 2 | |
| FUS | ERG | 12 | 3 | 2 | 2 | 2 | 2 | |
| SMCHD1 | NDC80 | 12 | 3 | 2 | 2 | 2 | 2 | |
| PTPN12 | CCDC146 | 11 | 4 | 2 | 2 | 2 | 2 | |
| ERBB2 | PSMB3 | 10 | 4 | 2 | 1 | 2 | 1 | |
| TFG | ALK | 10 | 3 | 2 | 2 | 2 | 2 | |
| ACO2 | ZC3H7B | 9 | 2 | 2 | 2 | 2 | 2 | |
| FGFR2 | BICC1 | 9 | 7 | 2 | 2 | 2 | 2 | |
| FGFR2 | ATE1 | 9 | 3 | 2 | 2 | 2 | 2 | |
| SDC4 | ROS1 | 9 | 3 | 2 | 2 | 2 | 2 | |
| TBCD | FOXK2 | 9 | 5 | 2 | 2 | 2 | 2 | |
| UBTF | MAML3 | 9 | 4 | 2 | 1 | 2 | 1 | |
| ERC1 | WNK1 | 8 | 5 | 2 | 2 | 2 | 2 | |
| EWSR1 | WT1 | 8 | 2 | 2 | 3 | 2 | 2 | 36900411 |
| STRN | ALK | 8 | 5 | 2 | 2 | 2 | 2 | |
| TC2N | TRIP11 | 8 | 3 | 2 | 2 | 2 | 2 | |
| UBE2K | LIAS | 8 | 2 | 2 | 2 | 2 | 2 | |
| ESR1 | MTHFD1L | 7 | 2 | 2 | 2 | 2 | 2 | |
| KMT2A | EPS15 | 7 | 1 | 2 | 2 | 2 | 2 | |
| AGBL4 | FAF1 | 6 | 2 | 2 | 2 | 2 | 2 | |
| BCR | JAK2 | 6 | 1 | 2 | 3 | 2 | 3 | |
| EFHD1 | EIF4E2 | 6 | 4 | 2 | 1 | 2 | 1 | |
| KMT2A | AFF3 | 6 | 1 | 2 | 2 | 2 | 2 | |
| PPFIA1 | SLC39A11 | 6 | 3 | 2 | 1 | 2 | 1 | |
| SMARCAD1 | GRID2 | 6 | 5 | 2 | 2 | 2 | 2 | |
| TAF15 | AP2B1 | 6 | 3 | 2 | 2 | 2 | 2 | |
| WHSC1L1 | ADAM32 | 6 | 6 | 2 | 1 | 2 | 1 | |
| MSH2 | TTC7A | 5 | 3 | 2 | 2 | 2 | 2 | |
| NEMF | C14orf182 | 5 | 2 | 2 | 2 | 2 | 2 | |
| PTPN11 | EPYC | 5 | 4 | 2 | 1 | 2 | 1 | |
| RAB3GAP1 | ACMSD | 5 | 3 | 2 | 2 | 2 | 2 | |
| SEC31A | ALK | 5 | 1 | 2 | 2 | 2 | 2 | |
| UBR1 | TGM5 | 5 | 5 | 2 | 2 | 2 | 2 | |
| ATXN2 | TRIM37 | 4 | 3 | 2 | 1 | 2 | 1 | |
| CTPS1 | NFYC | 4 | 3 | 2 | 1 | 2 | 1 | |
| CUX1 | RET | 4 | 1 | 2 | 2 | 2 | 2 | |
| DDX10 | NUP98 | 4 | 2 | 2 | 1 | 2 | 1 | |
| EHMT1 | GRIN1 | 4 | 3 | 2 | 2 | 2 | 2 | |