Table 2.
Patient’s neo-epitopes to which T cell reactivity was detected
| Patient ID | CMS | # Mut | # SLP | Genes | Mut cDNA | Mut aa. | Peptide | Peptide ID | Reactive T cell product | CD4/8 |
| NIC4 | 4 | 30 | 39 | ACTR10 | c.638G>A | p.R213H | SVPEGVLEDIKAHTCFVSDLKRGLK | L06 | TIL | CD4 |
| RAE1 | c.1106A>G | p.X369W | WWLETLAQPELFLSTLPHLCTNLGP | L20 | TIL | CD4 | ||||
| PDP1 | c.1024C>T | p.R342W | PKSEAKSVVKQDWLLGLLMPFRAFG | L29 | TIL, DP | CD8 | ||||
| NIC5 | 2 | 56 | 71 | – | – | – | – | – | – | – |
| NIC7 | 2 | 33 | 44 | – | – | – | – | – | – | – |
| NIC16 | 2 | 21 | 23 | ENGASE | c.260T>G | p.C87W | PPLSSQRPRTLLWHDMMGGYLDDRF | L12.1 | DP | CD8 |
| ENGASE | c.260T>G | p.C87W | PPLSSQRPRTLLWHDMMGGYLDDRD | L12.2 | DP | CD8 | ||||
| SMPD4 | c.646G>T | p.V216F | LITQKPLPVSLHFRTSDCAYFILVD | L15.1 | DP | CD8 | ||||
| NIC17 | 2 | 43 | 47 | – | – | – | – | – | – | – |
| NIC20 | 2 | 30 | 34 | MYOB1 | c.801A>C | p.E267D | RNAMQIVGFMDHDAESVLAVVAAVL | L16.2 | TIL, DP | CD4/8 |
| KMT2C | c.8950dupA | p.S2984fs | NVTVVSRVNHVFFSGCAGKPRAHSRSINS | L27.2 | DP | CD8 | ||||
| NIC22 | 2 | 30 | 34 | RRP15 | c.187A>G | p.I63V | SEKDHFYSDDDAVEADSEGDAEPCD | L02 | TIL | CD4 |
| CHEK2 | c.1418C>G | p.A473G | DLVKKLLVVDPKGRFTTEEALRHPW | L20 | TIL | CD4 | ||||
| NIC25 | 4 | 38 | 47 | – | – | – | – | – | – | – |
| NIC27 | 2 | 26 | 43 | – | – | – | – | – | – | – |
| NIC38 | 3 | 54 | 75 | RALGAPB | c.3410C>T | p.A1137V | EPANSRLPPHLIVLDSTIPGFFDDI | L36 | TIL | CD4 |
| GNAS | c.557G>A | p.R186H | DYVPSDQDLLRCHVLTSGIFETKFQ | L37 | TIL | CD4 | ||||
| SHH | c.962G>A | p.R321H | VRPGQRVYVVAEHDGDRRLLPAAVH | L48 | TIL | CD4 | ||||
| NIC39 | 3 | 57 | 66 | – | – | – | – | – | – | – |
aa, amino acid; CMS, consensus molecular subtype; DP, double-positive; Mut, mutation; SLP, synthetic long peptide.