Table 1. Ranking of the neo-antigens identified in four melanoma samples [17,20].
Column 2 shows the mutated neo-antigens (the mutated residue is highlighted in bold). Column 5 shows the ranking based on our predictions (i.e. number of peptide to be tested to find this neo-antigen). Columns 6 to 8 show the ranking based on NetMHC [8], NetMHCpan [12] and NetMHCstabpan [36], respectively. The last column shows the total number of neo-antigen candidates (i.e., all possible 9- and 10-mers encompassing all missense mutations).
| Sample | Sequence | Protein | Mutation | Rank | Net-MHC | Net-MHCpan | Net-MHC-stabpan | # Candi-dates |
|---|---|---|---|---|---|---|---|---|
| Mel8 | SPGPVKLEL | NOP16 | P169L | 2 | 7 | 7 | 14 | 1340 |
| Mel5 | YIDERFERY | SEPT2 | Q125R | 3 | 13 | 37 | 149 | 25807 |
| Mel5 | ETSKQVTRW | GABPA | E161K | 13 | 2088 | 1755 | 581 | 25807 |
| Mel15 | GRIAFFLKY | SYTL4 | S363F | 3 | 139 | 410 | 481 | 24766 |
| Mel15 | LPIQYEPVL | SEC23A | P52L | 7 | 1717 | 672 | 36 | 24766 |
| Mel15 | KLKLPIIMK | AKAP6 | M1482I | 21 | 198 | 100 | 44 | 24766 |
| Mel15 | GRTGAGKSFL | ABCC2 | S1342F | 243 | 1115 | 2085 | 3207 | 24766 |
| Mel15 | KLILWRGLK | NCAPG2 | P333L | 527 | 301 | 184 | 199 | 24766 |
| Mel15 | ASWVVPIDIK | MAP3K9 | E689K | 3978 | 1654 | 1351 | 3079 | 24766 |
| 12T | DANSFLQSV | MED15 | P747S | 38 | 4206 | 4176 | 3181 | 15750 |