Table 2.
Peptide sequences tested using ELISpot assay
| Peptide sequence | gene | NetMHC score | Isoform-detected samples | Isoform/frameshift | GENCODE | isoform type |
|---|---|---|---|---|---|---|
| TYMAGSEAW | NDST1 | 0.0327 | Case 6 | Frameshift | Frameshift | Frameshift |
| VWPTAWASL | NDST1 | 0.1467 | Case 6 | Frameshift | Frameshift | Frameshift |
| RYCRGVMLL | ARL8B | 0.2162 | Case 4 | Frameshift | Frameshift | Frameshift |
| SFTDISIYL | SENP2 | 0.3557 | Case 5 | Frameshift | Frameshift | Frameshift |
| KFSPEPSQF | CEACAM6 | 0.0565 | Case 4 | Isoform | Novel | Alternative last exon |
| SFPLVFLFF | CEACAM6 | 0.0857 | Case 4 | Isoform | Novel | Alternative last exon |
| NYFNLGMVV | ERO1A | 0.4236 | Case 2 | Isoform | Novel | Alternative last exon |
| TYTTIKINF | HOOK2 | 0.0185 | ABC-1, H1437, H1648, H1650, H2126, H322, II-18, PC-3, PC-9, RERF-LC-Ad1, RERF-LC-Ad2, RERF-LC-KJ, RERF-LC-OK, Case 6, Case 7, VMRC-LCD | Isoform | ENST00000589134 | Alternative last exon |
| AWPKHLDLM | MCEE | 0.3848 | ABC-1, H2126, H322, II-18, PC-3, RERF-LC-KJ, Case 1, Case 7 | Isoform | Novel | Alternative 5′ splice site |
| VYFTSDFKV | PKM | 0.2639 | ABC-1, H1299, H1437, H1648, H2126, H2347, H322, II-18, RERF-LC-Ad1, RERF-LC-Ad2, Case 4, VMRC-LCD | Isoform | Novel | Alternative last exon |
| SFLGFSILL | PKM | 0.3814 | ABC-1, H1299, H1437, H1648, H2126, H2347, H322, II-18, RERF-LC-Ad1, RERF-LC-Ad2, Case 4, VMRC-LCD | Isoform | Novel | Alternative last exon |
| QYSLATAFL | SCGB3A2 | 0.2403 | Case 6 | Isoform | Novel | Unannotated exon |
| SYFETIAAL | SELENBP1 | 0.0848 | Case1, Case 4, Case 6 | Isoform | ENST00000493560 | Intron retention |
| RFQPHGDGW | TMC4 | 0.2835 | H322, RERF-LC-Ad2, Case 1 | Isoform | Novel | Alternative last exon |
| TWLTSGPHL | TMEM45A | 0.2974 | Case4, Case7 | Isoform | Novel | Combination (unannotated exons) |
| FLLPAPFPF | TUFM | 0.3991 | A427, ABC-1, H1299, RERF-LC-Ad1, RERF-LC-Ad2, Case 1, VMRC-LCD | Isoform | Novel | Intron retention |
| KYEEVAQLY | UQCRB | 0.447 | H1819, Case 2, Case 3 | Isoform | ENST00000519322 | Alternative last exon |