Table 2. Output of TutuGenetics and comparison with Sanger sequencing results: Eight HLA/peptide associations are detailed.
For each sample and HLA, the first line shows the putative epitope described in the HxB2 reference sequence and the calculated IC50 (nM). For each epitope, the number of NGS reads as well as the percentage of variants is also shown. The mutated amino-acids are in bold. In the last column, “yes” means that this epitope obtained with NGS was retrieved in the Sanger sequence; “no” indicates that the epitope can be quantified by NGS but was not observed by Sanger.
| Sample ID | HLA | Subprotein | Epitope | Ic50 (nM) | nb reads | % variants | Concordance with Sanger |
|---|---|---|---|---|---|---|---|
| HxB2 | HLA-B*27:05 | p17 (19–27) | IRLRPGGKK | 192.5 | |||
| B03_Ba | HLA-B*27:05 | p17 (19–27) | IRLRPGGKK | 192.5 | 4949 | 93% | yes |
| B03_Ba | HLA-B*27:05 | p17 (19–27) | LRLRPGGKK | 144.5 | 71 | 1.3% | no |
| HxB2 | HLA-B*15:01 | p24 (137–145) | GLNKIVRMY | 392.9 | |||
| B01_Bg | HLA-B*15:01 | p24 (137–145) | GLNKIVRMY | 392.9 | 8336 | 96.8% | yes |
| B01_Bg | HLA-B*15:01 | p24 (137–145) | ELNKIVRMY | 1467.1 | 108 | 1.3% | no |
| HxB2 | HLA-A*24:02 | p17 (28–36) | KYKLKHIVW | 256.9 | |||
| M03_G0 | HLA-A*24:02 | p17 (28–36) | QYKLKHLVW | 405 | 896 | 89.8% | yes |
| M03_G0 | HLA-A*24:02 | p17 (28–36) | QYKLKHIVW | 517.9 | 53 | 5.3% | no |
| HxB2 | HLA-B*40:01 | p24 (44–52) | SEGATPQDL | 492.6 | |||
| B13_TEp | HLA-B*40:01 | p24 (44–52) | SEGATPQDL | 492.6 | 1160 | 76.5% | yes |
| B13_TEp | HLA-B*40:01 | p24 (44–52) | SERATPQDL | 600.9 | 312 | 20.6% | no |
| HxB2 | HLA-B*40:01 | p2p7p1p6 (118–126) | KELYPLTSL | 16.8 | |||
| B13_TEp | HLA-B*40:01 | p2p7p1p6 (118–126) | KELYPLASL | 14.7 | 2603 | 94.9% | yes |
| B13_TEp | HLA-B*40:01 | p2p7p1p6 (118–126) | KELYPLAPL | 11.9 | 38 | 1.4% | no |
| B13_TEp | HLA-B*40:01 | p2p7p1p6 (118–126) | EELYPLASL | 51.7 | 31 | 1.1% | no |
| HxB2 | HLA-A*29:02 | p17 (78–86) | LYNTVATLY | 25 | |||
| B04_Ce | HLA-A*29:02 | p17 (78–86) | LFNTVATLY | 12.1 | 5315 | 94.4% | yes |
| HxB2 | HLA-A*24:02 | p17 (28–36) | KYKLKHIVW | 256.9 | |||
| L01_H6 | HLA-A*24:02 | p17 (28–36) | QYRLKHIVW | 528.9 | 1360 | 88.3% | yes |
| L01_H6 | HLA-A*24:02 | p17 (28–36) | EYRLKHIVW | 1437.3 | 26 | 1.7% | no |
| L01_H6 | HLA-A*24:02 | p17 (28–36) | QYSLKHIVW | 244.2 | 49 | 3.2% | no |
| L01_H6 | HLA-A*24:02 | p17 (28–36) | EYSLKHIVW | 850.8 | 16 | 1% | no |
| HxB2 | HLA-B*40:01 | p17 (11–19) | GELDRWEKI | 358.3 | |||
| B11_Sy | HLA-B*40:01 | p17 (11–19) | GKLDKWERI | 20805.1 | 2114 | 95.4% | yes |
| HxB2 | HLA-B*35:01 | RT (118–127) | VPLDEDFRKY | 424.1 | |||
| M05_H9 | HLA-B*35:01 | RT (118–127) | VPLDEDFRKY | 424.1 | 532 | 76.9% | yes |
| M05_H9 | HLA-B*35:01 | RT (118–127) | VPLDEDFRKC | 29962.8 | 140 | 20.2% | no |