Table 4.
The orphan TCRs sent to test in the four rounds of experiments (distances < 0.15, probability of correct prediction > 50%) and the closest neighbor TCR with known specificities. The closest neighbors allowed us to infer the specificity of the orphans. The peptide, the TCRpcDist‐3D distance, the Enrichment Factor (if applied), and the figure correspondence are also present. The TCRs deorphanized and the closest neighbors are in bold.
| Round | Patient | Alpha Vseq | Alpha Jseq | CDR3α | Beta Vseq | Beta Jseq | CDR3β | peptide specificity | TCRpsDist‐3D | EF | Figure correspondance |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Mel#2 | TRAV12‐2 | TRAJ52 | CAVTTGGTSYGKLTF | TRBV11‐2 | TRBJ2‐7 | CASKGAPTIYYEQYF | orphan | 0.13 | 1.4 | |
| Mel#2 | TRAV12‐2 | TRAJ52 | CAVKGSGTSYGKLTF | TRBV9 | TRBJ2‐1 | CASSLTGYEQFF | GLYDGMEHL | ||||
| Mel#2 | TRAV1‐2 | TRAJ26 | CAVRFRDNYGQNFVF | TRBV5‐1 | TRBJ2‐1 | CASSLSWTSGNEQFF | orphan | 0.09 | 2.3 | ||
| Mel#2 | TRAV1‐2 | TRAJ28 | CAVRTGYSGAGSYQLTF | TRBV5‐1 | TRBJ2‐1 | CASSYGNEQFFG | TADFDITEL | ||||
| Mel#4 | TRAV17 | TRAJ12 | CATVVRMDSSYKLIF | TRBV7‐9 | TRBJ2‐1 | CASSLIGVSSYNEQFF | orphan | 0.11 | 4.5 | Figure 5 – TCR #2 | |
| Mel#2 | TRAV17 | TRAJ12 | CATVVRMDSSYKLIF | TRBV7‐9 | TRBJ2‐1 | CASSLVGEGWSDEQFF | TPRVTGGGAM | ||||
| Mel#2 | TRAV12‐2 | TRAJ49 | CAGSTGNQFYF | TRBV27 | TRBJ2‐3 | CASSPWGASDTQYF | orphan | 0.10 | 1.6 | ||
| Mel#2 | TRAV12‐2 | TRAJ49 | CAVNAGNQFYF | TRBV4‐1 | TRBJ2‐3 | CASSPDRSADTQYF | ELAGIGILTV | ||||
| Mel#2 | TRAV12‐1 | TRAJ42 | CVVNSYGGSQGNLIF | TRBV9 | TRBJ1‐2 | CASSVVSGGTYGYTF | orphan | 0.11 | 2.1 | ||
| Mel#2 | TRAV12‐2 | TRAJ37 | CAVKDGNTGKLIF | TRBV9 | TRBJ1‐2 | CASSLTGYGYTF | GLYDGMEHL | ||||
| Mel#4 | TRAV14/DV4 | TRAJ4 | CVSGGYNKLIF | TRBV12‐4 | TRBJ1‐6 | CASGSGNSPLHF | orphan | 0.11 | 4.5 | ||
| Mel#1 | TRAV14/DV4 | TRAJ4 | CAMRAGGYNKLIF | TRBV14 | TRBJ2‐5 | CASSHWTSGSGETQYF | ILRGSVAHK | ||||
| Mel#1 | TRAV13‐1 | TRAJ3 | CAAGLGRYSSASKIIF | TRBV20‐1 | TRBJ2‐5 | CSAKRTSGHQETQYF | orphan | 0.13 | 2.3 | ||
| Mel#1 | TRAV13‐1 | TRAJ3 | CAASDSSASKIIF | TRBV9 | TRBJ2‐5 | CASSVGKETQYF | FAFGEPREL | ||||
| Mel#1 | TRAV26‐2 | TRAJ30 | CILRDVGRDDKIIF | TRBV9 | TRBJ2‐5 | CASSARQGRGETQYF | orphan | 0.14 | 2.3 | ||
| Mel#1 | TRAV13‐1 | TRAJ3 | CAASDSSASKIIF | TRBV9 | TRBJ2‐5 | CASSVGKETQYF | FAFGEPREL | ||||
| Mel#1 | TRAV35 | TRAJ30 | CAGQVVMDDKIIF | TRBV9 | TRBJ2‐5 | CASSPPVGETQYF | orphan | 0.14 | 2.3 | ||
| Mel#1 | TRAV13‐1 | TRAJ3 | CAASDSSASKIIF | TRBV9 | TRBJ2‐5 | CASSVGKETQYF | FAFGEPREL | ||||
| Mel#4 | TRAV17 | TRAJ12 | CATVARMDSSYKLIF | TRBV7‐9 | TRBJ2‐3 | CASSLIGQGITDTQYF | orphan | 0.14 | 4.5 | Figure 5 – TCR #1 | |
| Mel#2 | TRAV17 | TRAJ12 | CATVVRMDSSYKLIF | TRBV7‐9 | TRBJ2‐1 | CASSLVGEGWSDEQFF | TPRVTGGGAM | ||||
| Mel#2 | TRAV13‐1 | TRAJ4 | CAVPGVLSGGYNKLIF | TRBV9 | TRBJ1‐1 | CASSVASPNTEAFF | orphan | 0.15 | 1.5 | ||
| Mel#2 | TRAV13‐1 | TRAJ37 | CASYSGNTGKLIF | TRBV9 | TRBJ2‐5 | CASSVTSGTLYF | TADFDITEL | ||||
| 2 | Mel #5 | TRAV12‐1 | TRAJ12 | CVVNGEDSSYKLIF | TRBV2 | TRBJ2‐2 | CASSEGQVAPGELFF | EBV – reactive | – | 7.6 | Figure S4 (Supporting Information) – TCR#1 |
| Mel #5 | TRAV12‐1 | TRAJ12 | CVVNGMDSSYKLIF | TRBV2 | TRBJ2‐2 | CASSAGQVAPGELFF | EBV – reactive | 0.00 | Figure S4 (Supporting Information) – TCR#2 | ||
| 10X genomics | TRAV12‐1 | TRAJ12 | CVVNGGDSSYKLIF | TRBV2 | TRBJ2‐2 | CASSEGQVSPGELFF | GLCTLVAML | 0.06 | |||
| GI #1 | TRAV5 | TRAJ31 | CAEDNNARLMF | TRBV20‐1 | TRBJ1‐2 | CSARDRTGNGYTF | orphan | – | 28.0 | Figure S4 (Supporting Information) – TCR#3 | |
| 10X genomics | TRAV5 | TRAJ31 | CAEDNNARLMF | TRBV20‐1 | TRBJ1‐2 | CSARDSTGNGYTF | GLCTLVAML | 0.02 | |||
| 3 | Lung #1 | TRAV26‐2 | TRAJ53 | CILSDGGSNYKLTF | TRBV2 | TRBJ2‐7 | CASSEPGYEQYF | orphan | 0.00 | not applied | Figure S5A (Supporting Information) – TCR#3 |
| Lung #1 | TRAV26‐2 | TRAJ53 | CILSDGGSNYKLTF | TRBV2 | TRBJ2‐7 | CASSDPGYEQYF | DSNDYHILR | ||||
| Lung #1 | TRAV26‐2 | TRAJ53 | CIPSDGGSNYKLTF | TRBV2 | TRBJ2‐1 | CASSVPGYEQFF | orphan | 0.00 | Figure S5A (Supporting Information) – TCR#2 | ||
| Lung #1 | TRAV26‐2 | TRAJ53 | CILSDGGSNYKLTF | TRBV2 | TRBJ2‐7 | CASSDPGYEQYF | DSNDYHILR | ||||
| Lung #1 | TRAV3 | TRAJ40 | CAVRDISTTSGTYKYIF | TRBV28 | TRBJ1‐2 | CASSPPGDPIYGYTF | orphan | 0.06 | Figure S5A (Supporting Information) – TCR#1 | ||
| Lung #1 | TRAV3 | TRAJ40 | CAVRDISTTSGTYKYIF | TRBV28 | TRBJ1‐6 | CASSSPGDSYNSPLHF | DSNDYHILR | ||||
| 4 | Mel #6 | TRAV14/DV4 | TRAJ26 | CAMEEYGQNFVF | TRBV27 | TRBJ2‐4 | CASSLSGGLYNEQFF | orphan | 0.02 | not applied | Figure 6 + Figure S5B (Supporting Information) – TCR #1 |
| Mel #6 | TRAV14/DV4 | TRAJ26 | CAIINYGQNFVF | TRBV27 | TRBJ2‐4 | CASSLSASGRVNIQYF | SLKLHYQL | ||||
| Mel #6 | TRAV12‐2 | TRAJ52 | CALGSAGGTSYGKLTF | TRBV6‐5 | TRBJ1‐2 | CASSPSGAPANYGYTF | orphan | 0.05 | Figure S5C (Supporting Information) – TCR #1 | ||
| 10X genomics | TRAV12‐2 | TRAJ52 | CAVNLGLTAGGTSYGKLTF | TRBV6‐4 | TRBJ1‐2 | CASRAGTEISGYGYTF | ELAGIGILTV | ||||
| Mel #6 | TRAV12‐2 | TRAJ49 | CAVNTGNQFYF | TRBV6‐1 | TRBJ1‐5 | CASSEAGVGQPQHF | orphan | 0.06 | Figure S5C (Supporting Information) – TCR #2 | ||
| 10X genomics | TRAV12‐2 | TRAJ49 | CAVPGSTGNQFYF | TRBV6‐3 | TRBJ1‐5 | CASSFGFGQPQHF | ELAGIGILTV | ||||
| Mel #6 | TRAV12‐2 | TRAJ47 | CAVTLTKYGNKLVF | TRBV11‐2 | TRBJ1‐2 | CASSLGGGPIGYTF | orphan | 0.06 | Figure S5C (Supporting Information) – TCR#3 | ||
| 10X genomics | TRAV12‐2 | TRAJ39 | CAANAGNMLTF | TRBV11‐2 | TRBJ1‐2 | CASSLGGGTEAFF | ELAGIGILTV | ||||
| Mel #6 | TRAV12‐2 | TRAJ45 | CAVNPGGGADGLTF | TRBV28 | TRBJ2‐1 | CASTPPGTSGKSSYNEQFF | orphan | 0.07 | Figure S5C (Supporting Information) – TCR#4 | ||
| 10X genomics | TRAV12‐2 | TRAJ32 | CAVNGGGATNKLIF | TRBV28 | TRBJ1‐1 | CAIPGPSNTEAFF | ELAGIGILTV |