Table 1 A list of somatic mutations identified in 25 ATL cells.
From: Full-length HLA sequencing in adult T cell leukemia–lymphoma uncovers multiple gene alterations
HLA locus | Sample ID | Allele | Mutation | Amino acid substitution* | Ratio of reads** | ||||
|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Position | ATL | Non-ATL | Position | ATL | Non-ATL | Â |
HLA-A | ATL 08 | A*31:01:02:01 | 1796 (exon 3) | T | C | 204 | Nonsense | Q | 97.3% |
|  | ATL 09 | A*02:06:01:01 | 894 (intron 1) | G/T | G | – | – | – | 49.6% |
| Â | ATL 13 | A*02:06:01:01 | 2657 (exon 4) | Del | G | 290 | F (fs*6) | L | 94.4% |
|  | ATL 19 | A*24:02:01:01 | 1021 (exon 2) | Ins C | – | 26 | L (fs*72) | S | 98.9% |
| Â | ATL 20 | A*11:01:01:01 | 863 (exon 1) | G | T | 17 | R | L | 100% |
| Â | Â | A*24:02:01:01 | 1277 (exon 2) | T | C | 111 | Nonsense | Q | 98.1% |
|  | ATL 23 | A*31:01:02:01 | 2407 (exon 4) | Ins C | – | 210 | Q (fs*10) | K | 90.0% |
| Â | ATL 27 | A*24:02:01:01 | 2517 (exon 4) | G/A | G | 251 | D/N | D | 45.6% |
| Â | Â | Â | 2823 (exon 5) | G/A | G | 319 | G/R | G | 47.8% |
HLA-C | ATL 20 | C*03:03:01:01 | 1731 (intron 2, 3′ splice site) | T | A | 115 | S (fs*3) | R | 100% |
| Â | Â | C*04:01:01:01 | 2725 (exon 4) | G | C | 250 | E | Q | 96.4% |
HLA-B | ATL 08 | B*56:01:01:03 | 2427 (exon 4) | A | C | 207 | E | D | 82.1% |
| Â | Â | Â | 2429 (exon 4) | A | C | 208 | H | P | 85.7% |
| Â | Â | Â | 2555 (exon 4) | T | A | 250 | L | Q | 92.6% |
|  | ATL 09 | B*35:01:01:02 | 2609 (exon 4) | Ins GT | – | 268 | W/C (fs*29) | W | 40.1% |
|  | ATL 11 | B*54:01:01:01 | 1330 (intron 2, 5′ splice site) | A | G | 115 | D (fs*3) | G | 96.8% |
| Â | ATL 19 | B*55:02:01:03 | 1646 (exon 3) | T | C | 139 | Nonsense | Q | 98.2% |
|  | ATL 27 | B*07:02:01:01 | 1840–1880 (exon 3-intron 3) | Del 41 bp | – | 203 | I (fs*35) | L | 100% |
