Table 1.
List of the identified HNF1B ASVs in eleven pools of different tissue types.
| Variant name | HGVS description | Functional annotation | Splicing biotype | Endometrioid endometrial carcinoma | Colorectal carcinoma | Healthy colon | Kidney carcinoma | Healthy kidney | Kidney oncocy-toma | Pancreatic carcinoma | Healthy pancreas | Prostate carcinoma | Paired healthy tissue | Prostate hyper-plasia | No. of pools with ASV | Novel (0), known (1) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Δ2 | c.345_544 del200 | FS | CΔ | 255 | 0 | 1 454 | 199 | 754 | 259 | 322 | 556 | 0 | 0 | 444 | 8 | 0 |
| Δ2,3p | c.345_622 del278 | FS | CΔ + SDSΔ | 0 | 143 | 0 | 127 | 436 | 163 | 64 | 0 | 0 | 136 | 385 | 7 | 0 |
| Δ2_4 | c.345_1045 del701 | FS | mCΔ | 68 | 0 | 57 | 468 | 166 | 216 | 143 | 91 | 0 | 0 | 0 | 7 | 0 |
| Δ2_5 | c.345_1206 del862 | FS | mCΔ | 0 | 0 | 0 | 34 | 14 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| Δ2_6 | c.345_1339 del995 | FS | mCΔ | 0 | 0 | 0 | 770 | 0 | 0 | 0 | 0 | 0 | 0 | 1 719 | 3 | 0 |
| Δ2_7,8p | c.345_1584 del1204 | FS | mCΔ + SASΔ | 0 | 0 | 0 | 0 | 117 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ2_8 | c.345_1653 del1309 | FS | mCΔ | 0 | 0 | 226 | 951 | 844 | 276 | 433 | 275 | 446 | 0 | 0 | 7 | 0 |
| 3p | c.545_622 del78 | IF | SASΔ | 89 082 | 166 213 | 185 492 | 178 626 | 179 688 | 130 503 | 182 721 | 163 105 | 227 604 | 199 210 | 273 908 | 11 | 1 |
| Δ3_4 | c.545_1045 del501 | IF | mCΔ | 19 | 138 | 89 | 199 | 237 | 74 | 303 | 221 | 0 | 0 | 0 | 8 | 0 |
| Δ3_5 | c.545_1206 del662 | FS | mCΔ | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ3_5,6p | c.545_1328 del784 | FS | mCΔ + SASΔ | 0 | 0 | 0 | 132 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ3_8 | c.545_1653 del1109 | FS* | mCΔ | 0 | 0 | 0 | 0 | 139 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ4_5,3q,6p | c.796_1222 del427 | FS | mCΔ + SDSΔ + SASΔ | 0 | 0 | 0 | 0 | 22 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ4,3q | c.799_1045 del247 | FS | CΔ + SDSΔ | 0 | 0 | 0 | 0 | 0 | 0 | 16 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ4_6,3q,7p | c.804_1359 del556 | FS | mCΔ + SDSΔ + SASΔ | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ4 | c.810_1045 del236 | FS | CΔ | 0 | 0 | 39 | 41 | 54 | 0 | 292 | 116 | 0 | 0 | 0 | 5 | 0 |
| Δ5_7,4q,8p | c.1039_1548 del510 | IF | mCΔ + SDSΔ + SASΔ | 0 | 0 | 59 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ5_6,4q,7p | c.1041_1520 del480 | FS | mCΔ + SDSΔ + SASΔ | 0 | 0 | 519 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ5 | c.1046_1206 del161 | FS | CΔ | 135 | 77 | 271 | 674 | 365 | 187 | 884 | 411 | 634 | 694 | 336 | 11 | 0 |
| Δ5,6p | c.1046_1222 del177 | IF | CΔ + SASΔ | 0 | 7 | 0 | 18 | 0 | 46 | 0 | 0 | 0 | 0 | 4 | 4 | 0 |
| Δ5,6p | c.1046_1225 del180 | IF | CΔ + SASΔ | 0 | 0 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| Δ5_6 | c.1046_1339 del294 | IF | mCΔ | 0 | 0 | 0 | 158 | 621 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| Δ5_7 | c.1046_1534 del489 | IF | mCΔ | 0 | 0 | 0 | 594 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Δ5_8 | c.1046_1653 del608 | IF* | mCΔ | 113 | 208 | 866 | 2 739 | 2 324 | 2 145 | 786 | 927 | 0 | 407 | 1 064 | 10 | 0 |
| Δ6_7,5q | c.1199_1534 del336 | IF | mCΔ + SDSΔ | 0 | 0 | 229 | 0 | 5 | 0 | 26 | 0 | 0 | 0 | 0 | 3 | 0 |
| Δ6 | c.1207_1339 del133 | FS | CΔ | 191 | 63 | 101 | 269 | 155 | 190 | 240 | 310 | 540 | 0 | 0 | 9 | 0 |
| Δ6_7 | c.1207_1534 del328 | FS | mCΔ | 0 | 0 | 0 | 545 | 152 | 411 | 263 | 108 | 0 | 0 | 0 | 5 | 0 |
| Variant name | ||||||||||||||||
| Δ6_8 | c.1207_1653 del477 | IF | mCΔ | 566 | 599 | 637 | 3 527 | 3 155 | 1 708 | 899 | 2 065 | 647 | 354 | 2 629 | 11 | 0 |
| Δ7,6q,8p | c.1336_1542 del207 | IF | CΔ + SDSΔ + SASΔ | 68 | 5 | 12 | 8 | 24 | 60 | 33 | 25 | 27 | 46 | 17 | 11 | 0 |
| Δ7 | c.1340_1534 del195 | IF | CΔ | 13 053 | 25 843 | 25 407 | 31 199 | 29 225 | 27 652 | 34 884 | 29 461 | 31 266 | 25 085 | 38 698 | 11 | 0 |
| Δ7_8 | c.1340_1653 del314 | IF* | mCΔ | 8 541 | 39 834 | 38 134 | 69 676 | 76 681 | 84 948 | 72 312 | 45 479 | 24 189 | 26 958 | 45 290 | 11 | 1 |
| Δ8 | c.1535_1653 del119 | IF* | CΔ | 1 399 | 4 506 | 5 749 | 6 095 | 6 421 | 5 017 | 3 441 | 3 690 | 871 | 1 713 | 1 098 | 11 | 0 |
| ▼106bp_i2 | c.545-899_549-793 ins106 | FS | C▼ | 64 | 0 | 0 | 0 | 0 | 17 | 0 | 5 | 0 | 0 | 0 | 3 | 0 |
| ▼153bp_i4 | c.1046-10281_1046-10129 ins153 | IF, PTC | C▼ | 7 | 7 | 6 | 7 | 7 | 0 | 7 | 19 | 6 | 2 | 0 | 9 | 0 |
| ▼157bp_i4 | c.1046-10281_1046-10125 ins157 | FS | C▼ | 30 | 26 | 16 | 29 | 17 | 4 | 26 | 24 | 9 | 11 | 6 | 11 | 0 |
| ▼91 bp_i4 | c.1046-10219_1046-10129 ins91 | FS | C▼ | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| ▼94 bp_i4 | c.1046-10219_1046-10125 ins94 | FS | C▼ | 0 | 0 | 4 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 2 | 0 |
| ▼91 bp_i4 | c.1046-1421_1046-1331 ins91 | FS | C▼ | 928 | 216 | 204 | 597 | 462 | 178 | 312 | 460 | 236 | 399 | 251 | 11 | 0 |
| ▼128bp_i4 | c.1046-765_1046-638 ins128 | FS | C▼ | 98 | 54 | 44 | 101 | 72 | 24 | 44 | 65 | 32 | 86 | 35 | 11 | 0 |
| ▼99 bp_i4 | c.1046-1421_1046-1331 ins91 + c.1046-8_1046-1 ins8 | IF | C▼ + SAS▼ | 24 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 14 | 0 | 0 | 3 | 0 |
| ▼79 bp_i5 | c.1206 + 1417_1206 + 1495 ins79 | FS | C▼ | 0 | 0 | 14 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 5 | 3 | 0 |
| ▼148bp_i5 | c.1206 + 1417_1206 + 1564 ins148 | FS | C▼ | 368 | 75 | 41 | 231 | 162 | 38 | 108 | 185 | 82 | 107 | 15 | 11 | 0 |
| ▼195bp_i6, Δ7_8 | c.1339 + 521_1339 + 715 ins195 + c.1340_1653 del314 | FS | C▼ + mCΔ | 0 | 0 | 0 | 52 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| ▼92 bp_i6 | c.1339 + 1620_1339 + 1711 ins92 | FS | C▼ | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 0 | 0 | 0 | 0 | 1 | 0 |
| ▼169bp_i6 | c.1340-1781_1340-1613 ins169 | FS | C▼ | 34 | 40 | 22 | 109 | 10 | 3 | 58 | 39 | 4 | 5 | 0 | 10 | 0 |
| ASV reads in pool together | 115 049 | 238 054 | 259 694 | 298 184 | 302 328 | 254 125 | 298 628 | 247 635 | 286 606 | 255 213 | 365 903 | |||||
| ASV reads in pool together (% of normalized million) | 11,5 | 23,8 | 26,0 | 29,8 | 30,2 | 25,4 | 29,9 | 24,8 | 28,7 | 25,5 | 36,6 | |||||
| No. of ASVs in pool | 21 | 18 | 25 | 31 | 28 | 24 | 27 | 22 | 16 | 15 | 17 | |||||
Cells with stated normalized sequencing coverage higher than 1000 are underlined. The “predominant” and the “predominant candidate” variants are in bold. The list includes the variant’s name, presumed HGVS nomenclature, presumed functional annotation (FS = frameshift; IF – in frame; FS* - frameshift in the last exon 9 with alternative STOP codon), splicing event biotype (Δ = deletion; ▼ = insertion; C = cassette/exon; mC = multicasette/multiexon; SDS = splice donor site shift; SAS = splice acceptor site shift).