Table 3.
Genetic Gain and Loss Regions in Isolated HG-PanIN Lesions
| CNA | Cytoband∗ | Start∗ | Stop∗ | Gene symbols | Patient ID | Sample ID | Lesion | LRR |
|---|---|---|---|---|---|---|---|---|
| Gain | 1q25.2–q31.1 | 180022343 | 187135612 | LAMC2, PLA2G4A, PTGS2, TPR | 45T | TH20 | HG-PanIN | 0.4864 |
| 29T | TH22 | HG-PanIN | 0.2516 | |||||
| 78T | TH23 | HG-PanIN | 0.5393 | |||||
| Gain | 8q24.21–q24.3 | 128213233 | 141524484 | MYC, KCNK9, WISP1, NDRG1 | 49T | TH14 | HG-PanIN | 0.4835 |
| 70T | TH16 | HG-PanIN | 0.4516 | |||||
| 22T | TH19 | HG-PanIN | 0.6603 | |||||
| Gain | 19q12 | 28771117 | 31050122 | CCNE1 | 70T | TH16 | HG-PanIN | 0.3467 |
| 19T | TH17 | HG-PanIN | 0.8888 | |||||
| 69T | TH18 | HG-PanIN | 0.3405 | |||||
| 45T | TH20 | LG-PanIN | 0.8365 | |||||
| 45T | TH21 | HG-PanIN | 0.8362 | |||||
| Gain | 19q13.2–q13.32 | 42676481 | 47465366 | BCL3, CADM, CBLC, CEACAM1, CIC, ERCC1, ERCC2, PPP1R13L, RELB, | 70T | TH16 | HG-PanIN | 0.3467 |
| 19T | TH17 | HG-PanIN | 0.5762 | |||||
| 69T | TH18 | HG-PanIN | 0.9417 | |||||
| Loss | 6p25.3–p24.3 | 204909 | 7374207 | DUSP22, IRF4, FOXC1, RREB1 | 39T | TH15 | HG-PanIN | –0.2883 |
| 22T | TH19 | HG-PanIN | –0.3551 | |||||
| 78T | TH23 | HG-PanIN | –0.4501 | |||||
| Loss | 6q11.1–q27 | 62351428 | 166070424 | BACH2, HACE1, IGF2R, LATS1, PLAGL1, PRDM1, CTGF, MYB, PTP4A1, TIAM2 | 39T | TH15 | HG-PanIN | –0.5373 |
| 22T | TH19 | HG-PanIN | –0.4003 | |||||
| 78T | TH23 | HG-PanIN | –0.6227 | |||||
| Loss | 9p24.3–p21.3 | 46587 | 21600424 | PTPRD, MLLT3, JAK2, KDM4C, TYRP1 | 39T | TH15 | HG-PanIN | –0.9140 |
| 70T | TH16 | HG-PanIN | –0.5040 | |||||
| 45T | TH20 | LG-PanIN | –0.4940 | |||||
| 45T | TH21 | HG-PanIN | –0.5439 | |||||
| 78T | TH23 | HG-PanIN | –0.5533 | |||||
| Loss | 9p21.3 | 21600424 | 22811336 | CDKN2A, CDKN2B | 39T | TH15 | HG-PanIN | –0.4654 |
| 70T | TH16 | HG-PanIN | –1.5687 | |||||
| 45T | TH20 | LG-PanIN | –1.2731 | |||||
| 45T | TH21 | HG-PanIN | –1.3433 | |||||
| 29T | TH22 | HG-PanIN | –1.8574 | |||||
| 78T | TH23 | HG-PanIN | –0.5535 | |||||
| Loss | 12q24.23–q24.31 | 120104173 | 124845413 | CDK2AP1, DIABLO, RSRC2 | 70T | TH16 | HG-PanIN | –0.3665 |
| 45T | TH21 | HG-PanIN | –0.2766 | |||||
| 78T | TH23 | HG-PanIN | –0.6194 | |||||
| Loss | 17p13.2–p11.2 | 18901 | 19703855 | TP53, ALOX15, CRK, HIC1, USP6, XAF1, MYBBP1A, PER1 | 37T | TH12 | HG-PanIN | –0.6747 |
| 39T | TH15 | HG-PanIN | –0.5327 | |||||
| 45T | TH20 | LG-PanIN | –1.0724 | |||||
| 45T | TH21 | HG-PanIN | –1.1674 | |||||
| 78T | TH23 | HG-PanIN | –0.5619 | |||||
| 780T | TH24 | HG-PanIN | –0.1895 | |||||
| Loss | 17q23–q24.3 | 60981969 | 68416552 | AXIN2, PRKAR1A, CD79B, KPNA2, MAP2K6, STRADA, GNA13 | 37T | TH12 | HG-PanIN | –0.6213 |
| 39T | TH15 | HG-PanIN | –0.4583 | |||||
| 78T | TH23 | HG-PanIN | –0.5323 | |||||
| Loss | 18q11.32–q23 | 24607196 | 78014582 | SMAD4, SMAD2, ME2, DCC, SERP1NB5, BCL2, MALT1, MBD2, PHLPP1 | 70T | TH16 | HG-PanIN | –0.4227 |
| 19T | TH17 | HG-PanIN | –0.5008 | |||||
| 22T | TH19 | HG-PanIN | –0.3881 | |||||
| 45T | TH20 | LG-PanIN | –0.4278 | |||||
| 78T | TH23 | HG-PanIN | –0.5228 |
Underlined genes indicate known oncogenes in regions of gain or tumor suppressor genes in regions of loss.
CNA, copy number alteration; HG-PanIN, high-grade pancreatic intraepithelial neoplasia; LG-PanIN, low-grade pancreatic intraepithelial neoplasia; LRR, log R ratio.
∗
Based on hg19 assembly.