Table 3. Recurrently altered regions in vulvar SCCs by HPV status.
| HPV status | Event | Chr | Map position | Size | Cytoband | Freq | Cancer-related genes |
|---|---|---|---|---|---|---|---|
| HPV (+) | CN Gain | 1 | 144 214 303–144 596 037 | 381734 | q21.1 | 50% | |
| CN Gain | 3 | 118 644 873–159 947 520 | 41302647 | q13.32–q25.33 | 67% | GATA2, RPN1, CNBP, FOXL2, ATR, WWTR1, GMPS, MLF1 | |
| CN Gain | 3 | 160 282 987–198 022 430 | 37739443 | q25.33–q29 | 83% | MECOM, TBL1XR1, PIK3CA, SOX2, MAP3K13, ETV5, EIF4A2, BCL6, LPP, TP63, TFRC | |
| CN Gain | 5 | 140 372–23 884 365 | 23743993 | p15.33–p14.2 | 50% | SDHA, TERT | |
| CN Gain | 5 | 31 552 901–34 688 160 | 3135259 | p13.3–p13.2 | 50% | ||
| CN Loss | 11 | 96 124 552–99 487 602 | 3363050 | q21–q22.1 | 50% | ||
| CN Loss | 11 | 101 762 008–103 349 792 | 1587784 | q22.1–q22.3 | 50% | BIRC3 | |
| CN Gain | 13 | 100 336 156–101 714 451 | 1378295 | q32.3–q33.1 | 50% | ||
| CN Gain | 18 | 2 796 420–17 200 000 | 14403580 | p11.32–q11.1 | 67% | ||
| CN Gain | 18 | 18 517 121–34 840 647 | 16323526 | q11.1–q12.2 | 50% | ZNF521, SS18 | |
| CN Gain | 18 | 43 422 074–45 567 137 | 2145063 | q12.3–q21.1 | 50% | SMAD2 | |
| CN Gain | 18 | 46 645 092–47 957 549 | 1312457 | q21.1 | 50% | ||
| CN Gain | 18 | 51 690 882–67 872 291 | 16181409 | q21.2–q22.2 | 50% | MALT1, BCL2, KDSR | |
| CN Gain | 20 | 3 847 585–21 402 481 | 17554896 | p13–p11.22 | 50% | ||
| CN Gain | 20 | 47 465 498–58 744 996 | 11279498 | q13.13–q13.33 | 50% | NFATC2, SALL4, GNAS | |
| HPV (−) | CN Loss | 2 | 3 698 900–3 698 947 | 47 | p25.3 | 43% | |
| CN Loss | 2 | 192 746 283–196 581 520 | 3835237 | q32.3 | 57% | ||
| CN Loss | 2 | 202 625 760–203 620 248 | 994488 | q33.1–q33.2 | 43% | ||
| CN Loss | 3 | 49 949 001–50 191 322 | 242321 | p21.31 | 43% | ||
| CN Loss | 3 | 50 683 675–50 816 138 | 132463 | p21.2 | 43% | ||
| CN Loss | 3 | 51 497 186–51 696 851 | 199665 | p21.2 | 43% | ||
| CN Loss | 3 | 81 792 616–87 027 712 | 5235096 | p12.2–p12.1 | 43% | ||
| CN Loss | 4 | 187 630 720–189 660 328 | 2029608 | q35.2 | 43% | FAT1 | |
| CN Gain | 7 | 766 289–2 771 308 | 2005019 | p22.3 | 43% | ||
| CN Gain | 7 | 5 256 327–5 692 158 | 435831 | p22.1 | 43% | ||
| CN Gain | 7 | 16 131 179–48 567 889 | 32436710 | p21.2–p12.3 | 57% | HNRNPA2B1, HOXA9, HOXA11, HOXA13, JAZF1, SFRP4 | |
| CN Gain | 8 | 141 542 615–142 489 103 | 946488 | q24.3 | 57% | ||
| CN Gain | 8 | 145 918 761–146 364 022 | 445261 | q24.3 | 43% | ||
| CN Loss | 10 | 99 426 796–99 473 736 | 46940 | q24.2 | 43% | ||
| CN Gain | 14 | 22 386 737–23 012 133 | 625396 | q11.2 | 43% | ||
| CN Loss | 21 | 5305–13 200 000 | 13194695 | p13–q11.1 | 43% | ||
| CN Loss | X | 0–2 616 478 | 2616478 | p22.33 | 43% | CRLF2, P2RY8 | |
| CN Loss | X | 61 686 735–62 569 812 | 883077 | q11.1 | 43% |
Abbreviations: CN gain, copy number gain; CN loss, copy number loss; Freq, frequency.
CNAs occurring in more than 40% of samples were defined as recurrently altered regions.