Table 3.
Top 20 CNA chromosome regions with recurrent somatic CNAs (deletions >100 kb) in the cases; not observed in the reference group.
| Cytoband | Start | Stop | # of Sub. with Del*. | Deletions in Subjects | No. of Markers | Length (bp) | Cancer-Related Genes |
|---|---|---|---|---|---|---|---|
| 19p13.3 | 766,463 | 2,357,625 | 10 | I (2), II (1), III (3), SCC (4) | 1497 | 1,591,163 | STK11 |
| 19p13.3 | 2,860,429 | 3,984,025 | 10 | I (2), II (1), III (3), SCC (4) | 1154 | 1,123,597 | MATK, DAPK3 |
| 16p13.3 | 895,986 | 1,883,511 | 10 | I (2), II (1), III (3), SCC (4) | 1022 | 987,526 | AXIN1 |
| 19p13.3 | 3,984,025 | 4,738,536 | 9 | I (2), II (1), III (3), SCC (3) | 672 | 754,512 | |
| 1p36.33-1p36.32 | 1,825,510 | 2,545,368 | 9 | I (2), II (0), III (3), SCC (4) | 732 | 719,859 | HES5 |
| 1p36.32 | 2,545,368 | 3,230,848 | 9 | I (2), II (0), III (3), SCC (4) | 678 | 685,481 | PRDM16 |
| 16p13.3 | 377,287 | 895,986 | 10 | I (2), II (1), III (3), SCC (4) | 525 | 518,700 | AXIN1, MSLN |
| 1p36.33 | 1,282,654 | 1,799,975 | 9 | I (2), II (0), III (3), SCC (4) | 242 | 517,322 | |
| 16p13.3 | 2,816,699 | 3,271,935 | 8 | I (2), II (0), III (3), SCC (3) | 469 | 455,237 | BSG, FGF22, AXIN1 |
| 7p22.3 | 93,965 | 534,503 | 8 | I (2), II (0), III (3), SCC (3) | 265 | 440,539 | |
| 19p13.3 | 366,342 | 762,497 | 10 | I (2), II (1), III (3), SCC (4) | 604 | 396,156 | HBA2 |
| 16p13.3 | 2,408,963 | 2,706,379 | 8 | I (2), II (0), III (3), SCC (3) | 142 | 297,417 | |
| 16p13.3 | 84,130 | 377,287 | 10 | I (2), II (1), III (3), SCC (4) | 284 | 293,158 | AXIN1 |
| 16p13.3 | 2,132,651 | 2,397,391 | 10 | I (2), II (1), III (3), SCC (4) | 141 | 264,741 | TSC2 |
| 1p36.33 | 1,021,380 | 1,282,654 | 9 | I (2), II (0), III (3), SCC (4) | 233 | 261,275 | |
| 16p13.3 | 1,888,316 | 2,115,231 | 10 | I (2), II (1), III (3), SCC (4) | 210 | 226,916 | |
| 1p36.33 | 810,836 | 1,021,380 | 9 | I (2), II (0), III (3), SCC (4) | 221 | 210,545 | |
| 19p13.3 | 2,532,493 | 2,735,499 | 10 | I (2), II (1), III (3), SCC (4) | 228 | 203,007 | |
| 19p13.3 | 2,367,858 | 2,532,493 | 10 | I (2), II (1), III (3), SCC (4) | 191 | 164,636 | |
| 19p13.3 | 254,506 | 365,334 | 10 | I (2), II (1), III (3), SCC (4) | 108 | 110,829 |
# of Sub. with Del *: number of subjects with deletion. Serine/threonine kinase 11 (STK11); maturase K (MATK); Death-associated protein kinase 3 (DAPK3); axis inhibition protein 1 (AXIN1); hairy/enhancer of split, drosophila, homolog of, 5 (HES5); PR domain containing 16 (PRDM16); mesothelin (MSLN); basignin (BSG); fibroblast growth factor 22 (FGF22); haemoglobin A2 (HBA2); tuberous sclerosis complex 2 (TSC2).