Table 3. ‘Cancer census genes’ most frequently involved in a copy number loss or gain in the LP-WGS-data.
| ‘Cancer census genes’ most frequently involved in a copy number lossa | ‘Cancer census genes’ most frequently involved in a copy number gaina | ||||||
|---|---|---|---|---|---|---|---|
| Gene name | Chromosome position | OG or TSb | Frequency loss (%)c | Gene name | Chromosome position | OG or TSb | Frequency gain (%)c |
| EP300 | chr22:41,488,614-41,576,081 | / | 71.43 | PMS2 | chr7:6,012,870-6,048,737 | / | 33.33 |
| SETD2 | chr3:47,057,898-47,205,467 | TS | 66.67 | FCGR2B | chr1:161,632,905-161,648,444 | / | 23.81 |
| PBRM1 | chr3:52,579,368-52,713,739 | TS | 66.67 | EIF4A2 | chr3:186,501,361-186,507,685 | / | 23.81 |
| ROS1 | chr6:117,609,530-117,747,018 | OG | 66.67 | TERT | chr5:1,253,287-1,295,162 | / | 23.81 |
| ZNF198 | chr13:20,532,810-20,665,968 | / | 66.67 | HNRNPA2B1 | chr7:26,229,556-26,240,413 | / | 23.81 |
| RB1 | chr13:48,877,883-49,056,026 | TS | 66.67 | EGFR | chr7:55,086,725-55,275,031 | / | 23.81 |
| CHEK2 | chr22:29,083,731-29,137,822 | TS | 66.67 | MET | chr7:116,312,459-116,438,440 | OG | 23.81 |
| TRIM33 | chr1:114,935,399-115,053,781 | / | 61.90 | RAD21 | chr8:117,858,173-117,887,105 | / | 23.81 |
| CACNA1D | chr3:53,529,076-53,846,492 | OG | 61,90 | KLF6 | chr10:3,818,188-3,827,473 | / | 23.81 |
| FLT3 | chr13:28,577,411-28,674,729 | OG | 61.90 | NAB2 | chr12:57,482,677-57,489,259 | OG | 23.81 |
| FOXO1 | chr13:41,129,801-41,240,734 | OG/TS | 61.90 | MLLT6 | chr17:36,861,873-36,886,056 | / | 23.81 |
| MKL1 | chr22:40,806,292-41,032,690 | / | 61.90 | CIC | chr19:42,788,817-42,799,949 | OG/TS | 23.81 |
| EPS15 | chr1:51,819,935-51,984,995 | / | 57.14 | FAM131B | chr7:143,050,493-143,059,840 | / | 19.05 |
| WHSC1 | chr4:1,873,123-1,983,934 | / | 57.14 | PLAG1 | chr8:57,073,468-57,123,859 | OG | 19.05 |
| PTPN13 | chr4:87,515,468-87,736,328 | TS | 57.14 | CHCHD7 | chr8:57,124,315-57,131,176 | / | 19.05 |
| RAP1GDS1 | chr4:99,182,527-99,365,012 | / | 57.14 | RECQL4 | chr8:145,736,667-145,743,210 | / | 19.05 |
| FBXW7 | chr4:153,242,410-153,456,185 | / | 57.14 | NUTM2B | chr10:81,462,983-81,472,513 | / | 19.05 |
| FAT1 | chr4:187,508,937-187,644,987 | TS | 57.14 | NUTM2A | chr10:88,985,205-88,994,733 | / | 19.05 |
| NFIB | chr9:14,081,842-14,314,045 | / | 57.14 | ETNK1 | chr12:22,778,076-22,843,608 | / | 19.05 |
| MLLT3 | chr9:20,344,968-20,622,514 | OG | 57.14 | DICER1 | chr14:95,552,565-95,608,085 | TS | 19.05 |
| BRCA2 | chr13:32,889,617-32,973,809 | TS | 57.14 | CD79B | chr17:62,006,098-62,009,704 | OG | 19.05 |
| LHFP | chr13:39,917,029-40,177,356 | / | 57.14 | PRKAR1A | chr17:66,507,921-66,529,570 | / | 19.05 |
| LCP1 | chr13:46,700,058-46,756,459 | / | 57.14 | ZNF521 | chr18:22,641,888-22,932,214 | / | 19.05 |
| MAPK1 | chr22:22,113,947-22,221,970 | OG | 57.14 | ||||
aThe 20 ‘Cancer census genes’ most frequently involved in a copy number loss or gain were identified. However, as some ‘Cancer census genes’ showed exactly the same frequency of loss or gain, this list can contain more than 20 genes.
bClassified as an oncogene or tumor suppressor gene according to the ‘Cancer census gene’ list.
cFor ‘Cancer census genes’ smaller than 50 kb, the frequency of copy number loss or gain in the 50 kb-region containing at least 90% of the gene was considered. ‘Cancer census genes’ smaller than 50 kb, that were not located for at least 90% in one bin, were excluded from this analysis. For the analysis of ‘Cancer census genes’ bigger than 50 kb, additional bins with the exact chromosomal location of these genes were analyzed.
OG: oncogene; TS: tumor suppressor gene