Table 2. ‘Cancer census genes’ most frequently involved in a copy number loss or gain in the TCGA-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 | / | 69.41 | TERT | chr5:1,253,287-1,295,162 | / | 27.06 |
| PDGFB | chr22:39,619,685-39,640,957 | OG | 68.24 | SDHA | chr5:218,356-256,814 | TS | 24.71 |
| MKL1 | chr22:40,806,292-41,032,690 | / | 68.24 | DROSHA | chr5:31,400,602-31,532,282 | TS | 23.53 |
| MYH9 | chr22:36,677,323-36,784,063 | / | 68.24 | IL7R | chr5:35,856,977-35,879,705 | / | 22.35 |
| APOBEC3B | chr22:39,378,404-39,388,784 | OG/TS | 64.71 | LIFR | chr5:38,475,065-38,595,507 | / | 22.35 |
| ZNF278 | chr22:31,721,790-31,742,249 | / | 63.53 | FCGR2B | chr1:161,632,905-161,648,444 | / | 21.18 |
| NF2 | chr22:29,999,545-30,094,589 | TS | 62.35 | CDC73 | chr1:193,091,088-193,223,942 | TS | 21.18 |
| MN1 | chr22:28,144,265-28,197,486 | / | 62.35 | PTPRC | chr1:198,608,098-198,726,605 | / | 20.00 |
| CHEK2 | chr22:29,083,731-29,137,822 | TS | 62.35 | MDM4 | chr1:204,485,507-204,527,248 | OG | 20.00 |
| EWSR1 | chr22:29,663,998-29,696,515 | / | 62.35 | ELK4 | chr1:205,566,695-205,602,000 | / | 20.00 |
| BCR | chr22:23,522,552-23,660,224 | OG | 60.00 | SLC45A3 | chr1:205,626,981-205,649,630 | / | 20.00 |
| SMARCB1 | chr22:24,129,150-24,176,705 | / | 60.00 | HLF | chr17:53,342,321-53,402,426 | OG | 20.00 |
| MAPK1 | chr22:22,113,947-22,221,970 | OG | 57.65 | MSI2 | chr17:55,333,931-55,757,299 | / | 20.00 |
| CLTCL1 | chr22:19,167,712-19,279,239 | TS | 55.29 | RNF43 | chr17:56,431,038-56,494,931 | / | 20.00 |
| SEPT5 | chr22:19,704,743-19,711,102 | / | 55.29 | CLTC | chr17:57,697,050-57,774,317 | TS | 20.00 |
| LZTR1 | chr22:21,336,558-21,353,326 | TS | 55.29 | PPM1D | chr17:58,677,544-58,743,640 | OG | 20.00 |
| CDKN2A | chr9:21,967,751-21,975,132 | TS | 50.59 | BRIP1 | chr17:59,756,547-59,940,920 | TS | 20.00 |
| SETD2 | chr3:47,057,898-47,205,467 | TS | 44.71 | CD79B | chr17:62,006,098-62,009,704 | OG | 20.00 |
| BAP1 | chr3:52,435,020-52,444,121 | TS | 43.53 | DDX5 | chr17:62,494,374-62,502,484 | OG | 20.00 |
| NCKIPSD | chr3:48,711,278-48,723,334 | / | 42.35 | AXIN2 | chr17:63,524,683-63,557,740 | TS | 20.00 |
| PBRM1 | chr3:52,579,368-52,713,739 | TS | 42.35 | PRKAR1A | chr17:66,507,921-66,529,570 | / | 20.00 |
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.
cWhen a ‘Cancer census gene’ was spread over multiple segments, the frequency of the segment containing the largest part of the gene was considered.
OG: oncogene; TS: tumor suppressor gene