Table 2.
Gene copy alterations from colorectal cancer cell lines and samples
| Cluster 1 frequency (%) | Cluster 2 frequency (%) | No. probes | Chromosome | Nucleotide | Ideogram | Genes or genetic markers | |
|---|---|---|---|---|---|---|---|
| Cell line deletions | |||||||
| 33.0 | 0.0 | 1 | 2 | 216062244 | — | 2q35 | FN1 |
| 33.0 | 0.0 | 1 | 2 | 216882889 | — | 2q35 | XRCC5 |
| 33.0 | 0.0 | 1 | 10 | 104582361 | — | 10q24.32 | CYP17A1 |
| 0.0 | 100.0 | 5 | 18 | 48943142 | 49190846 | 18q21.2 | DCC |
| 50.0 | 50.0 | 1 | 18 | 54383666 | — | 18q21.31 | D18S881 |
| 50.0 | 50.0 | 1 | 18 | 54850718 | — | 18q21.32 | D18S531 |
| 0.0 | 100.0 | 27 | 18 | 59194458 | 70195190 | 18q21.33-18q22.3 | VPS4B, SERPINB12, SERPINB13, SERPINB4, SERPINB3, SERPINB7, SERPINB2, SERPINB10, SERPINB8, CDH7, CDH19, TXNDC10, CD226, RTTN, SOCS6, GTSCR1, CBLN2, NETO1, FBXO15, CYB5 |
| Cell line amplifications | |||||||
| 16.7 | 16.7 | 1 | 8 | 102034675 | — | 8q22.3 | YWHAZ |
| 16.7 | 16.7 | 1 | 8 | 128820024 | — | 8q24.21 | MYC |
| 0.0 | 33.3 | 2 | 20 | 45684415 | 45686101 | 20q13.12 | NCOA3 |
| Primary tumor deletions | |||||||
| 94.0 | 0.0 | 1 | 5 | 133685387 | — | 5q31.1 | CDKL3 |
| 94.0 | 0.0 | 1 | 5 | 137921004 | — | 5q31.2 | HSPA9B |
| 94.0 | 12.0 | 1 | 6 | 57154822 | — | 6p12.1 | BAG2 |
| 0.0 | 35.3 | 2 | 6 | 144323338 | 144329507 | 6q24.2 | PLAG1 |
| 94.0 | 12.0 | 1 | 8 | 31058227 | — | 8p12 | WRN |
| 62.0 | 0.0 | 1 | 11 | 77456756 | — | 11q14.1 | THRSP |
| 62.0 | 0.0 | 1 | 11 | 101725901 | — | 11q22.2 | BIRC2 |
| 62.0 | 0.0 | 1 | 11 | 101744386 | — | 11q22.2 | BIRC2 |
| 94.0 | 6.0 | 1 | 18 | 27126956 | — | 18cen | D18S521 |
| 94.0 | 6.0 | 1 | 18 | 28078724 | — | 18q12.1 | D18S518 |
| 94.0 | 6.0 | 14 | 18 | 64574936 | 70195190 | 18q12.2-18q21.1 | NPM1P1, PIK3C3, RIT2SYT4, SETBP1, SLC14A2, SLC14A1, CD33L3, KIAA1632, PSTPIP2 |
| 94.0 | 24.0 | 1 | 18 | 47940111 | — | 18q21.1 | D18S89 |
| 94.0 | 24.0 | 1 | 18 | 48085326 | — | 18q21.1 | D18S88 |
| 62.5 | 35.3 | 1 | 18 | 54383666 | — | 18q21.31 | D18S881 |
| 62.5 | 35.3 | 1 | 18 | 54850718 | — | 18q21.32 | D18S531 |
| 100.0 | 6.0 | 4 | 18 | 66883827 | 68156526 | 18q22.2-18q22.3 | Q14754_HUMAN, ENSG00000196512 |
| Primary tumors amplifications | |||||||
| 25.0 | 53.0 | 1 | 2 | 113305137 | — | 2q13 | ILB1 |
| 25.0 | 53.0 | 1 | 2 | 191688469 | — | 2q32.2 | STAT1 |
| 56.0 | 35.0 | 1 | 3 | 41255650 | — | 3p21 | CTNNB1 |
| 56.0 | 35.0 | 1 | 3 | 47428610 | — | 3p12.31 | PTPN23 |
| 56.0 | 35.0 | 2 | 3 | 52410179 | 52414177 | 3p21.31-p21.2 | BAP1 |
| 87.5 | 35.3 | 1 | 8 | 102034675 | — | 8q22.3 | YWHAZ |
| 87.5 | 35.3 | 1 | 8 | 128820024 | — | 8q24.21 | MYC |
| 75.0 | 47.0 | 2 | 10 | 104154700 | 104155176 | 10q24 | PSD |
| 24.0 | 56.3 | 1 | 20 | 44075483 | — | 20q13.12 | MMP9 |
| 24.0 | 56.3 | 2 | 20 | 45684415 | 45686101 | 20q13.12 | NCOA3 |
| 58.0 | 6.0 | 2 | 20 | 48891730 | 48926584 | 20q13.13 | BCAS4 |