Table 2.
Replication timing for a list of curated cancer genes that are frequently amplified or deleted in many cancer types (as listed in the Cancer Gene Census)
| Gene | Type | Locus | Replication timing | Common SCNA event | Replication timing of the SCNA boundaries | Frequencies (early: late replication timing) |
|---|---|---|---|---|---|---|
| MYC | Oncogene | 8q24.21 | Constant early | Amplification |
|
(23:1) |
| ERBB2 | Oncogene | 17q12 | Constant early | Amplification |
|
(66:3) |
| CDK4 | Oncogene | 12q14.1 | Constant early | Amplification |
|
(8:2) |
| MDM2 | Oncogene | 12q15 | Constant early | Amplification |
|
(16:1) |
| FGFR1 | Oncogene | 8p12 | Constant early | Amplification |
|
(31:24) |
| CRKL | Oncogene | 22q11.21 | Constant early | Amplification |
|
(28:2) |
| PRKCI | Oncogene | 3q26.2 | Constant early | Amplification |
|
(1:8) |
| CDK6 | Oncogene | 7q21.3 | Constant early | Amplification |
|
(13:1) |
| MET | Oncogene | 7q31.2 | Constant early | Amplification |
|
(1:0) |
| JUN | Oncogene | 1p32.1 | Constant early | Amplification |
|
(6:0) |
| BIRC2 | Oncogene | 11q22.2 | Constant early | Amplification |
|
(1:3) |
| MDM4 | Oncogene | 1q32.1 | Constant early | Amplification |
|
(20:1) |
| ETV6 | Tumor suppressor | 12p13.2 | Constant early | Deletion |
|
(42:0) |
| NF1 | Tumor suppressor | 17q11.2 | Constant early | Deletion |
|
(47:4) |
| ATM | Tumor suppressor | 11q23.1 | Constant early | Deletion |
|
(1:7) |
| PAX5 | Tumor suppressor | 9p13.2 | Constant early | Deletion |
|
(66:1) |
| TP53 | Tumor suppressor | 17p13.1 | Constant early | Deletion |
|
(19:1) |
| APC | Tumor suppressor | 5q21.1 | Constant early | Deletion |
|
(3:16) |
In the pie charts, dark and light gray indicates the proportion of SCNA boundaries in early- and late-replication timing regions.