Table 1.
Top candidate cancer genes in breast and colorectal cancer amplifications
| Tumor type | Minimal affected region |
Candidate cancer gene | Total number of amplifications | Total number of point mutations | Passenger probability | ||
|---|---|---|---|---|---|---|---|
| Chr | Left boundary | Right boundary | |||||
| Breast | 19 | 34,933,380 | 35,097,525 | CCNE1 | 4 (5) | 0 | <0.01 |
| 17 | 34,634,168 | 35,387,448 | ERBB2 | 4 (8) | 0 | <0.01 | |
| 11 | 68,626,681 | 69,411,832 | CCND1 | 3 | 0 | <0.01 | |
| 11 | 93,740,661 | 93,972,379 | MRE11A | 1 | 2 | 0.01 | |
| 7 | 25,728,296 | 27,195,245 | HOXA3 | 1 | 2 | 0.01 | |
| 6 | 40,917,990 | 43,889,896 | TREM1 | 1 | 1 | 0.01 | |
| 1 | 149,032,752 | 149,156,966 | FLG2 | 1 (2) | 1 | 0.02 | |
| Colon | 8 | 128,750,181 | 128,848,183 | MYC | 2 | 0 | <0.01 |
| 17 | 19,136,024 | 19,211,040 | EPPB9 | 2 | 0 | <0.01 | |
| 7 | 54,862,624 | 55,406,733 | EGFR | 2 | 0 | <0.01 | |
| 13 | 109,108,212 | 109,557,712 | IRS2 | 1 | 1 | <0.01 | |
| 19 | 57,427,110 | 57,619,851 | ZNF480 | 1 | 1 | <0.01 | |
| 19 | 49,127,007 | 49,207,192 | ZNF155 | 1 | 1 | 0.01 | |
| 15 | 88,561,995 | 89,253,599 | NEUGRIN | 1 | 1 | 0.01 | |
| Combined breast and colon | 19 | 34,933,380 | 35,097,525 | CCNE1 | 5 (6) | 0 | <0.01 |
| 17 | 34,634,168 | 35,387,448 | ERBB2 | 5 (9) | 0 | <0.01 | |
| 6 | 41,419,345 | 42,485,546 | FOXP4 | 2 | 1 | <0.01 | |
| 8 | 37,767,164 | 40,003,731 | GPR124 | 2 (5) | 1 | <0.01 | |
| 20 | 61,788,664 | 61,840,441 | ARFRP1 | 1 (4) | 1 | 0.01 | |
| 10 | 123,231,784 | 123,471,190 | FGFR2 | 1 | 1 | 0.02 | |
| 20 | 29,297,270 | 29,721,415 | HM13 | 1 (4) | 1 | 0.03 | |
Top seven candidate cancer genes for each tumor type are indicated. The combined group corresponds to genes that are altered in both tumor types, with at least one observed amplification. Minimal affected region is defined as the smallest overlapping interval affecting candidate cancer gene. Total number of amplifications indicates the number of focal amplifications or the number of focal and complex amplifications (in parentheses) in the indicated tumor type(s). Candidate cancer gene refers to either known cancer genes or the gene with the highest driver probability within the minimal affected region. Candidate genes were required to be entirely contained within the minimal affected region. The passenger probability provides a combined probability that the number of amplifications and point mutations observed were passengers alterations; these analyses used the intermediate passenger rate for point alterations (see SI Methods for additional information). All amplified genes and their passenger probabilities are indicated in Table S4 and the samples analyzed for such alterations are indicated in Table S6.