Table 1.
| Chromosome | minimally overlapping amplification region (kb) | loci marked by gene* | gene_ID | number of tumors with gene amplification^ | other genes in minimally overlapping amplificatin region | ||
|---|---|---|---|---|---|---|---|
| region_start | region_end | interval | |||||
| 3 | 178000 | 178800 | 800 | TBL1XR1 | 79718 | 3 | |
| 3 | 180200 | 180800 | 600 | PIK3CA | 5290 | 10 | KCNMB3 ZNF639 MFN1 GNB4 ACTL6A MRPL47 |
| 5 | 2700 | 3000 | 300 | IRX2 | 153572 | 3 | CEI |
| 6 | 106200 | 108200 | 2000 | PRDM1 | 639 | 2 | ATG5 AIM1 QRSL1 MIRN587 PDSS2 SCML4 |
| 7 | 54900 | 55200 | 300 | EGFR | 1956 | 3 | |
| 8 | 36500 | 38800 | 2300 | FGFR1 | 2260 | 12 | ASH2L LSM1 etc ∼ 20 genes |
| 8 | 62400 | 62800 | 400 | ASPH | 444 | 5 | |
| 8 | 102200 | 103800 | 1600 | NCALD | 83988 | 16 | ZNF706 GRHL2 RRM2B EDD1 ODF1 KLF10 |
| 8 | 128300 | 128800 | 500 | MYC | 4609 | 11 | PVT1 |
| 10 | 122700 | 123700 | 1000 | FGFR2 | 2263 | 2 | ATE1 |
| 11 | 68900 | 69300 | 400 | CCND1 | 595 | 11 | ORAOV1 FGF19 FGF4 |
| 11 | 73900 | 74050 | 150 | POLD3 | 10714 | 6 | |
| 12 | 4100 | 5300 | 1200 | CCND2 | 894 | 3 | FGF23 FGF6 etc ∼ 10 genes |
| 12 | 42200 | 42600 | 600 | IRAK4 | 51135 | 3 | PUS7L TWF1 |
| 17 | 35090 | 35170 | 80 | ERBB2 | 2064 | 23 | GRB7 |
| 17 | 57800 | 58500 | 700 | TLK2 | 11011 | 3 | EFCAB3 METTL2A MRC2 RNF190 MIRN633 |
| 19 | 15110 | 15260 | 150 | BRD4 | 4854 | 2 | NOTCH3 ABHD9 |
*
Genes highlighted with red, green or blue are novel findings. Red indicates a single gene in the minimal amplification region/locus. Green indicates 3 genes in the minimal amplification region/locus. Blue indicates more than 3 genes in the minimal amplification region/locus.
^
The number of tumors with gene amplification are tumors that have log2ratio > 0.6.