Table 1.
Frequency of Copy Number Change by Array CGH and Metaphase CGH in Breast Cancer
| Gene | Location | a (%)* | b (%)† | c (%)‡ | ||||
|---|---|---|---|---|---|---|---|---|
| A. Genes previously reported to be amplified in breast cancer | ||||||||
| NRAS | 1p13.2 | 8/27 (30) | 2/4 (50) | 5/19 (26) | ||||
| FGFR1 | 8p11.2-p11.1 | 5/25 (20) | 1/4 (25) | 3/17 (18) | ||||
| MYC | 8q24.12-q24.3 | 18/27 (67) | 11/13 (85) | 5/10 (50) | ||||
| HRAS | 11p15.5 | 8/28 (29) | 3/5 (60) | 2/19 (11) | ||||
| CCND1 | 11q13 | 8/28 (29) | 6/9 (67) | 1/15 (7) | ||||
| FGF4/FGF3 | 11q13 | 7/28 (25) | 6/9 (67) | 0/15 (0) | ||||
| EMS1 | 11q13 | 10/28 (36) | 6/9 (67) | 1/15 (7) | ||||
| GARP | 11q13.5-q14 | 9/28 (32) | 5/8 (63) | 2/16 (13) | ||||
| MDM2 | 12q14.3-q15 | 6/27 (22) | 2/3 (67) | 2/20 (10) | ||||
| AKT1 | 14q32.3 | 11/28 (39) | 5/7 (71) | 2/17 (12) | ||||
| TOP2A | 17q21-q22 | 6/28 (21) | 1/6 (17) | 3/18 (17) | ||||
| ERBB2 | 17q21.2 | 11/28 (39) | 4/6 (67) | 4/18 (22) | ||||
| AIB1 | 20q12 | 10/28 (36) | 8/17 (47) | 2/7 (29) | ||||
| STK15 | 20q13 | 12/27 (44) | 10/17 (59) | 2/6 (33) | ||||
| CSE1L | 20q13 | 14/26 (54) | 8/15 (53) | 3/7 (43) | ||||
| MYBL2 | 20q13.1 | 9/28 (32) | 5/17 (29) | 4/7 (57) | ||||
| PTPN1 | 20q13.1-q13.2 | 14/28 (50) | 11/17 (65) | 2/7 (29) | ||||
| ZNF217 | 20q13.2 | 11/28 (39) | 9/17 (53) | 2/7 (29) | ||||
| B. Genes suspected to be amplified in breast cancer | ||||||||
| MYCN | 2p24.1 | 6/28 (21) | 1/4 (25) | 3/20 (15) | ||||
| RAF1 | 3p25 | 7/27 (26) | 3/4 (75) | 2/18 (11) | ||||
| MYB | 6q22 | 7/23 (30) | no amp. | 6/19 (32) | ||||
| EGFR | 7p12.3-p12.1 | 7/28 (25) | 3/6 (50) | 3/18 (17) | ||||
| PGY1 | 7q21.1 | 8/28 (29) | 4/7 (57) | 3/17 (18) | ||||
| MOS | 8q11 | 6/27 (22) | 2/5 (40) | 4/18 (22) | ||||
| KRAS2 | 12p12.1 | 10/27 (37) | 3/5 (60) | 7/22 (32) | ||||
| IGFR1 | 15q25-q26 | 6/28 (21) | 3/7 (43) | 2/17 (12) | ||||
| FES | 15q26.1 | 7/28 (25) | 1/6 (17) | 3/18 (17) | ||||
| RPS6KB1 | 17q23 | 13/28 (46) | 6/8 (75) | 5/16 (31) | ||||
| JUNB | 19p13.2 | 6/24 (25) | 3/4 (75) | 1/16 (6) | ||||
| PDGFB | 22q12.3-q13.1 | 8/28 (29) | 5/5 (100) | 2/19 (11) | ||||
| AR | Xq11-q12 | 5/23 (22) | 3/3 (100) | 2/16 (13) | ||||
| C. Novel genes amplified in breast cancer | ||||||||
| FGR | 1p36.2-p36.1 | 6/22 (27) | 2/6 (33) | 3/13 (23) | ||||
| LAMC2 | 1q25-q31 | 9/28 (32) | 4/6 (67) | 3/18 (17) | ||||
| TERC | 3q26.3 | 7/24 (29) | 2/4 (50) | 5/17 (29) | ||||
| PDGFRA | 4q12 | 6/28 (21) | no amp. | 4/24 (17) | ||||
| MET | 7q31 | 7/25 (28) | 3/4 (75) | 4/18 (22) | ||||
| GLI | 12q13.2-q13.3 | 6/28 (21) | 1/5 (20) | 2/19 (11) | ||||
| INSR | 19p13.2 | 8/25 (32) | 3/4 (75) | 3/17 (18) | ||||
| CCNE1 | 19q13.1 | 6/28 (21) | 3/12 (25) | 2/12 (17) | ||||
*a; Number of cancers with copy number gains per total samples tested (in 28 samples).
†b; Fraction of amplicons detected by CGH in which a specific oncogene amplification was identified by array CGH (in a total of 24 cases).
‡c; Fraction of cancers (in 24 cases) without a specific chromosomal band amplicon by classical CGH in which array CGH detected oncogene amplification.
no amp.; no amplification was detected by metaphase CGH.