Comparative genomic hybridization analysis of breast tumors with predetermined profiles of DNA amplification

In a separate study (F. Courjal et al., Cancer Res., 57: 4360-4367, 1997), we have analyzed by Southern blotting the relationship between DNA amplification and clinicopathological features of breast cancer. Six regions of recurrent amplifications were tested (8p12, 8q24, 11q13, 12q13, 17q12, and 20q13), and the results suggested that there was a relationship between DNA amplification profiles and breast tumor phenotype. We had delineated three subgroups of tumors showing distinct DNA amplification profiles and clinicopathological characteristics: group A, tumors showing amplification at 11q13 and/or 8p12 and/or 20q13; group B, tumors amplified at ERBB2 and/or MYC and/or MDM2/SAS; and group C, tumors with no detectable amplification. The aim of the present work was to characterize extensively the amplification profiles in the different subgroups of tumors. Sixty-one breast tumors distributed in all three subgroups were studied by comparative genomic hybridization (CGH). There was an overall good agreement between Southern blotting results and CGH data. As expected, CGH revealed gains undetected by Southern blotting. Most of these gains occurred in regions for which no adapted probes were available but also revealed nondetected amplifications at 8q24 or 20q13. Tumors showed multiple aberrations with a medium number of 5.6 copy number variations/tumor, whereas, according to Southern blotting results, 38% of the tumors analyzed were devoid of any amplification. This proportion fell to 6.5% after CGH analysis. Recurrent gains were observed in tumors from all three subgroups, albeit at varying incidences, and involved 1q, 8q, 17q23-q24, and 20q13. Gains covered large regions of DNA and could possibly include several cores of amplification. Some events, such as gains at 16p11-p12 and 14q or losses at 22q, showed more restricted distributions, suggesting the existence of additional sets of preferential coamplifications. The complexity of genetic profiles revealed by CGH indicates that breast cancer development depends on a large (yet undetermined) number of genetic events. The description of molecular phenotypes in breast cancer may therefore prove to be complex, and it should be interesting to see how many breast tumor subtypes will be defined in the end.