Evaluation of breast cancer polyclonality by combined chromosome banding and comparative genomic hybridization analysis

Cytogenetically unrelated clones have been detected by chromosome banding a nalysis in many breast carcinomas. Because these karyotypic studies were pe rformed on short-term cultured samples, it may be argued that in vitro sele ction occurred or that small clones may have arisen during culturing. To ad dress this issue, we analyzed 37 breast carcinomas by G-banding and compara tive genomic hybridization (CGH), a fluorescent in situ hybridization-based screening technique that does not require culturing or tumor metaphases. A ll but two of the 37 karyotypically abnormal cases presented copy number ch anges by CGH. The picture of genomic alterations revealed by the two techni ques overlapped only partly. Sometimes the CGH analysis revealed genomic im balances that belonged to cell populations not picked up by the cytogenetic analysis and in other cases, especially when the karyotypes had many marke rs and chromosomes with additional material of unknown origin, CGH gave a m ore reliable overall picture of the copy number gains and losses. However, besides sometimes revealing cell populations with balanced chromosome aberr ations or unbalanced changes that nevertheless remained undetected by CGH, G-banding analysis was essential to understand how the genomic imbalances a rose in the many cases in which both techniques detected the same clonal ab normalities. Furthermore, because CGH pictures only imbalances present in a significant proportion of the test sample, the very detection by this tech nique of imbalances belonging to apparently small, cytogenetically unrelate d clones of cells proves that these clones must have been present in vivo. This constitutes compelling evidence that the cytogenetic polyclonality obs erved after short-term culturing of breast carcinomas is not an artifact.