Genome profiling of breast cancer cells selected against in vitro shows copy number changes.

About 20% of breast carcinomas show no clonal chromosome abnormalities when analyzed after short-term culturing. An interesting question is whether this subset of breast carcinomas really is karyotypically normal or if selection for normal cells occurred in vitro. To address this issue, 26 breast carcinomas that had shown no cytogenetic changes by chromosome banding analysis were examined by comparative genomic hybridization (CGH), a technique that does not require culturing or tumor metaphase cells. All but one case showed copy number changes by CGH (median, four). A comparison of these findings with those of a karyotypically abnormal series analyzed using the same CGH protocol found that the cytogenetically "normal" cases were typically genetically less complex (median, four and eight, respectively; P = 0.0058). Although largely the same alterations were found in both series, some differences with respect to the frequencies of specific imbalances were seen. Gains of 3p and 6q and losses of 10q, 14q, and 17p more often were found in the cytogenetically abnormal series than in the normal tumors. We conclude that in most instances cells found to be normal by chromosome banding analysis after short-term culture do not belong to the tumor parenchyma. Furthermore, when we compared the distribution of the number of imbalances detected by CGH in the total data set according to the mitotic index in vivo (scored from 1 to 3), the median values were three, seven, and 18, respectively (P < 0.001). These data indicate not only that karyotypically normal breast carcinomas may represent a genetically simpler subgroup that grows poorly in vitro but also that this subset of tumors already has a slow growth rate in vivo.