Chromosomal aberrations in breast cancer: A comparison between cytogenetics and comparative genomic hybridization

The analysis of chromosomal imbalances in solid tumors using comparative ge netic hybridization (CGH) has gained much attention. A survey of the litera ture suggests that CGH is more sensitive in detecting copy number aberratio ns than is karyotyping, although careful comparisons between CGH and cytoge netics have not been performed. Here, we compared cytogenetics and CGH in 2 9 invasive breast cancers after converting the karyotypes into net copy num ber gains and losses. We found 15 tumors (56%) with a significant agreement between the two methods and 12 tumors (44%) where the methods were in disa greement (two cases failed CGH analysis). Interestingly, in 13 of the 15 tu mors where the two methods were concordant, there was also a strong correla tion between chromosome index and DNA index by flow cytometry. In the oppos ite situation, i.e., when chromosome and DNA indices were not matching, the re was disagreement between cytogenetics and CGH in 10 of the 12 tumors. Of the discordant cases, all except one had a "simple" abnormal karyotype. Un resolved chromosomal aberrations (marker chromosomes, homogeneously stainin g regions, double minutes) could not completely explain the differences bet ween CGH and karyotyping. A likely explanation for the discrepancies is tha t the methods analyzed different cell populations. Gains and losses found b y CGH represented the predominant (often aneuploid) clone, whereas the abno rmal, near-diploid karyotypes represented minor cell clone(s), which, for u nknown reasons, had a growth advantage in vitro. (C) 1999 Wiley-Liss, Inc.