Comparative genomic hybridization of fine needle aspirates from breast carcinomas

Detailed knowledge of chromosomal aberrations in a specific tumor may facil itate the development of individually tailored chemotherapy, hormone or gen e therapy. Unfortunately, karyotype analysis requires living cells and is c omplicated by the low number of good metaphase spreads obtained. Comparativ e genomic hybridization (CCH), however, is capable of detecting and mapping genome-wide amplifications and deletions using an equimolar mixture of nor mal and tumor cell DNA, We show here that even the few cells from a fine ne edle aspirate of a tumor are sufficient for a direct CGH assay, independent of DNA amplification. Ten primary breast cancers were analyzed by CCH, A f resh frozen fine needle aspirate and a formalin-fixed and paraffin-embedded section were used for each tumor. Metaphases from each CGH reaction were i maged, and a sum ratio profile was determined for every chromosome. The rat io profiles of DNA isolated from the 2 material sources were then compared, Fine needle aspirates and the paraffin-embedded material of a single tumor yielded the same fluorescence ratio profiles, albeit with slightly differe nt confidence intervals. Different tumors showed a variety of aberrations. The most frequently observed changes were 1q+, 8q+, 14q-, 16p+, 16q-, 17p-, 17q+, 19q+, 20q+, 21q- and 22q-, The ability of CGH to assess chromosomal changes in breast cancer from fine needle aspirates could facilitate geneti c evaluation of tumors prior to surgery. (C) 2000 Wiley-Liss, Inc.