The application of comparative genomic hybridization to previously karyotyped cervical cancer cell lines

This investigation is concerned with the application of comparative genomic hybridization (CGH) to DNA from previously fully karyotyped cervical cancer cell lines using G-banding and fluorescence in situ hybridization (FISH) to compare the chromosome copy numbers observed in karyotypes with the profile shifts seen in CGH analysis. It has demonstrated that diploid DNA can be used as a reference to cohybridize with a test sample of any modal number because of the proportional representation of every chromosome arm and region in equal volumes of both test and reference DNAs. Profile shifts in the near-diploid line gave a clear indication of over and under-representation of either the whole or parts of chromosome arms. In near-tetraploid samples, profile shifts, either gain or loss due to copy number changes from four to five, five to six, or four to three were smaller and were not always seen; however, the points of profile shift would have allowed us to work out most of the breakpoints if karyotype information had not been available. The profiles, however, did not provide accurate information on the ploidy status; this would need to be measured by other means for the CGH data to be interpreted correctly. The 3q and 8q gain in all the squamous cell carcinoma cell lines appeared very clearly. Comparative genomic hybridization revealed a new breakpoint at 7q31 which was not detected originally on the karyotype in DE3. A breakpoint on 9q was reassigned on the basis of the profile shift from 9q13 to 9q22 in JE6. Clarification of the origin of a small fragment from chromosome 20 constantly present in JE6 showed it to be 20q22-qter.