ANALYSES OF BRAIN-TUMOR CELL-LINES CONFIRM A SIMPLE-MODEL OF RELATIONSHIPS AMONG FLUORESCENCE IN-SITU HYBRIDIZATION, DNA INDEX, AND COMPARATIVE GENOMIC HYBRIDIZATION

Several techniques are commonly used for genetic analysis of interphas e nuclei. Flow cytometry assays the distribution of DNA content in pop ulations of nuclei stained with a DNA-specific fluorochrome. Fluoresce nce in situ hybridization (FISH) quantifies the number of copies of a specific DNA sequence in single nuclei. Comparative genomic hybridizat ion (CGH) assesses the relative copy number of DNA sequences throughou t a test genome by comparing the signal intensities of test and refere nce DNA samples hybridized to a template of normal metaphase chromosom es. In principle, there are specific relationships among data obtained from these measurements, and combined measurements should provide a m ore comprehensive view of the sample that is analyzed. We applied thes e three techniques to nine brain tumor cell lines and find that a mode l of CGH that includes unsuppressed repeat sequences describes the dat a well. We estimate that up to 35% of the fluorescence intensity in we ll-blocked CGH preparations may not represent unique sequences. Taking these factors into account, our results are, in general, mutually con sistent, and highlight issues critical for interpreting CGH preparatio ns. (C) 1997 Wiley-Liss, Inc.