title: Analyses of brain tumor cell lines confirm a simple model of relationships among fluorescence in situ hybridization, DNA index, and comparative genomic hybridization.
abstract: Several techniques are commonly used for genetic analysis of interphase nuclei. Flow cytometry assays the distribution of DNA content in populations of nuclei stained with a DNA-specific fluorochrome. Fluorescence in situ hybridization (FISH) quantifies the number of copies of a specific DNA sequence in single nuclei. Comparative genomic hybridization (CGH) assesses the relative copy number of DNA sequences throughout a test genome by comparing the signal intensities of test and reference DNA samples hybridized to a template of normal metaphase chromosomes. In principle, there are specific relationship among data obtained from these measurements, and combined measurements should provide a more comprehensive view of the sample that is analyzed. We applied these three techniques to nine brain tumor cell lines and find that a model of CGH that includes unsuppressed repeat sequences describes the data well. We estimate that up to 35% of the fluorescence intensity in well-blocked CGH preparations may not represent unique sequences. Taking these factors into account, our results are, in general, mutually consistent, and highlight issues critical for interpreting CGH preparations.
authors.affiliation: Cancer Genetics Program, UCSF Cancer Center 94143-0808, USA.
authors.forename: G
authors.initials: G
authors.lastname: Mohapatra
authors.forename: D H
authors.initials: DH
authors.lastname: Moore
authors.forename: D H
authors.initials: DH
authors.lastname: Kim
authors.forename: L
authors.initials: L
authors.lastname: Grewal
authors.forename: W C
authors.initials: WC
authors.lastname: Hyun
authors.forename: F M
authors.initials: FM
authors.lastname: Waldman
authors.forename: D
authors.initials: D
authors.lastname: Pinkel
authors.forename: B G
authors.initials: BG
authors.lastname: Feuerstein
mesh_terms: D000465:Algorithms; D000818:Animals; D001932:Brain Neoplasms / Q000235:genetics*; D015342:DNA Probes; D004273:DNA, Neoplasm / Q000032:analysis*; D005434:Flow Cytometry; D018628:Gene Dosage; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: D015342:DNA Probes; D004273:DNA, Neoplasm