Genetic analysis of drug resistance by fluorescence in situ hybridization

Tumor progression is driven by the accumulation of genetic changes, which, in aggregate, confer the malignant phenotype (1). Thus, tumor development proceeds via clonal divergence with selection for cells with, for example, a proliferative advantage, metastatic potential, or drug resistance phenotype (2-5). Although Southern blotting and polymorphic microsatellite markers are invaluable in providing information about the genetic alterations that underlie the development of solid tumors, the spatial relationships between tumor cells are destroyed during tissue processing (6-8). This leads to a loss of information on genetic heterogeneity and small subpopulations and presents an averaging of the genetic changes. Conventional karyotyping would determine both numerical and structural chromosome anomalies, but is largely impractical for the study of solid tumors, owing to the necessity for cell culture to produce metaphase spreads. Fluorescence in situ hybridization (FISH) is a powerful method for the analysis of genetic change in solid tumors (7,9-12). In particular, it allows the visualization of the genetic makeup of individual cells within their histological context (7). In general, FISH uses chromosome and region specific probes to assess rapidly copy number and rearrangements of chromosomes and genes. The genetically abnormal cells are detected by their aberrant hybridization pattern in the interphase nuclei. Thus, this method of analysis is generally termed "interphase cytogenetics" (9,10,12).