Refined characterisation of chromosome aberrations in tumours by multicolour banding and electronic mapping resources

Acquired chromosome abnormalities in tumours often reflect pathogenetic events at the gene level. Multicolour fluorescence in situ hybridisation (FISH) with single-copy probes offers extensive possibilities to characterise chromosome breakpoints in relation to the physical map of the human genome. This approach is based on the construction of comprehensive EST- based maps, combinatorial labelling of probes, and tumour cell preparations optimised for metaphase FISH. Information from several electronically available databases is combined into an integrated physical map, to which clones carrying yeast and bacterial artificial chromosomes are anchored. Extracted DNA or PCR products from these clones are then fluorescently labelled by one or several fluors, allowing simultaneous FISH detection of multiple loci. To improve hybridisation efficiency and reduce background fluorescence, standard methods for chromosome preparation from cultured tumour cells are complemented with a prolonged trypsin treatment to obtain complete disaggregation of cells, and exposure of the metaphase spreads to detergent and saline at high temperature, followed by pepsin digestion to remove extracellular matrix and cytoplasmic debris. The resulting colour-banding allows the characterisation of chromosome abnormalities in relation to expressed sequences, even in tumours exhibiting highly complex rearrangements.