High resolution detection of chromosome abnormalities with single copy fluorescence in situ hybridization

Precise delineation of rearranged chromosomes in genetic diseases and cancer by fluorescence in situ hybridization can identify the primary etiologies of these disorders. We present a novel approach for defining these abnormalities based on sequential fluorescence in situ hybridization (FISH) of arrays of single copy genomic probes. These arrays consist of sequence-defined synthetic DNA products that can be produced at significantly higher genomic densities than recombinant probes used in conventional FISH. Single copy FISH (scFISH) probes are 50-100 fold shorter than those used for conventional FISH. With scFISH, chromosome abnormalities can be determined at a resolution equivalent to molecular genetic approaches such as Southern analysis. We show how line minimization and bracketing techniques can be used to select probes to optimize strategies for translocation breakpoint determination.