Differentially painting human chromosome arms with combined binary ratio-labeling fluorescence in situ hybridization

Recently we developed a novel strategy for differentially painting all 24 h uman chromosomes. It is termed COBRA-FISH, short for combined binary ratio labeling-fluorescence in situ hybridization. COBRA-FISH is distinct from th e pure combinatorial approach in that only 4 instead of 5 fluorophores are needed to achieve color discrimination of 24 targets. Furthermore, multipli city can be increased to 48 by introduction of a fifth Fluorophore. Here we show that color identification by COBRA-FISH of all of the p and q arms of human chromosomes is feasible, and we apply the technique for detecting an d elucidating intra- and interchromosomal rearrangements. Compared with 24- color whole chromosome painting FISH, PQ-COBRA-FISH considerably enhances t he ability to determine the composition of rearranged chromosomes as demons trated by the identification of pericentric inversions and isochromosomes a s well as the elucidation of the arm identity of chromosomal material invol ved in complex translocations that occur in solid tumors.