Chromosome Orientation fluorescence in situ hybridization or strand-specific FISH.

Chromosome Orientation FISH (CO-FISH) is a technique that can be used to extend the information obtainable from standard FISH to include the relative orientation of two or more DNA sequences within a chromosome. CO-FISH can determine the absolute 5'-to-3' direction of a DNA sequence relative to the short arm-to-long arm axis of the chromosome, and so was originally termed "COD-FISH" (Chromosome Orientation and Direction FISH). CO-FISH has been employed to detect chromosomal inversions associated with isochromosome formation, various pericentric inversions, and to confirm the origin of lateral asymmetry. More recent and sophisticated applications of CO-FISH include distinction between telomeres produced via leading- vs. lagging-strand DNA synthesis, identification of interstitial blocks of telomere sequence that result from inappropriate fusion to double-strand breaks (telomere-DSB fusion), discovery of elevated rates of mitotic recombination at chromosomal termini and sister chromatid exchange within telomeric DNA (T-SCE), establishing replication timing of mammalian telomeres throughout S-phase (ReD-FISH) and to identify chromosomes, in combination with spectral karyotyping (SKY-CO-FISH).