Color-Changing Karyotyping (CCK), an M-FISH/SKY Alternative

Multicolor karyotyping of human chromosomes is a valuable tool for defining marker chromosomes as well as small, cryptic or complex chromosome translocations. Two procedures, multiplex FISH (M-FISH) and spectral karyotyping (SKY) use combinatorial labeling schemes involving 5–6 different fluorophores to label DNA painting probes specific for all human (or mouse) chromosomes. Although the results obtained are excellent, both procedures require expensive equipment for detection and specialized software for analysis. In many laboratories, research projects often only occasionally require multicolor karyotyping, and so expensive investment in specialized accessory hardware cannot be justified. To minimize costs and yet enable color karyotyping using only the most basic equipment, we have developed an alternative technique called color-changing karyotyping (CCK), which uses DNA probes labeled with only three fluorescent dyes. Image capture can be accomplished using a conventional digital camera, and image processing can be performed with generic imaging software. An optimized procedure for cytogenetic slide preparation and efficient chromosome hybridization is also detailed.