Eigenanalysis of DAPI-stained chromosomes: tools and strategies toward computer-assisted analysis of FISH experiments

The fluorescent dye 4',6-diamidino-2-phenylindole (DAPI) is widely used as a chromosome counterstain in fluorescence in situ hybridization (FISH) studies. It produces a Q-banding pattern that allows for both chromosome identification and the assignment of molecular probes to specific chromosome bands. Using a statistical procedure based on eigenanalysis, we have extracted features from digital images of DAPI-stained chromosomes and constructed prototypes of each of the 24 human chromosomes. The features of these prototypes are directly proportional, in intensity profile and band location, to those of real chromosomes. The prototype's intensity profile can be translated into cytogenetic bands to provide a computer-based strategy for chromosome mapping and analysis amenable to automation. Data presented here were obtained using images from the 24 human chromosomes and mouse X chromosome. Moreover, the same procedure is general and can be used for the analysis of chromosomes from other species, as well as with banding techniques other than those using DAPI.