Improved Detection of a Small Marker Chromosome with Repetitive Sequence-Depleted FISH Probe

Characterization of small marker chromosomes plays an important role in cytogenetic diagnosis and genetic counseling. While array-based comparative genomic hybridization (CGH) has become a powerful technique for the detection of unbalanced chromosome abnormalities, including marker chromosomes, multiplex fluorescence in situ hybridization (M-FISH) using 24 color painting probes remains as a complementary method for the detection of small marker chromosomes with unknown chromosome origin, especially when the marker is presented in a mosaic form. To test the hypothesis that a repeats-depleted FISH probe may result in improved detection of small marker chromosomes, we compared three procedures to remove repetitive sequences in the FISH probe and provided evidence that such probes can facilitate cytogenetic diagnoses of challenging cases.