Detection of segmental chromosome copy number gains by improved fluorescence in situ hybridization techniques

Fluorescence in situ hybridization (FISH) techniques are used for the targeted investigation of microduplication, microdeletion and structural rearrangements. More recently FISH techniques using probes specific to the region of interest have been applied to confirm genomic copy number variation (CNV). However, there are limitations in the assessment of FISH signal patterns. Tandem duplication of small CNVs appear as an increased signal size when standard FISH methods are applied. As such, interpretation of signal patterns is subjective and further complicated in the presence of mosaicism. Here we describe a pre-treatment that enhances the demonstration of tandem duplication. We assessed the sensitivity to CNVs of a minimum of 120 kb in size and determined that the lower limit of detection of mosaicism is 10 percent. In contrast to some methods of chromatin extension and elongation, this technique is done using fixed cell preparations from routine cytogenetic harvesting, and can be applied to freshly harvested or stored fixed cell suspensions. This modification to standard FISH preparations has the scope to be used as a screening tool for family and prenatal investigations.