Technology
Besides the high failure rates, another challenge faced by cytogeneticists is the resolution in standard cytogenetic preparations for POC and cancer samples, which is about or less than 400 bands.
Identification of “cryptic” rearrangements and precise characterization of breakpoints is crucial for structural chromosome abnormalities as they often are diagnostic and/or prognostic. Additionally, when the origin of chromosome material cannot be determined by the classical banding methods, terms such as marker and “add” are used. While molecular genetic methods are available to characterize the nature of the “marker” and “add” material, it is a prerequisite to have sufficient metaphase preparations. There may or may not have any material left to conduct such additional studies, and in the case of a successful study it adds extra time and cost. Interphase Chromosome Profiling (ICP) provides an alternative way of profiling individual chromosomes with sufficient resolution to address the above detailed concerns.
Concept
The ICP concept is very simple. Individual chromosomes are studied in their uncondensed state in an interphase nucleus using a panel of FISH probes that target DNA sequences in an equidistant fashion along the entire length of the chromosome. Using only three fluorophores for each chromosome arm, one can “walk” along the whole chromosome in a sequential manner using standard fluorescence microscopy. The resolution obtained with the ICP approach is approximately 600 bands, sufficient to detect numerical changes and all clinically relevant structural abnormalities from POC and oncology samples. Some targets are read once while others are read twice with two different fluorophores and the resulting “banding pattern” is distinct with each target molecularly different from its neighboring target or any other target on that chromosome.