Which assay would you recommend to test for chromosomal rearrangements such as the BCR/ABL translocation seen in CML?

• A. FISH
• B. PCR
• C. Microarray
• D. Next generation sequencing

Answer: (A)

Detecting chromosomal rearrangements requires a method that reveals structural changes in chromosomes directly. Fluorescence in situ hybridization uses labeled DNA probes that bind specifically to the BCR and ABL gene regions. In normal cells, the probes appear as separate signals; when the t(9;22) Philadelphia translocation is present, the signals either fuse or show a rearranged pattern, indicating the BCR-ABL fusion. This makes FISH well-suited for identifying balanced translocations, and it can be done on interphase cells, not just metaphase spreads, giving a rapid and practical readout for clinical samples.

While PCR can detect the BCR-ABL fusion transcripts and is very sensitive, it focuses on the sequence of the fusion product and may miss atypical breakpoints or require knowledge of the exact junction. Microarrays primarily detect copy-number changes and are not reliable for balanced translocations. Next-generation sequencing can identify rearrangements as well, but it is more complex and resource-intensive for routine testing. Thus, FISH is the most straightforward and reliable choice for testing chromosomal rearrangements like BCR-ABL in CML.