Not all MYC FISH probes are created equal

Abstract

Abstract Background The MYC gene plays a critical role in the diagnosis, prognosis, and treatment of hematological malignancies, including B-cell lymphomas, and both acute myeloid and lymphoid leukemia. The MYC fluorescence in situ hybridization (FISH) break-apart probe (BAP) is used in clinical testing to detect MYC gene rearrangements. Since MYC genomic abnormalities include various breakpoints and more than 35 translocation partner genes, false-negative results could significantly affect patient care. Due to the COVID-19 pandemia, our validated Abbott MYC BAP became unavailable in May 2023 after 20 years of clinical use. To ensure uninterrupted clinical testing, we validated MYC BAPs from three companies using three bone marrow samples with known MYC abnormalities. Results Two of the three tested probe sets from three manufacturers (CytoCell, MetaSystems, and Empire Genomics) showed concordant results with Abbott’s BAP for all samples, while one manufacturer’s MYC BAP (Empire Genomics) showed concordance in only 1 of the 3 samples. Using reference loci provided by each company’s probe map, we demonstrated that the discordant results were due to the proximity of the 5’ and 3’ probes, which prevented detection of the known MYC rearrangements, resulting in false-negative results. Conclusions Our findings reveal high-risk vulnerabilities in diagnostic testing when presuming equivalency between commercially available MYC BAPs. We recommend that clinical laboratories, in their initial validation process, include probes from multiple sources to account for supply chain disruptions. Additionally, laboratories should carefully compare probe designs when selecting probe manufacturers to ensure consistent and accurate detection of all frequent MYC genomic abnormalities.