Enhancing Cytogenetic Diagnostics: Incorporating Optical Genome Mapping in the Laboratory Routine

Introduction Optical Genome Mapping (OGM) is a is a novel high-throughput diagnostic technique that overcomes the limitations of conventional cytogenetic methods. The objective of this study was to evaluate the application of OGM in the daily workflow of the cytogenetics laboratory and compare it with standard techniques. Methods A total of 180 adult or pediatric patients referred to the Cytogenetics Laboratory at Hospital La Fe during disease onset or relapse were included. The patients had the following diagnoses: aplastic anemia (AA) n = 6, B-cell acute lymphoblastic leukemia (B-ALL) n = 39, T-cell acute lymphoblastic leukemia (T-ALL) n = 9, acute myeloid leukemia (AML) n = 51, myelofibrosis (MF) n = 36, polycythemia vera (PV) n = 3, essential thrombocythemia (ET) n = 2, multiple myeloma (MM) n = 11, and myelodysplastic syndromes (MDS) n = 22. Chromosome banding analysis (CBA) was performed on bone marrow samples, and in selected cases, fluorescence in situ hybridization (FISH) was carried out using specific probes following diagnostic recommendations. For OGM analysis, high molecular weight DNA was extracted and labeled from peripheral blood (PB, n = 62) or bone marrow (BM, n = 118) following the manufacturer's protocol (Bionano, San Diego, CA, USA). Results CBA was performed on all patients except MM, where an initial FISH panel targeting IGH rearrangement, TP53 deletion, and 1q amplification was applied. Among the CBA, 61/169 (36%) patients showed a CBA without alterations, 62/169 (37%) were abnormal and 46/169 (27%) were unsuccessful. OGM successfully detected cryptic alterations in 60% (37/61) of cases previously classified as normal with CBA. Additionally, OGM identified further alterations in 56% (35/62) of cases with abnormal CBA findings. Notably, OGM demonstrated a remarkable 93% success rate in resolving previously uninformative CBA results. •AA OGM did not detect clinically significant alterations or copy neutral loss of heterozygozity (CN-LOH) on chromosome 6 in this subgroup of patients.•B-ALL: OGM detected alterations in all patients with a normal or uninformative karyotype. Regarding cases with a previous abnormal CBA, OGM discovered 2 cases with masked hypodiploidy. Copy Number Alterations (CNA) affecting IKZF1, PAX5, ETV6, RB1, BTG1, EBF1, CDKN2A, CDKN2B, PAR1 region, and ERG were detected in 27/39 (69%) patients, 3 of whom harbored the IKZF1plus Moreover, several cryptic rearrangements were uncovered, such as MEF2D::BCL9, RUFY1::ETV6,