Optical genome mapping improves detection and characterisation of cytogenetic abnormalities in non-Hodgkin lymphomas.

Classical cytogenetics (CC) encompassing fluorescence in situ hybridisation (FISH) and karyotype remains central to the diagnostic work-up of non-Hodgkin lymphoma (NHL). However, karyotype is limited by restricted access to fresh tumour tissue and low resolution, while FISH provides targeted information. Optical genome mapping (OGM) has emerged as a genome-wide, high-resolution approach capable of detecting both translocations and copy number variations in a single assay. To assess its feasibility and diagnostic performance in routine practice, we prospectively compared OGM to CC in 105 patients with NHL. OGM was technically feasible in both fresh and frozen tissue specimens. Among 511 cytogenetic abnormalities (CAs) directly compared, 91.1% were concordant between the two methods. Using the low allele fraction guided assembly pipeline, OGM identified all 77 immunoglobulin loci rearrangements, with a sensitivity threshold of 5%. Overall, OGM detected diagnostically relevant CAs in 99/105 patients (94.2%). OGM outperformed CC in 10/105 patients (9.5%), revealing cryptic rearrangements involving major target genes (MYC, BCL2 and BCL6) as well as diagnostically relevant CAs in cases with uncertain diagnoses or non-informative karyotypes. In conclusion, OGM demonstrated feasibility in routine practice and superior diagnostic performance compared with CC, supporting its integration into the standard genetic work-up of NHL.