Combining next-generation sequencing and optical genome mapping techniques to analyze genomic abnormalities in marginal zone lymphoma

Abstract Introduction: Optical genome mapping (OGM) is a novel DNA-based technology enabling comprehensive genome-wide analysis of cytogenomic aberrations, including alterations frequently missed by conventional cytogenetics. Next-generation sequencing (NGS) provides comprehensive mutational profiling at the nucleotide level, detecting point mutations, insertions, deletions, and copy number variations (CNVs). This study aims to assess the clinical value of combining NGS with OGM in the diagnosis of MZL. It seeks to optimize the diagnostic approach for MZL through the integration of these technologies and to explore their clinical relevance. Methods A total of 25 MZL patients diagnosed and treated at Second Affiliated Hospital of Army Medical University (Xinqiao Hospital), Chongqing (July 2024–July 2025) were enrolled. All patients underwent at least one of the following genetic testing methods: OGM, NGS, FISH, or karyotype analysis. Cytogenomic findings detected by NGS and OGM were classified as pathogenic/likely pathogenic or of uncertain clinical significance. Clinical data including staging and subtypes were collected. Results The cohort comprised 25 MZL patients, including 13 cases of MALT lymphoma (52%), 3 of splenic MZL (SMZL, 12%), 2 of nodal MZL (8%), and 7 of disseminated MZL (28%). NGS and OGM were performed in 84.0% (n=21) of patients, while 8.0% (n=2) underwent only NGS or OGM. Notably, in one patient with 21q deletion detected by karyotyping, OGM not only confirmed this deletion but also identified an additional duplication of chromosome 3.For chromosomal variations with definite clinical significance (Class Ⅰ/Ⅱ), 56.5% (n=13) of patients were at stage Ⅳ, with 38.5% harboring such variations; no variations were detected in 43.5% (n=10) of patients at stage Ⅲ or lower. The detection rate of chromosomal variations was significantly higher in stage Ⅳ than in stage Ⅲ or lower (p≈0.044), suggesting a potential association between disease progression and increased genomic instability, which may affect treatment response (pending validation in larger cohorts). In terms of disease dissemination, 30.4% (n=7) were disseminated MZL, with 57.1% showing chromosomal variations; only 6.3% of non-disseminated cases (69.6%, n=16) had variations, with a significant difference between groups (p≈0.023), indicating that enhanced genomic instability may be associated with the abnormal proliferation and migration of tumor cells.Specifically, ins 22q11.2/SLC25A18 (50.0% vs 6.7%, p≈0.03) and ins 2p25.3/LINC01250 (37.5% vs 0.0%, p≈0.03) were significantly more frequent in disseminated cases. Among 73.9% (n=17) of intermediate/high-risk patients, OGM detected more structural variants (SVs) and CNVs, with median counts of 31 (range, 5–51) and 3 (range, 1–11), respectively. The most common aberrations included dup 1p13.3/SLC2A14 (47.8%), ins 19p13.3/GNA15 (30.4%), and del 7q11.21/STAG3L4 (26.1%).NGS profiling was performed in 92% (n=23) of patients, with 95.7% (n=22) harboring at least one genetic variant. The most frequent mutations involved ARID1B (100%), KMT2C (95.7%), PCLO (91.3%), SETD1B (87.0%), and KMT2D (78.3%), predominantly missense mutations; frameshift and nonsense mutations were less common. Recurrently mutated genes included epigenetic regulators (KMT2C, KMT2D, KMT2A, SETD1B), tumor suppressors (FAT1, NF1, PTPN6), signaling pathway-related genes (MAP2K2, MAP3K14), and immune regulatory genes (CIITA, SP140, CD70). Additionally, STAT6 (13.0%) and TP53 (13.0%) mutations were exclusively observed in disseminated cases, suggesting a close association with disease risk stratification. Conclusion Integrated genomic analysis combining NGS and OGM facilitates comprehensive characterization of cytogenomic aberrations in MZL, providing new insights for clinical diagnosis and precision therapy of MZL.