Application of Optical Genome Mapping for the Diagnosis and Risk Stratification of Myeloid and Lymphoid Malignancies

Abstract

Optical genome mapping (OGM) is a novel, high-resolution technology for genome-wide detection of structural variants, offering clear advantages over conventional cytogenetics in hematologic malignancies. We applied OGM to a large cohort of patients with acute myeloid leukemia (AML), myelodysplastic syndromes (MDSs), and B-cell acute lymphoblastic leukemia (B-ALL) to evaluate its clinical utility. In AML and MDS, it revealed high-risk alterations such as deletions in 5q31-5q32 and 7q22, and cryptic fusions like NUP98::NSD1 that were missed by karyotyping or FISH. It also identified chromoanagenesis, a catastrophic chromosomal event linked to poor prognosis and often undetectable by standard methods. In B-ALL, OGM uncovered clinically relevant deletions in CDKN2A/B, PAX5, and IKZF1, as well as high-risk ploidy changes like hypodiploidy and hyperdiploidy, all important for risk assessment and frequently underdetected. OGM not only refines diagnosis and improves risk stratification but can also uncover cryptic and complex genomic abnormalities. Our findings support its integration into routine diagnostics to enhance classification, guide treatment decisions, and improve patient outcomes.

Keywords: OGM; chromosomal alterations; cryptic rearrangements; hematologic malignancies; optical genome mapping.

Figure 1

Optical genome mapping results illustrating cytogenetic complexity profiles: (a) Circos plot of a patient with acute myeloid leukemia (AML) associated with myelodysplasia. Deletions in 17p and 7q are indicated, along with multiple rearrangements involving chromosomes 5, 7, 12, and 17, consistent with a complex karyotype. Findings from optical genome mapping (OGM) together with a TP53 mutation confirmed by next-generation sequencing (NGS) indicate biallelic inactivation of TP53; (b) Circos plot of a patient with myelodysplastic syndrome (MDS). The analysis revealed a ~1 Mb deletion in 17p encompassing the TP53 gene, detected by OGM but not identified by conventional karyotyping or FISH. This deletion, in combination with a TP53 mutation detected by NGS, supports biallelic inactivation of the gene. Additional abnormalities include monosomy seven and deletion of 5q; (c) Circos plot of a patient with therapy-related acute myeloid leukemia (t-AML). A deletion in 17p, a large deletion affecting nearly the entire chromosome 7, a deletion in 5q, and complex rearrangements involving chromosomes 1, 4, 8, and 18 were observed. As in the previous cases, the presence of a TP53 mutation identified by NGS, together with the 17p deletion, indicates biallelic inactivation of TP53. From the outer to the inner rings of the circos plot, the following layers are displayed: (1) chromosomes and cytobands, (2) masked regions (heterochromatic, difficult to analyze), (3) structural variant (SV) region, (4) copy number variation (CNV) profile, and (5) in the center, inter- and intrachromosomal translocations represented as pink lines connecting the involved genomic loci. SVs < 1 Mb were filtered out from the circos plot unless they involved clinically significant regions. All alterations depicted in the circos plots are summarized in Supplementary Table S2.

Figure 2

Visualization of structural alterations by optical mapping in hematological neoplasms: (a) Genome browser image of patient nº 4 with acute myeloid leukemia (AML). Optical genome mapping (OGM) revealed the translocation t(5;11)(q35;p15.5), resulting in the NUP98::NSD1 gene fusion; (b) Genome browser image of patient nº 3 with AML. OGM detected a rearrangement between regions 16p13.11 and 16q22.1, leading to the MYH11::CBFB fusion; (c) Circos plot of patient nº 6 with T-cell acute lymphoblastic leukemia (T-ALL). OGM revealed several structural variants not detected by conventional karyotyping or FISH, including a deletion in 9p involving loss of CDKN2A/B and a t(1;14) translocation resulting in a TAL1::TRD fusion; (d) Whole genome view of patient nº 8 with B-cell acute lymphoblastic leukemia (B-ALL). A 55 Mb deletion in the short arm of chromosome 7 affecting the IKZF1 gene was identified, along with multiple chromosomal gains, suggesting a hyperdiploid profile consistent with a complex karyotype; (e) Whole genome view using De Novo Assembly algorithm, patient nº 10 with B-ALL and Li-Fraumeni syndrome. High hyperdiploidy was detected, including trisomies of chromosomes X, 4, 6, 8, 10, 14, 17, and 18, as well as tetrasomy of chromosome 21. Secondary analysis showed no loss of heterozygosity, confirming true hyperdiploidy and ruling out masked hypodiploidy.