Application of Next-Generation Cytogenetics in a Clinical Laboratory for Diagnostic Work-up of Myelodysplastic Syndromes/Neoplasms (MDS)

Background. Optical genome mapping (OGM) is a novel, non-sequencing-based technique for genome-wide detection of various types of chromosomal structural abnormalities (losses, gains, translocations, inversions, partial tandem duplications) at a very high (10⁴X) resolution compared to chromosome banding analysis (CBA). We published our experience with OGM for cytogenomic profiling of a large retrospective cohort of newly diagnosed myelodysplastic syndrome/ neoplasm (MDS) patients using OGM (Yang et al., Leukemia 2022). Our findings revealed that OGM identified multiple cryptic abnormalities, with over half being undetectable by CBA across 34% of patients. Additionally, OGM results independently predicted overall survival. Subsequently, we implemented OGM as a clinical assay in our clinical cytogenetic laboratory. In this study, we present the results of an additional 105 MDS patients who underwent OGM prospectively as part of the routine diagnostic work-up in a clinical diagnostic laboratory.

Methods. All patients diagnosed with MDS (2023-2024) who underwent OGM were identified. Clinicopathological data including standard-of-care cytogenetic studies were collected from medical records. All cases were classified using WHO (5^th ed.) and International Consensus Classification (ICC) criteria.

Results. The cohort included 105 MDS patients [67 (%) men, 38 (%) women] with age ranging from 40 to 92 and median age of 65 years. The median blast percentage was 7%. The distribution based on WHO (4^th ed.) showed MDS with multilineage dysplasia (n=49), MDS excess blasts-1 (n=23), MDS with excess blasts-2 (n=27) and MDS with isolated del(5q) (n=6). Based on CBA, 26 (24%), 51 (48%) and 28 (26.7%) patients had normal, non-complex and complex karyotypes respectively.

OGM was performed on 104 patients (in one patient, there were not enough cells). OGM allowed precise gene/exon-level mapping of clinically relevant biomarkers for application of AMP/ASCO/CAP classification tiers. Sixty-nine (66%) of MDS patients had at least one Tier 1 or 2 abnormality (clinically significant). The abnormalities detected in the remaining 35 (33%) patients did not meet the criteria for Tier 1/2. Due to inherent higher resolution compared to CBA, OGM showed additional clinically significant abnormalities in 33 (31%) of patients. Of these, 7 cases showed abnormalities that changed the WHO5/ICC classification (diagnostic) [additional del(17p) loss in 2 patients, del(5q) in 2 patients, MECOM rearrangement (2 patients), MLF::NPM1 and del(7q). In 5 patients had a change in the prognostication based on detection of biallelic TP53 alteration (n=2). or KMT2A-partial tandem duplication (n=3). Further, 18 cases showed chromoanagenesis, a genomic catastrophe resulting in multiple chromosomal rearrangements and copy number changes, only 15 of these patients showed complex karyotype by CBA. In contrary, even though limit of detection of OGM is similar to CBA (10-20%), OGM missed clonal (seen in at least 2 metaphases) abnormalities in 5 cases due to absence of proliferative bias, underscoring the necessity of performing CBA work-up in parallel.

Conclusions. OGM is a powerful tool for identification of genome-wide chromosomal abnormalities and can be used to accurately apply WHO5 and ICC classification criteria.

Sasaki:Chugai: Other: Lecture fees; Enliven: Research Funding; Otsuka: Other: Lecture fees; Daiichi-Sankyo: Consultancy; Pfizer: Consultancy; Novartis: Consultancy, Research Funding. Montalban-Bravo:Rigel: Research Funding; Takeda: Research Funding. Chien:AbbVie: Consultancy; Rigel Pharmaceuticals: Consultancy. Garcia-Manero:Astex: Research Funding; Onconova: Research Funding; Helsinn: Research Funding; Merck: Research Funding; Novartis: Research Funding; Curis: Research Funding; Genentech: Research Funding; Genentech: Other: Personal fees; Janssen: Research Funding; H3 Biomedicine: Research Funding; AbbVie: Research Funding; Bristol Myers Squibb: Other: Personal fees, Research Funding; Amphivena: Research Funding; Forty Seven: Research Funding; Aprea: Research Funding; Astex: Other: Personal fees; Helsinn: Other: Personal fees.