Optical Genome Mapping Combined with High-Throughput Sequencing Is Effective for the Diagnostic and Prognostic Genomic Classification of Acute Myeloid Leukemia and Myelodysplastic Neoplasms

Cytogenetic and molecular analyses are crucial for the diagnosis, choice of treatment and prognostic evaluation of acute myeloblastic leukemia (AML) and myelodysplastic neoplasms (MDS). Optical genome mapping (OGM) is a recent technology enabling a genome-wide high-resolution detection of structural abnormalities (SVs) and copy number variations (CNV) developed by the Bionano® company. The clinical value of OGM in AML and MDS and its positioning in relation to conventional karyotype and FISH (K&F) and targeted high throughput panel sequencing (HTS) has been little evaluated.

Here, the primary objective was to evaluate prospectively the ability of OGM to apply the diagnosis (WHO 2022) and prognostic cytogenetic classification of AML (ELN 2022) and MDS (IPSSm) in comparison with K&F and HTS. The secondary objectives were to evaluate the proportion of informative cases in intention-of-analysis and among them the level of concordance of OGM versus K&F, the amount of additional information (OGM vs KF), and the potential reclassification (OMS 2022, ELN 2022, IPSSm) in addition to K&F and a targeted HTS panel (i.e. including ASXL1, CEBPA, DNMT3A, IDH1, IDH2, FLT3, KRAS, NPM1, NRAS, RUNX1, SRSF2, TP53, WT1) used in real-life.

A two-stage prospective selection of bone marrow or blood samples was carried out at Nantes University Hospital between May 2022 and June 2023. A 1st collection of samples from 67 patients (pts) with AML (n=58) or MDS (n=9) was selected and cryopreserved according to pre-analytical criteria (cell count, time after collection). A 2nd final selection of 39 pts including 34 AML and 5 MDS was carried out according to their cytogenetic and/or molecular data, in order to evaluate the performance of OGM in different profiles of clinical interest (Table 1). Of these 39 intention-to-analyze patients, 35 were informative for OGM comparison with K&F (3 OGM failures, 1 K not realized). Interpretation criteria with Bionano access software considered SVs and CNVs >200 and >500 kbp respectively, or smaller if a gene of interest was found. Further details will be presented at the conference.

OGM showed concordance with K&F in 30/35 (86%) of informative pts, but 5 had subclonal (<20%) gains undetected i.e. +8, +21, +6p or poorly detected i.e. t(1;15) with centromeric break. None of these OGM false negatives modify the diagnosis or prognosis. Additional information was found with OGM in 19/35 pts, with a median of 1 cryptic anomaly/patient (range = 1-13). Cryptic abnormalities were identified in 9/18 pts with normal K (7 AML, 2 MDS), including 5 pts with pathogenic SV, notably KMT2A with partial tandem duplication (PTD) and TET2 deletion, and 4 pts with SV of unknown significance (-6p, +4q, +15q, +19p, +20q). Finally, the WHO diagnosis was confirmed with OGM in all informative pts but not modified in any of them.

OGM confirmed ELN prognostic classification of all the AML cases without modification. Two AML cases had >3 anomalies with OGM (range = 5-6) of which >2 were cryptic without complex karyotype (CK) (size = 226-1221 kbp, VAF% = 3-100) including gains (3q, 11q, Xp) or losses (3p, 4p, 21q) of undetermined or pathogenic ( RUNX1 deletion) significance. In this context of multiple cryptic anomalies, there is no precise definition of abnormal or CK with OGM. One is a MDS-related AML cases that also had MDS-associated somatic mutations (i.e. ASXL1, SRSF2 ELNadverse) and the other was an AML with NUP98 rearrangement and FLT3-ITD mutation (i.e ELN intermediate).

OGM confirmed the IPSSm prognostic cytogenetic category in 3 pts and modified it in 2/5 MDS pts (40%). Among the two latter, K was normal (e.g. favorable) but OGM identified cryptic KMT2A- PTD of poor prognosis. These two SMD-IB2 changes the IPSSm risk category from Moderate-High or High to Very-High risk group. The combination of OGM and HTS techniques provided a more accurate prognostic classification of MDS cases.

Confirmations of cryptic pathogenic anomalies detected by OGM using a 2nd technique will be presented at the congress.

OGM technology is powerful for identifying pathogenic anomalies, but the criteria for abnormal K and CK need to be clarified in order to apply international diagnosis and prognosis classifications. To this end, the OGM+HTS combination is highly effective. The positioning of OGM as a complement and/or replacement for conventional cytogenetic and molecular tools, and its impact on therapeutic choice, still needs to be evaluated in AML and MDS.