Optical Genome Mapping Reclassifies Patients with Intermediate Risk Acute Myeloid Leukemia

Introduction

Acute myeloid leukemia (AML) prognosis is stratified based on cytogenetic and molecular alterations as per the European LeukemiaNet (ELN) 2022 guidelines. Conventional cytogenetic techniques, including chromosomal karyotyping and fluorescence in situ hybridization (FISH), are widely employed in the diagnostic evaluation of AML. Optical genome mapping (OGM) is an emerging genome-wide cytogenetic technology that utilizes imaging of ultra-long labeled single DNA molecules to generate high-resolution genomic assemblies, detecting both balanced and unbalanced structural variants. This study evaluates the efficacy of OGM compared to conventional cytogenetics in classifying AML patients.

Methods

Conventional cytogenetic testing using karyotyping and high-risk FISH probes targeting chromosomes 3 (MECOM), 5 (monosomy or loss of q arm), 7 (monosomy or loss of q arm), 11 (KMT2A break apart probe), and 17 (loss of p arm) was performed in 74 patients with AML at a large tertiary care medical center between February 2023 and April 2024. Twenty-two patients from this cohort were categorized as intermediate risk AML according to the ELN 2022. Additionally, a next-generation sequencing (NGS) mutational panel was performed for all patients to refine their risk classification by ELN 2022.

Results

The median age of the patients was 60 years, with a gender distribution of 9 females and 13 males. All 22 patients exhibited a normal karyotype with no abnormalities detected by the specified FISH probes. Additionally, none of the patients had NPM1 mutations, inv(16), or t(8;21). Eight patients exhibited FLT3-ITD or FLT3-TKD mutations, classifying them as intermediate risk by ELN 2022 based solely on cytogenetics.

OGM identified structural abnormalities in 8 patients (36%) that reclassified their cytogenetic risk to an adverse category. Five patients had KMT2A gene alterations: four exhibited partial tandem duplications (PTD) of exons 3 through 5 (KMT2A-PTD), associated with secondary AML (Yazi et al., Nature 2022), and one had a duplication of the long arm of chromosome 11 (11q) involving the KMT2A gene. Two patients had NUP98 translocations, which, despite not being classified as adverse by ELN 2022, have been associated with high-risk disease in pediatric AML. One patient exhibited trisomy 8, undetected by conventional karyotyping, classifying this patient as having AML with myelodysplasia-related cytogenetic abnormalities. Notably, only one of these 8 patients had an FLT3-ITD mutation, and none of the other 7 FLT3-mutated patients showed adverse cytogenetics by OGM.

The NGS panel for these 8 patients with OGM-detected abnormalities revealed secondary-type mutations in two patients: one patient with trisomy 8 had AXSL1 and BCOR mutations, and the patient with 11q duplication had SRSF2 mutations. The remaining 6 patients did not have mutations affecting their risk stratification.

Conclusion

The high resolution of OGM enhances classification, prognostic prediction, and management of intermediate risk AML. In this cohort, OGM reclassified over one-third of patients initially categorized as intermediate risk by traditional cytogenetics, to an adverse risk group. Among the 22 patients, 8 had FLT3 mutations. Importantly, 7 out of the remaining 14 patients (50%) had findings on OGM not detected by conventional cytogenetics, underscoring the critical role of OGM in cases where conventional cytogenetic or molecular drivers for AML are not apparent. Detecting novel structural variants and cryptic translocations facilitates better risk stratification in AML patients. Additionally, the NGS panel contributed to the risk stratification of two patients with OGM findings, emphasizing the role of high-resolution cytogenetics in AML risk assessment.

In summary , OGM has the potential to become the new standard for prognostic classification of patients with AML .