Optical Genome Mapping as a Diagnostic Tool in Pediatric Acute Myeloid Leukemia

SIMPLE SUMMARY: Treatment of pediatric acute myeloid leukemia (AML) is stratified according to multiple recurrent genetic aberrations, which require for detection of different diagnostic methods such as karyotyping and fluorescence in situ hybridization (FISH). The aim of this study was to analyze whether optical genome mapping (OGM), as a new all-in-one methodological approach, can identify all stratification-relevant genetic aberrations that were described by karyotyping. Therefore, frozen bone marrow and blood cells from 24 pediatric patients with AML, bi-lineage leukemia, and mixed-phenotype acute leukemia collected at diagnosis were analyzed by OGM. The results of OGM were compared with routine diagnostic results from karyotyping and FISH. We show that OGM has much potential to address limitations of cytogenetics and even identify new structural aberrations that can be useful for monitoring minimal residual disease (MRD) in patients without an MRD marker. ABSTRACT: Pediatric AML is characterized by numerous genetic aberrations (chromosomal translocations, deletions, insertions) impacting its classification for risk of treatment failure. Aberrations are described by classical cytogenetic procedures (karyotyping, FISH), which harbor limitations (low resolution, need for cell cultivation, cost-intensiveness, experienced staff required). Optical Genome Mapping (OGM) is an emerging chip-based DNA technique combining high resolution (~500 bp) with a relatively short turnaround time. Twenty-four pediatric patients with AML, bi-lineage leukemia, and mixed-phenotype acute leukemia were analyzed by OGM, and the results were compared with cytogenetics. Results were discrepant in 17/24 (70%) cases, including 32 previously unknown alterations called by OGM only. One newly detected deletion and two translocations were validated by primer walking, breakpoint-spanning PCR, and DNA sequencing. As an added benefit, in two cases, OGM identified a new minimal residual disease (MRD) marker. Comparing impact on risk stratification in de novo AML, 19/20 (95%) cases had concordant results while only OGM unraveled another high-risk aberration. Thus, OGM considerably expands the methodological spectrum to optimize the diagnosis of pediatric AML via the identification of new aberrations. Results will contribute to a better understanding of leukemogenesis in pediatric AML. In addition, aberrations identified by OGM may provide markers for MRD monitoring.