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

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.

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

“…Around 20% of leukemic blasts are required for SNP-array in a diagnostic setting for large CN alterations. 34,35 Our study and others 14,36,37 showed that OGM performance on samples with blast amounts of about 20%-30% could also detect observed by conventional diagnostic methods. Hence, OGM could be an attractive option for routine diagnostic workup of hematological malignancies, as it has a fast turnaround time of ≈5 days from sample acquisition to data analysis.…”

“…The applicability of this approach has recently been shown for various hematological malignancies, and some researchers even advocate for further replacing the existing routine diagnostics methods of those neoplasms with optical genome mapping (OGM). 11–17…”

“…The applicability of this approach has recently been shown for various hematological malignancies, and some researchers even advocate for further replacing the existing routine diagnostics methods of those neoplasms with optical genome mapping (OGM). [11][12][13][14][15][16][17] Here, we present a study focusing on 60 HD and ETV6::RUNX1+ BCP-ALL cases analyzed by whole exome sequencing (WES) and OGM to decipher the landscape of genomic alterations in both entities, with a special focus on their SVs. We report several novel recurrently altered genes, which are not described in previous studies that applied SNP-arrays or WGS.…”

Optical Genome Mapping for Cytogenetic Diagnostics in AML

“…As for the adult population, one patient was re-classified, leading to changes in treatment. For two patients, an MRD marker could be identified [ 32 ].…”

Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia

“…Nowadays, there are some cytogenetic and molecular methods used in SV detection, with different advantages and limitations. Methods used to detect genetic aberrations vary in their resolutions, which may affect the more precise assignment of the gene being tested [4]. For instance, karyotyping analysis allows for the identification of balanced and unbalanced structural anomalies, limited by the proliferation index of the blast, as well as by the poor quality of the metaphases obtained and the low resolution (about 5 Mbp) [5].…”