Electronic Genome Mapping Enables High-Resolution Cytogenomic Profiling of Hematologic Malignancies: A Proof-of-Principle Study

Source abstract

Background/Objectives: Many myeloid malignancies are defined by recurrent structural variants (SVs) and copy-number alterations (CNAs) under the current World Health Organization (WHO) and International Consensus Classification (ICC) frameworks. Detecting these abnormalities typically requires several standard-of-care (SOC) assays, each with its own blind spots, and then laboratories and clinicians are left to piece the results together. Genome mapping has emerged as a mainstream technology with the potential to serve as a high-resolution alternative to several standard-of-care cytogenetic assays such as karyotyping (KT), fluorescence in situ hybridization (FISH) or chromosomal microarray (CMA). Our laboratory at Augusta University has published numerous publications on the analytical and clinical utility of optical genome mapping (OGM) as a first-line assay for hematological malignancies. Electronic genome mapping (EGM) pursues the same goal with an electronic rather than optical readout. The objective of this study was to demonstrate the performance and utility of EGM as a valuable tool to detect clinically relevant SVs and CNAs found by SOC testing. Cytogenomic characterization of hematologic malignancies commonly requires multiple complementary assays, including karyotyping, FISH, and chromosomal microarray, each with distinct analytical limitations. Electronic genome mapping (EGM) provides genome-wide interrogation of structural variants and copy-number alterations using electronic single-molecule detection. We evaluated the feasibility and analytical performance of EGM in previously characterized myeloid malignancies. Methods: EGM was performed on the Nabsys OhmX platform using five previously characterized bone marrow aspirates from cases with acute myeloid leukemia (AML) or chronic myeloid leukemia (CML). EGM calls were compared with findings from karyotyping (KT), fluorescence in situ hybridization (FISH), and OGM. Results: All five samples passed quality control, with contig N50 values ranging from 1.8 to 3.8 Mb and more than 90% of reference labels represented in the assembled contigs. EGM detected every SOC-reported abnormality including two t(9;22)(q34.12;q11.23)/BCR::ABL1 rearrangements, trisomy 4, trisomy 21, and monosomy 7. In the most complex case, EGM resolved a del(20q) reported by KT and FISH into an intrachromosomal fusion, fus(20;20)(q11.21;q13.12), showing not only what was lost but where the chromosome rejoined. Like OGM, EGM identified an approximately 1.8 Mb loss at 7q22.1 involving 45 of genes of which only CUX1 is associated with cancer. This 7q loss was not detected by KT or FISH. Interestingly, EGM also detected the KMT2A-PTD variant previously detected by OGM. Collectively, EGM demonstrated 100% concordance (6/6 SOC-reported abnormalities; 9/9 OGM calls). Conclusions: In this pilot study on five hematological malignancy specimens, EGM matched SOC and OGM across translocations, aneuploidies, insertions and deletions, including BCR::ABL1 rearrangements in both AML and CML, and added high-resolution breakpoint detail beyond karyotype resolution. These results support larger studies across more subtypes to establish EGM as a first-line genome-wide cytogenomic tool for hematological malignancies. Keywords: Genome mapping, Electronic genome mapping, hematological malignancies, structural variants, copy number variants