P067: Detection of leukemia-associated structural variants using electronic genome (EGM) mapping

Introduction: Structural variants (SVs) such as TP53 deletions and gene fusions drive many hematological malignancies.Reliable identification of these specific SVs is crucial for diagnosis, prognosis, and guiding therapies.Detection remains challenging using conventional cytogenetic and sequencing methods in clinical laboratories.Conventional methods, such as chromosomal karyotype and fluorescence in situ hybridization, often struggle to achieve adequate diagnostic resolution.The progression of next-generation sequencing (NGS) platforms, from short-read to long-read solutions, underscores the need to reliably resolve large and complex structural variants at low cost.Optical genome mapping (OGM) enables genome-wide SV analysis for clinical diagnosis but struggles to detect smaller SVs due to limitations in optical resolution and label density.Electronic genome mapping (EGM), a novel, solid-state nanochannel platform, delivers both genome-wide and targeted SV analysis at a higher resolution, bridging the gap between cytogenetic and molecular NGS techniques.Methods: EGM was used to identify TP53 deletions, gene fusions, and copy number variants (CNVs) in human leukemia-derived cell lines and blood/BMA samples.High molecular weight (HMW) DNA was isolated using the NEB Monarch kit.The HMW DNA was processed using a dual-enzyme workflow for nicking, labeling, tagging, and coating, and data were collected using the OhmX Platform.SVs were detected using Human Chromosome Explorer de novo assembly and confirmed with SV-Verify, a targeted, alignment-based variant detection application.Copy number variants (CNVs) were detected using an alignment-based CNV pipeline.Variants were confirmed using orthogonal techniques, including sequencing, OGM, and CMA.Results: EGM accurately called TP53 deletions ranging from 3.8-87 kb, as well as fusions such as BCR::ABL1, PML::RARA, and RUNX1::RUNX1T1, with accompanying CNV data.These results exhibit strong concordance with complementary methodologies and previously published data.Conclusion: EGM is a robust, high-resolution tool for detecting SVs and CNVs associated with hematological malignancies, complementing traditional cytogenetic and molecular NGS technologies.The cost-effectiveness and precision of EGM using the OhmX Platform make it a strong candidate for integration into hematopathology testing workflows.