PhD Scientific Days 2025

Poster Session I. - D: Pathological and Oncological Sciences

Resolving Complex Rearrangements and Improving Variant Analysis in Pediatric B-ALL Using Optical Genome Mapping

Name of the presenter

Bekő Anna

Institute/workplace of the presenter

Department of Pathology and Experimental Cancer Research, Semmelweis University

Authors

Anna Bekő¹, Borbála Péterffy¹, Alex Hughes¹, Janka Jakab¹, Katalin Csonka¹, Gergő Papp¹, Dóra Kapczár¹, Bettina Aranka Bohusné Barta¹, Bálint Egyed², Irén Haltrich², Lajos Hegyi¹, Anne Benard-Slagter³, Suvi Savola³, Donát Alpár¹, Csaba Bödör¹

1: Department of Pathology and Experimental Cancer Research, Semmelweis University
2: Pediatric Center, Semmelweis University
3: MRC Holland, Amsterdam, the Netherlands

Text of the abstract

Introduction: Detection of structural variants (SVs) and copy number variations (CNVs) is crucial in pediatric B-cell acute lymphoblastic leukemia (p-B-ALL) diagnostics. However, limitations of FISH and chromosome banding analysis (CBA) may challenge the accurate cytogenetic characterization, while optical genome mapping (OGM) offers a reliable solution by enabling genome-wide detection of CNVs and SVs.
Aims: To detect chromosomal aberrations in p-B-ALL using OGM and to test its feasibility for clinical diagnostics compared to CBA, FISH, targeted RNA sequencing (RNA-seq), and digitalMLPA. Additionally, to develop a more precise variant interpretation.
Method: CBA, FISH, targeted RNA-seq (TruSight RNA Pan-Cancer Panel, Illumina), and OGM (Bionano Genomics) were performed on diagnostic bone marrow samples from 51 p-B-ALL patients at Semmelweis University. digitalMLPA was conducted at MRC Holland. OGM variant analysis was performed in Bionano Access v1.8.1. Statistical analyses were performed in SPSS v.28.0.1.
Results: CBA detected aberrations in 13/51 patients; OGM fully confirmed the findings in 10 cases. OGM detected high hyperdiploidy in 5 cases with normal karyotypes and generated digital karyotypes for all 21 CBA-failed cases. OGM data and results of the FISH probes were congruent in 91%. In 93% of CNV discordancies, digitalMLPA confirmed OGM findings. OGM detected 156 translocations, 40% (n=62) overlapping with RNA-seq panel genes (38 validated, 24 unvalidated). Among the unvalidated fusions, in 11 variants, ETV6 or RUNX1 genes were involved in complex ETV6::RUNX1 fusions (8/11 validated by FISH). CNVs identified by OGM and digitalMLPA showed almost perfect overall agreement (Cohen’s Kappa (CK)=0.93). For the 153 genes associated with ALL, agreement between CNV values was perfect (CK=1) in 76%. In the regions on the variants’ periphery in the OGM analysis, in grey-zones, by applying a novel evaluation strategy, the concordant CNV values significantly increased. After re-evaluating grey-zone areas, CK interpretation level was updated in 10/11 genes.
Conclusion: Application of OGM revealed complex rearrangements challenging to detect by other methods and led to improved classification of the patients. Notably, our newly introduced evaluation approach also offers a novel, more accurate OGM variant analysis.
Funding: SE250+ grant, KDP-2023-00016