Molecular subtypes of pediatric B lymphoblastic leukemia (B-ALL) discovered in recent years by comprehensive genomic profiling are increasingly becoming essential determinants of treatment, but frequently remain undetected by routine clinical assays. Serial multi-step testing at our institution [consisting of karyotyping, FISH, Chromosomal Microarray and a custom next-generation sequencing panel (OncoKids®)], fails to detect primary genetic drivers in approximately 15% of B-ALL cases. To address this gap, we investigated whether capture-based transcriptome sequencing (RNA-Seq) and optical genome mapping (OGM) could detect molecular subtypes of B-ALL which remain unidentified by the current multi-modal assessment. RNASeq was performed on 53 banked B-ALL samples with unknown oncogenic drivers. A subtype-defining abnormality was identified in 16/53 cases (30%). These included 12 known fusions (IGH::DUX4 (3 cases), MEF2D::BCL9 (2), and 1 each of MEF2D::SS18, MEF2D::FOXJ2, EP300::ZNF384, TCF3::PBX1, SPTBN1::PDGFRB, ACIN1::NUTM1 and IGH::CEBPA), and 4 previously unreported fusions (RBM26::JAK2, STRBP::JAK2, PAX5::HIPK3 and ETV6::MFN2). OGM was completed for 19 B-ALL cases, either in house or at the Bionano Genomics Service Laboratory. It identified the subtype in 6/19 cases (31%), revealing a known fusion in 3 cases (MEF2D::FOXJ2, MEF2D::SS18 and SPTBN1::PDGFRB), and a novel fusion in 3 cases (RBM26::JAK2, STRBP::JAK2 and PAX5::HIPK3). Among the 19 cases tested by both methods, 12 were negative, 6 had concordant abnormalities, and one showed a TCF3::PBX1 fusion by RNAseq but was negative by OGM. While OGM revealed the nature of genomic rearrangements resulting in abnormal fusions and detected secondary structural abnormalities, RNAseq confirmed expression of detected fusions and allowed base-resolution mapping of fusion junctions. The majority of the known and novel fusions detected in this study define specific subtypes of B-ALL, have established prognostic significance and/or predict response to targeted treatments. Our pilot study thus shows clinical utility, discovery potential of, and high concordance between OGM and RNAseq, and highlights complementarity between the two assays.

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DOI: https://doi.org/10.1016/j.cancergen.2022.05.013

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