Application of Targeted RNA-Sequencing in High-Risk B-Cell Acute Lymphoblastic Leukemia (B-ALL): Identifying Fusions, IKZF1 Deletions, and CRLF2 Expression in an Indian Cohort.

Introduction: B-cell acute lymphoblastic leukemia (B-ALL) is genetically heterogeneous. We assessed the utility of FusionPlex ALL targeted RNA sequencing panel in detecting gene fusions and other genomic lesions in B-ALL.

Methods: The high-risk B-ALL, negative for common recurrent gene fusions (RGF), that is, BCR::ABL1, ETV6::RUNX1, TCF3::PBX1 and KMT2A::AFF1, were analysed with RNA-based targeted sequencing 81-gene-panel FusionPlex ALL (IDT, USA). Multiplex ligation-dependent probe amplification (MLPA) was used for IKZF1 deletions and flow-cytometry for CRLF2 expression and ploidy analysis.

Results: Out of 32 samples, 27 were high-risk B-ALL cases (median age 16 (1-41) years) and 5 B-ALL controls with known fusions for validation. The fusions were detected in 6/27 (22%) RGF-negative B-ALL cases; 2 with EPOR::IGH and 1 each P2RY8::IGH, PAX5::ETV6, SNX2::ABL1, IKZF1::CIITA. In addition, IKZF1 and/or PAX5 gene deletions resulting in the formation of oncogenic/novel isoforms were detected in 75% (15/20) samples positive on MLPA. Flow-cytometry CRLF2 overexpression was noted in 60% (9/15) tested samples which correlated well with targeted RNAseq CRLF2 gene expression.

Conclusion: The targeted sequencing approach can help in detecting known and novel fusions in B-ALL, novel breakpoints in the known fusions, gene deletions as oncogenic/novel isoforms and CRLF2 expression.