Decoding the genetic complexity in a pediatric case of B-ALL through long-read genomic sequencing and RNA sequencing

B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous hematologic malignancy caused by diverse genetic alterations. While cytogenetic methods such as karyotyping and FISH are routinely used in diagnostics, cryptic and novel oncogenic gene fusions often go undetected. We report a 15-year-old male diagnosed with high-risk B-ALL, presenting with anemia, leukocytosis, and significant lymphoblast burden. Initial karyotyping identified an abnormal clone with a t(7;20)(q34;q13.3) and FISH detected a partial deletion of the ABL1 gene. Chromosome microarray analysis revealed a deletion at 9p21.3 encompassing CDKN2A/CDKN2B and several contiguous copy number aberrations at 9q34.12q34.2. Further long-read genomic sequencing uncovered cryptic NUP214::ABL1 and ABL1::TSC1 fusions, as well as a novel VAPB::TRBV30 rearrangement from the t(7;20). RNA sequencing confirmed the transcripts for both ABL1 fusions and a noncoding rearrangement involving the TCRB locus. Notably, the presence of NUP214::ABL1 identified a clinically actionable target, supporting the use of tyrosine kinase inhibitors (TKIs) such as imatinib. This case underscores the critical role of integrated sequencing approaches in identifying cryptic genetic alterations in B-ALL for precise classification of oncogenic drivers and for targeted therapeutic strategies to improve patient outcomes.