Transcriptome Sequencing Allows Comprehensive Genomic Characterization of Pediatric B-Acute Lymphoblastic Leukemia in an Academic Clinical Laboratory

Abstract

Studies have shown the power of transcriptome sequencing [RNA sequencing (RNA-Seq)] in identifying known and novel oncogenic drivers and molecular subtypes of B-acute lymphoblastic leukemia (B-ALL). The current study investigated whether the clinically validated RNA-Seq assay, coupled with a custom analysis pipeline, could be used for a comprehensive B-ALL classification. Following comprehensive clinical testing, RNA-Seq was performed on 76 retrospective B-ALL cases, 28 of which had known and 48 had undetermined subtype. Subtypes were accurately identified in all 28 known cases, and in 38 of 48 unknown cases (79%). The subtypes of the unknown cases included the following: PAX5alt (n = 12), DUX4-rearranged (n = 6), Philadelphia chromosome-like (n = 5), low hyperdiploid (n = 4), ETV6::RUNX1-like (n = 3), MEF2D-rearranged (n = 2), PAX5 P80R (n = 2), ZEB2/CEBP (n = 1), NUTM1-rearranged (n = 1), ZNF384-rearranged (n = 1), and TCF3::PBX1 (n = 1). In 15 of 38 cases (39%), classification based on expression profile was corroborated by detection of subtype-defining oncogenic drivers missed by clinical testing. RNA-Seq analysis also detected large copy number abnormalities, oncogenic hot-spot sequence variants, and intragenic IKZF1 deletions. This pilot study confirms the feasibility of implementing an RNA-Seq workflow for clinical diagnosis of molecular subtypes in pediatric B-ALL, reinforcing that RNA-Seq represents a promising global genomic assay for this heterogeneous leukemia.