Identification of SPAG9 as a novel JAK2 fusion partner gene in pediatric acute lymphoblastic leukemia with t(9;17)(p24;q21).

We have identified a novel SPAG9-JAK2 fusion in a B-cell precursor acute lymphoblastic leukemia (ALL) with t(9;17)(p24;q21) and a poor outcome, using paired-end transcriptome sequencing. Homozygous and hemizygous deletions of CDKN2A/2B, and hemizygous deletions of PAX5, BTG1, CDK6, ADARB2, and IKZF1 were also identified by multiple ligation-dependent probe amplification and single nucleotide polymorphism array analyses. Having both a tyrosine kinase-activating rearrangement and genomic lesions affecting lymphoid transcription factors suggested that the leukemia was of the Philadelphia chromosome (Ph)/BCR-ABL1-like ALL subtype and that JAK2 inhibitors might be able to overcome this aggressive ALL with SPAG9-JAK2.