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The t(12;21)(p13;q22) ETV6- RUNX1 gene fusion is one of the most common chromosomal translocation in childhood acute lymphoblastic leukemia ( ALL). It is associated with favorable prognosis. The identification of the genomic sequence of the breakpoint flanking regions of the ETV6- RUNX1 translocation should be the best strategy to monitor minimal residual disease ( MRD) in patients with ETV6- RUNX1-positive ALL. In this study, the ETV6- RUNX1 translocation was sequenced by next-generation sequencing ( NGS) in 26 patients with ETV6- RUNX1-positive ALL and re-sequenced by using the Sanger method. Interestingly, the three-way translocation, including ETV6- RUNX1, was detected in five patients. Four of them relapsed during or after therapy, while 21 patients without the three-way translocation were still in remission ( P < 0.0001). The three-way translocation pattern was identical between the diagnosis and relapse samples in three patients, excluding one patient ( SCMC-001245). The relapse samples retained the translocation of ETV6- RUNX1 relative to the three-way translocation t(8;12;21) at diagnosis, suggesting that the three-way translocation might be an important risk factor for relapse in patients with ETV6- RUNX1-positive ALL and should be further studied. [ABSTRACT FROM AUTHOR]