CBFA2T3-GLIS2 fusion transcript is a novel common feature of pediatric CN-AML, predicting poorer outcome. (A) Schematic representation of the fusion between CBFA2T3 and GLIS2 and predicted sequence of the fusion proteins found in CN-AML. The exon-intron gene structures are indicated. The purple blocks represent untranslated exons. Black arrows indicate the fusion breakpoint. (B) RT-PCR analysis and Sanger sequencing performed in order to validate the detection of the CBFA2T3-GLIS2 fusion. Detection of the GAPDH transcript was used as an RNA quality control. A library negative for the CBFA2T3-GLIS2 fusion transcript was used as negative control (Neg). Black arrows indicate the fusion breakpoint. (C) Probability of 5-year EFS in children with CBFA2T3-GLIS2 fusion transcript in CN-AML. EFS of CBFA2T3-GLIS2–positive patients (27.4%, SE 10.5) vs CBFA2T3-GLIS2–negative patients (59.6%, SE 3.6; P = .01). (D) Probability of 5-year EFS in pediatric CN-AML with or without CBFA2T3-GLIS2 fusion transcript stratified according to FAB subgroups (M7 vs non-M7): EFS of non-M7 CN-AML without CBFA2T3-GLIS2 = 59.4%, SE 3.5 vs EFS of non-M7 CN-AML with CBFA2T3-GLIS2 = 30.0%, SE 14.4 (P = .04). EFS of FAB-M7 CN-AML without CBFA2T3-GLIS2 = 60.7%, SE 8.3 vs EFS of FAB-M7 CN-AML with CBFA2T3-GLIS2 = 26.6%, SE 15.0 (P = .04).