In conclusion, this study demonstrated that panel-based RNA-seq, supplemented by FISH analysis, and CGH+SNP arrays are a reliable combination of methods to detect the genetic markers BCR-ABL1, ETV6-RUNX1, hypodiploidy, IKZF1plus as well as rearrangements of KMT2A and TCF3 necessary for risk stratification in pediatric BCP-ALL. Here, BCR is linked to acute lymphoblastic leukemia.