Using gc-HTS in the BCR-ABL1-positive ALL group we observed rare failures in the identification of genomic breakpoints that were potentially due to AT-rich- or repetitive sequences at probe hybridization sites or gaps in probe design targeting intron 1 of ABL1. Improved probe design with greater coverage at these sites may eliminate such drawbacks in the future. Here, ABL1 is linked to acute lymphoblastic leukemia.