Reinforcing the accuracy of WGS, 19 cases harboured established chromosomal abnormalities, which were previously undetected due to limited material and incomplete standard-of-care testing at the time of diagnosis: high hyperdiploidy (n = 5), iAMP21-ALL (n = 3), ETV6::RUNX1 (n = 1), TCF3::PBX1 (n = 8), TCF3::HLF (n = 1), low hypodiploidy (n = 1) (Supplementary Table 1, Supplementary Information, Fig. 1). Here, RUNX1 is linked to acute lymphoblastic leukemia.