Overall, most (>90%) genomic regions were in the same compartment in the leukemia samples as in the GM12878 cell line and more than 98% of genomic regions were in the same compartment in high hyperdiploid ALL and ETV6/RUNX1-positive cases, in line with previous studies showing that depletion of CTCF does not lead to compartment switching37. Here, RUNX1 is linked to acute lymphoblastic leukemia.