Transcriptional activity from ALL cells representing seven different pre-B-ALL cytogenetic subtypes was assayed using GRO-seq (both primary patient and cell line samples, see Supplementary file 1 and Materials and methods), and jointly analyzed with WGS data from the ETV6-RUNX1 (51 cases; Papaemmanuil et al., 2014), high hyperdiploid (HeH, 16 cases; Paulsson et al., 2015), hypodiploid (20 cases; Holmfeldt et al., 2013) and MLL-rearranged (22 cases at diagnosis and 2 relapses; Andersson et al., 2015) subtypes of precursor B-ALL. Here, RUNX1 is linked to acute lymphoblastic leukemia.