(A) Somatic JAK3 mutations were significantly enriched in T-ALL patients with germline RUNX1 variants. Whole-genome sequencing of remission samples for 17 T-ALL patients, 6 and 11 with germline variants or somatic mutations in RUNX1, respectively. (B) RNA-Seq was analyzed for 267 T-ALL patients, including 252, 4, and 11 subjects with WT RUNX1 carrying germline variants or somatic mutations in this gene. Unsupervised clustering shows that RUNX1-variant patients, either germline or somatic, clustered tightly with T-ALL with ETP and near-ETP immunophenotypes.