This study discovered crucial lncRNAs (RP11-170J3.2, RP11-135F9.1 and RP1-151B14.9) characterizing two ALL phenotypes, and identified lncRNA-associated genes (ACTN1, TNFRSF21 and NLRP3) that influenced the clinical outcome of patients with ALL. Here, TNFRSF21 is linked to acute lymphoblastic leukemia.