T-cell count during remission was associated with relapse-free survival in children with ALL. (A) The prevalence of different immune cell populations in patients with ALL during remission was inferred by applying the CIBERSORT deconvolution algorithm to the global gene expression profile of peripheral blood leukocytes collected in week 1 of consolidation therapy. The level of each type of immune cell was inferred on the basis of the expression of a panel of marker genes of this population. A total of 102 children with ALL from the St. Jude Total Therapy XV clinical trial^32,33 with gene expression profiles available were included in this analysis. T cells, monocytes, and neutrophils accounted for the highest cell populations. (B) The expression-based estimates of lymphocyte level (B cells and T cells; x-axis) were highly correlated with actual lymphocyte count measured during routine complete blood count tests of these patients at this time point (y-axis). (C,D) Event-free survival (C) and relapse-free survival (D) of patients with ALL based on their T-cell levels during remission. Patients were classified as T-cell high vs low, using a cutoff of 0.42, with n indicating the number of patients. (E,F) Event-free survival (E) and relapse-free survival (F) of patients with ALL based on their T cell/monocyte ratio during remission. Patients were classified as T cell/monocyte ratio high vs low using a cutoff of 2, with n indicating the number of patients. The differences in survival were detected by log-rank (Mantel-Cox) test.