Patient characteristics.

Diagnostic blast immunophenotypic analysis (in bulk patient samples) and DNA sequencing (in the CD34+ cell population) were performed for 12 pediatric T-ALL patient samples. Patient age range was 2–23 and mean age was 11.3 years. Diagnostic samples included patients 1–11 while sample 12 was donated by a patient with relapsed T-ALL. Diagnostic blast immunophenotypes were not available (N/A) for 2 of 12 patients. Treatment was performed according to protocol COG 05-01 for patients 1 to 7; protocol COG 9404 for patients 8 to 10; the Larson protocol for patient 11, and patient 12 received COG-ALL043 treatment. Targeted exon sequencing performed on T-ALL CD34+ LIC revealed NOTCH1 HD or PEST domain mutations in 6 of 12 T-ALL (patients 01, 03, 05, 08, 11, 12) samples. PTEN mutations and/or deletions were detected in 4 of 12 samples (patients 01, 05, 06, 11). Patient 5 also had a PIK3R1 mutation. # Indicates NOTCH1Mutated patient samples, and * indicates NOTCH1 activation in the absence of NOTCH1 mutation (NOTCH1High) by qRT-PCR.