Supplementary Figures 1-19 from Acute Lymphoblastic Leukemia with Myeloid Mutations Is a High-Risk Disease Associated with Clonal Hematopoiesis

Supplemental Figure 1. WHO/ICC subtypes for the B-ALL cohort.

Supplemental Figure 2. Lymphoid clonal hematopoiesis (CH) mutations are less common in adults with ALL.

Supplemental Figure 3. Blast percentage in the pre-treatment sample and detected variant allelic frequencies (VAF) of mutations in ALL patients with myeloid mutations.

Supplemental Figure 4. Germline testing in the adult ALL cohort.

Supplemental Figure 5. Associations of gene mutations and WHO/ICC disease subtypes in B-ALL.

Supplemental Figure 6. Overall survival in adults with B-ALL.

Supplemental Figure 7. Kaplan-Meier overall survival curves for Ph-negative B-ALL patients stratified based on the presence of TP53 and non-TP53 MyM (A), and treatment with different chemotherapy protocols (B, C, D). LH, low hypodiploidy.

Supplemental Figure 8. T-lineage ALL with myeloid mutations (MyM).

Supplemental Figure 9. Expression levels of lineage-specific surface markers.

Supplemental Figure 10. Single cell DNA and protein sequencing to study the clonal architecture of Tlineage ALL with MyM.

Supplemental Figure 11. A, Flow plots showing ETP-lymphoblast, myeloid, and mature lymphocytic compartments of ETP-ALL1, which were sorted for DNA extraction and sequencing. B, Distribution of variant allelic frequencies (VAFs) for myeloid (IDH2, DNMT3A) and NRAS mutations across subpopulations of cells in ETP-ALL1.

Supplemental Figure 12. Clonal dynamics of ALL with MyM.

Supplemental Figure 13. Two CH mutations (TP53 and DNMT3A) were detectable seven years before the diagnosis of therapy-related ALL22.

Supplemental Figure 14. Clonal evolution of B-ALL2.

Supplemental Figure 15. Lymphoblasts from B-ALL with MyM are characterized by their resistance to cytotoxic chemotherapy.

Supplemental Figure 16. Curves showing viability of primary human B-ALL samples with TP53 mutation (n= 14), MyM (n= 16) and no MyM/TP53 (n= 24), treated with vincristine, doxorubicin, and blinatumomab at escalating doses.

Supplemental Figure 17. Flow cytometry plots showing ALL22 (TP53-mutated B-ALL) sample treated with escalating doses of blinatumomab.

Supplemental Figure 18. A, CR with MRD negativity rates in Ph-negative B-ALL patients treated with pediatric regimens, stratified based on age, gender, and treatment site. B, CR with MRD negativity rates in Ph-negative B-ALL patients treated with hyper-CVAD, stratified based on age, gender, and treatment site. C, CR with MRD negativity rates in Ph-negative B-ALL patients treated with inotuzumab.

Supplemental Figure 19. A, MHC class I and II antigen expression in blasts from B-ALL with MyM vs B-ALL without MyM/TP53. B, Comparison of genes implicated in blinatumomab resistance in B-ALL with vs without MyM/TP53.