(A) Schematic of the phenotypic, genetic, and epigenetic characterization of KMT2A-AFF1 cells generated through CRISPR/Cas9-mediated gene editing. PDX, patient-derived xenograft. (B) FISH analysis of cells (day 26 in vitro culture) for KMT2A translocation using KMT2A break apart probes. (C) Survival curves for xeno-transplanted mice showing mean latencies for development of primary (n = 18) and secondary (n = 9) leukemias, respectively. P value was generated using Mantel-Cox log-rank test. **P < 0.01; ***P < 0.001. (D) Percentage of cells from gene-edited KMT2A-AFF1 BCP-ALL and diagnostic KMT2A-AFF1 BCP-ALL patient bone marrow classified into developmental populations. HSC, hematopoietic stem cell; CLP, common lymphoid progenitor. (E) t-SNE projections of normal controls, gene-edited BCP-ALL, patient samples, and PDX and human cell lines, where each cell is represented by a dot within color-coded clusters. (F) Unsupervised hierarchical clustering of Spearman’s correlations from ATAC-Seq data of gene-edited KMT2A-AFF1 BCP-ALLs, gene-edited KMT2A-MLLT3 leukemias (acute myeloid leukemia [AML], ALL, mixed-phenotype acute leukemia [MPAL]), KMT2A-AFF1 patient samples, and KMT2A-AFF1 human cell lines. (G) Principal component analysis of RNA-Seq data from gene-edited BCP-ALLs, gene-edited leukemias (AML, ALL, MPAL), patient samples, and human cell lines.