Figure 2.
Genetic architecture of the established leukemia mouse models. (A) Mutations induced by CRISPR/Cas9 gene editing and spontaneously acquired during leukemia clonal evolution. Each column is a different mouse. For each gene, all variants are reported in supplemental Tables 11 and 12. In metadata, each tumor model is represented by a different color. (B) Copy number changes from whole-exome sequencing and visualized by Integrative Genomics Viewer (Igv) show gross aneuploidies in samples with Trp53 mutations. Blue indicates deletions; red indicates gains. (C) Schematic workflow of single-cell DNA-sequencing performed on representative established mouse models of AEL (n = 8, samples: 2 primary, 4 secondary, 1 tertiary, and 1 quaternary tumor). Bar plot showing cooccurrence of mutations in cells from mouse #587 (secondary passage) (D) and from mouse #588 (E) sample. In panel D, the large non-frameshift deletion in Trp53 (p.R155-172del) was not detectable by this assay and not included in this analysis. However, from bulk sequencing, variant allele frequency was 77%, suggesting it can be a founder event. (F) Fish plot showing acquisition of mutations in serial transplants (from primary to quaternary passage, mouse IDs are 768, 583, 941, and 962, respectively). The genes with homozygous mutations are in bold. In secondary passage, gain of Kit and Fancd2 mutations drove clonal expansion (blue clone). Minor clones include cells with a different heterozygous or homozygous combination of mutations of Tp53, Dnmt3a, and Kif1a. Bcor deletions are reported in supplemental Table 13. However, because the mean amplicon number among cells was low, we chose not to use it for clonal analysis. (G) Fish plot showing acquisition of mutations from a primary mouse model with AEL (mouse ID 1695) to a secondary passage with mixed AEL/B-ALL (mouse ID 594). The suffix “_2” in TP53 T167fs_2 describes a frameshift mutation due to a deletion of 2 nucleotides. In TP53 T167fs, the frameshift mutation is due to a nucleotide insertion. The genes with homozygous mutations are in bold. In panels F and G, the symbol “/” means “and” (cooccurrence of mutations). GFP, green fluorescent protein; RFP, red fluorescent protein; WT, wild type.

Genetic architecture of the established leukemia mouse models. (A) Mutations induced by CRISPR/Cas9 gene editing and spontaneously acquired during leukemia clonal evolution. Each column is a different mouse. For each gene, all variants are reported in supplemental Tables 11 and 12. In metadata, each tumor model is represented by a different color. (B) Copy number changes from whole-exome sequencing and visualized by Integrative Genomics Viewer (Igv) show gross aneuploidies in samples with Trp53 mutations. Blue indicates deletions; red indicates gains. (C) Schematic workflow of single-cell DNA-sequencing performed on representative established mouse models of AEL (n = 8, samples: 2 primary, 4 secondary, 1 tertiary, and 1 quaternary tumor). Bar plot showing cooccurrence of mutations in cells from mouse #587 (secondary passage) (D) and from mouse #588 (E) sample. In panel D, the large non-frameshift deletion in Trp53 (p.R155-172del) was not detectable by this assay and not included in this analysis. However, from bulk sequencing, variant allele frequency was 77%, suggesting it can be a founder event. (F) Fish plot showing acquisition of mutations in serial transplants (from primary to quaternary passage, mouse IDs are 768, 583, 941, and 962, respectively). The genes with homozygous mutations are in bold. In secondary passage, gain of Kit and Fancd2 mutations drove clonal expansion (blue clone). Minor clones include cells with a different heterozygous or homozygous combination of mutations of Tp53, Dnmt3a, and Kif1a. Bcor deletions are reported in supplemental Table 13. However, because the mean amplicon number among cells was low, we chose not to use it for clonal analysis. (G) Fish plot showing acquisition of mutations from a primary mouse model with AEL (mouse ID 1695) to a secondary passage with mixed AEL/B-ALL (mouse ID 594). The suffix “_2” in TP53 T167fs_2 describes a frameshift mutation due to a deletion of 2 nucleotides. In TP53 T167fs, the frameshift mutation is due to a nucleotide insertion. The genes with homozygous mutations are in bold. In panels F and G, the symbol “/” means “and” (cooccurrence of mutations). GFP, green fluorescent protein; RFP, red fluorescent protein; WT, wild type.

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