Leukemic CD34⁺ and CD34⁻ populations share clonal structures. (A–D) Partial differentiation arrest leads to expansion of an LSC-containing CD34⁻CD117⁺ population. (i) Clonal composition of FACS-purified populations using data from single-cell mutation–specific genotyping. (ii) Clonal hierarchy of AML based on single-cell genotyping. Numbers within the circles indicate the percentage that each clone comprises within a Lin⁻ MNC population. Numbers outside the circles indicate the number of cells called with each genotype. The asterisk indicates genotypes that were detected in less than three cells where they were called with <99% confidence because of ADO. Genotypes detected in more than two cells could be called with 99% confidence. (iii) The proportions of normal BM CD34⁺, GM-pre (CD34⁻117⁺), GM-mat (CD34⁻117⁻), other myeloid mature, and NK cell populations and erythroid precursors (Ery-pre; CD34⁻244⁺117⁺) are shown on the left for comparison with that observed in CD34⁻ AML (right), showing expansion or contraction of populations. Within each leukemic population, the contribution of each clone is shown using data from panel i. Data are also in Table S6 G. (iv) Numbers of cells of FACS-purified populations injected into immunodeficient mice, estimated number of cells of each clone based on results in panel iii, and type of leukemic clones engrafted in each mouse are shown. Where more than one clone is detected in a mouse, circle size denotes major and minor clones. Engrafted clones may be serially engrafted in subsequent secondary and tertiary transplants. NE, no engraftment. Data from four patients and the number of single cells analyzed per population are shown. (A) Patient #880: CD34⁺, n = 18; CD34⁻CD117⁺, n = 20; CD34⁻CD117⁻, n = 20. (B) Patient #1037: CD34⁺, n = 16; CD34⁻CD117⁺, n = 18; CD34⁻CD117⁻, n = 20. (C) Patient #044: CD34⁺, n = 18; CD34⁻CD117⁺, n = 32; CD34⁻CD117⁻, n = 18. (D) Patient #059: CD34⁺, n = 25; CD34⁻CD117⁺, n = 14; CD34⁻CD117⁻, n = 14.