Longitudinal tracking of malignant cell clones reveals insufficient clearing from progenitor cell populations. (A) Median variant allele frequency of recurrent somatic mutations in bone marrow aspirates of responders (blue) and NR (red) at screening, after 4 cycles of decitabine and ipilimumab (C4) and at end of treatment. Statistical testing using Wilcoxon rank-sum test. (B) Cancer cell fractions calculated from whole exome sequencing of bone marrow aspirates at screening and C4 in AML1007, AML1008 and AML1019 (all responders). (C) Identification of 2 distinct AML subclones defined by amp(8) in pink and amp(21) in cyan using inferCNV. Longitudinal tracking of both clones within the HSC-like compartment (right). (D) Longitudinal tracking of donor chimerism across myeloid cell subsets of responders (blue) and NRs (red). Disease burden (% blasts) obtained from routine clinical diagnostics with 5% mark indicated by horizontal bar. Grey indicates no data available. (E) Longitudinal detection of copy number changes across myeloid subsets. Grey indicates no data available or too few cells to perform analysis of copy number changes.