Figure S2.

Colony genotyping mutation tracing to phenotypic HSCs in JMML–QC (related to Fig. 3). (A) Diagram of the workflow for single-cell genotyping. (B) Pathway for samples analysis. (C–E) Variant allele frequency (VAF) and coverage of amplicons sequenced and that passed QC from patient-derived colonies and CB controls. (ID1, n = 129 cells used for analysis; ID15, n = 71 cells used for analysis; and ID5, n = 34 cells used for analysis). (F) VAF and coverage of amplicons sequenced from patient-derived colonies (ID5) after BMT and CB controls (ID5 after BMT, n = 65 cells used for analysis). (G) Examples of coverage of amplicons from heterozygous SNPs used to calculate the allelic dropout of the method. (H) Summary of amplicons from heterozygous SNPs for each sequencing run; coverage applied and allelic dropout for each amplicon. Six independent experiments; details for number of colonies are outlined in the Materials and methods section.