Fig. 1

Epigenetic biomarker for hematopoietic stem and progenitor cells. A Candidate CpG sites to discriminate HSPCs (GSE72867) from other leukocytes (GSE35069) were selected based on the difference in mean DNAm levels (β-value) and variation of β-values within these two groups. B DNAm levels of the three candidate CpGs are depicted in independent DNAm profiles (n = 301) of 42 studies (Additional file 1: Table S1). C DNAm levels at the three relevant CpGs in the genes MYO1D, STK17A, and SP140 were analyzed with pyrosequencing in dilutions of CD34⁺ HSPCs from mobilized peripheral blood (mPB, n = 2) and cord blood (CB, n = 3), measured with flow cytometry. D Multivariable models for the three CpGs were trained on the dilution data for mPB or CB. These models were then applied to estimate the fraction of HSPCs in different types of frozen samples (mPB model for PB, mPB, CD34⁺ BM cells, and apheresis samples; CB model for CB). E Estimates of HSPC counts based on the mPB multivariable model were compared to flow cytometric CD34 measurements in mPB (n = 9). F The CB HSPC predictor was applied to individual colonies in colony forming units (CFUs). G Correlation of DNAm at the CpG in MYO1D (cg00164282) with manual counts of blasts in leukemic samples (n = 39). Correlations were assessed by Pearson correlation coefficient r