Fig. 1

Enhanced probe mapping and applicability of EPICv2 in diverse human populations. A Total number of Infinium DNA methylation BeadChip studies and deposited datasets in GEO. B Probe counts for HM450, EPICv1, EPICv2, and unique prefix counts for EPICv2. Abbreviations: “cg”: CpG cytosine methylation probes; “ch”: non-CG cytosine methylation probes; “rs”: common SNP probes; “nv”: probes for somatic mutations found in cancer; and “ct”: quality control probes. C Venn diagram illustrating the percentage of EPICv2 probes retained from predecessor arrays. D Infinium-I and Infinium-II chemistry ratios for EPICv1 and EPICv2 probes. EPICv2 data is from all probes, same as panel B. E Infinium-I and Infinium-II chemistry ratios for shared EPICv1-v2 probes and exclusive EPICv1/EPICv2 probes. F Mapping quality of EPICv1 and EPICv2 probes, differentiated by allele A and allele B. G Proportion of probes masked due to ancestry-specific SNP overlaps. Abbreviations: AFR, African population; AMR, Admixed American; EAS, East Asian; EUR, European; SAS, South Asian. H Percentage of probes with cross-reactivity and sequence polymorphism influence issues, comparing shared EPICv1-EPICv2 and EPICv1-only probes