Fig. 6

Cross-reactivity of EPICv2 probes. a) Proportion of cross-hybridising EPICv2 probes targeting cytosines present on EPICv2 or previous versions of the Illumina methylation array. Number denotes the platform on which the probe first appeared. b) Composition of predicted off-target nucleotides for all cross-hybridising cg probes. c) Dinucleotide composition for all off-target cytosines. d) Scatterplot of root mean square errors (RMSE) between the methylation of 17,928 EPICv2 probes and matched WGBS methylation for the corresponding on-target CpG (x-axis), and between that probe and its most similar off-target CpG (y-axis). e) Root mean squared error (RMSE) between methylation of EPICv2 probes and their matched on-target WGBS methylation, grouped by evidence for cross-hybridisation. f-j) Scatterplots of EPICv2 M-values against matched WGBS methylation from Illumina manifest MAPINFO on-target (blue) and off-target CpGs (red) for five selected EPICv2 probes, with IlmnID in title. Black line represents the expected value of WGBS given EPICv2