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Fig. 2 | Genome Biology

Fig. 2

From: Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications

Fig. 2

Manifestation of how SNPs at CpG/SBE sites can affect the Infinium assay. U/M plots, MAF estimation, and probe design of a SNPs disguising as A U (SNP = U) or B M epiallele (SNP = M), C of a SNP causing probe failure (SNP = PF) and D of a SNP at an SBE site of a type I probe causing detection channel switch or E not. Cluster counts were estimated from U/M plots via bivariate Gaussian mixture models; only concordant monozygotic twin pairs were taken into account in the computation of MAF (genetic control); MZ twin-to-twin agreement matrices are also available on the plots employing the same color coding as the clusters in the U/M plot. Probe designs are highlighted in yellow boxes and SNPs are denoted in bold red. Reported MAFs correspond to 1000 genomes (phase 3) of EUR ancestry (n = 1006)

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