Fig. 2
From: “Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Predicted 450k signal for SNPs present at the interrogated CpG site. On the left, in the “DNAm state” column, we show the expected signal for methylated and unmethylated CpG states, when no SNP is present, for both Type I and II probe designs. Middle (“C site SNP”) and right columns (”G site SNP”) provide expected signals for SNPs in the C and G nucleotide positions, respectively. For all columns, S signal, NS no signal, G and R denote red and green channel signals, respectively. mCG represents methylated cytosine. IM and IU denote probe design type I methylated and unmethylated probe types, respectively; II denotes probe type II. For type I design, methylated probes fluoresce and unmethylated probes yield no signal when methylation is present. The type II design fluoresces in the green and red channels for methylated and unmethylated states, respectively. For forward strand interrogated CpG sites (top), a C to G SNP mimics the methylated state; C to A and C to T SNPs mimic the unmethylated state for Type II probes but result in no signal for the Type I design. One exception is for a C to T SNP because it mimics post-bisulfite converted unmethylated Cs. G site SNPs on the forward strand produce no signal for both probe designs because they inhibit single-base extension. Reverse strand probes (bottom) are defined relative to the top strand, so the expected signal scenarios are the converse of what is expected for the forward strand (i.e., G site with some signal, C site with comprehensively no signal)