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Table 1 Predicted impact of SNPs in the interrogated CpG on methylation readout using Infinium I probes

From: Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies

  1. *see also Fig. 4c.
  2. Interrogated CpG sites are underlined and bolded. BCD — bisulfite converted DNA; NR — not relevant (no CpG in the genomic sequence); strikethrough — mismatch between the probe and the interrogated locus; highlighted italics — incorporated fluorescently labeled ddNTPs; highlighted dots adjacent to the 3′-most position of the probe — no probe extension; lower case “gc” and “ac” in the, respectively, M and U probe sequences should be complementary to CpGs and TpGs under a probe (methylation status concordant with that of the interrogated dicnucleotide); “YG” in the BCD sequence indicates that the methylation status of the under-a-probe CpGs cannot be predicted when the interrogated dinucleotide contains SNP