I have DNA methylation data from the Illumina EPIC beadchip (information on 850 000 CpG site). Since SNPs can influence the methylation results, it is advised to filter CpG sites located close to SNPs. The question is how close.
I read that 10 base pairs is commonly used. But in the article of Zhou (2017, Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes) it is noted that the 10 base pair distance is too stringent, since >50% of the EPIC probes carry SNP annotations with a distance < 10 bp. They advice to use a distance of 5 base pairs.
Do you agree with this?
this link is useful
Article Bis-SNP: combined DNA methylation and SNP calling for Bisulf...
regards.
For the ones who are interested: I decided to go with the article of Zhou and used the 5 base pairs as cut off.
I realize this is an old post, but a SNP effects the methylation values across the full length of the probe (ie 50bp). See in the paper below for the me450 array.
"...we observed that the probe effect is present throughout the entire length of the 50 bp." Article SNPs located at CpG sites modulate genome-epigenome interaction
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