Are probes flagged as cross-reactive on Illumina's Methylation 450K still flagged on the EPIC methylation array?

Question

[dodausp]

Hi there!

My question is pretty straightforward: are those probes described on Chen et al., 2012 paper for Illumina's 450K methylation array still valid for the EPIC version? If not, would there be an updated list of probes? Or would you skip that filtering step from your pipeline when performing EPIC array analysis?

Thanks in advance!

Answer 1

[Basti]

Hi, I personally use the dropXreactiveLoci function from the maxprobes package in my pipeline. As you can see on their GitHub page, they collected cross-reactive identified probes on both EPIC and 450k from 4 studies : https://github.com/markgene/maxprobes