Comparison of Infinium MethylationEPIC v2.0 to v1.0 for human population epigenetics: considerations for addressing EPIC version differences in DNA methylation-based tools.
Beryl C ZhuangMarcia Smiti JudeChaini KonwarCalen P RyanJoanne WhiteheadHannah-Ruth EngelbrechtJulia L MacIsaacKristy DeverTran Khanh ToanKim KorinekZachary ZimmerKim M HuffmanNanette R LeeThomas W McDadeChristopher W KuzawaDaniel W BelskyMichael S KoborPublished in: bioRxiv : the preprint server for biology (2024)
Our findings indicate that EPIC version differences predominantly explain DNA methylation variation and influence estimates of DNA methylation-based tools, and therefore we recommend caution when combining cohorts run on different versions. We demonstrate the importance of calculating DNA methylation-based estimates separately for each EPIC version or accounting for EPIC version either as a covariate in statistical models or by using version correction algorithms.