Correlation of Infinium HumanMethylation450K andMethylationEPIC BeadChip arrays in cartilage

BackgroundDNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying 865859 CpG sites, almost double the number of sites present on the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms.\n\nMethodsDNA methylation was measured in 21 human cartilage samples using the Illumina Infinium Methylation450K BeadChip and the Infinium methylationEPIC array. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833 respectively. Data were processed using the Bioconductor package Minfi. Additionally, DNA methylation of six CpG sites was validated for the same 21 cartilage samples by use of pyrosequencing.\n\nResultsIn cartilage samples, overall sample correlations between methylation values generated by the two arrays were high (Pearson correlation coefficient r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulfite pyrosequencing did not highlight one array as generating more accurate methylation values that the other. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour and whole blood, reflecting the difference in methylation variance between cell types. These patterns can be observed across different tissues with different CpG site variances. When performing differential methylation analysis, the mean probe correlation co-efficient increased with increasing {Delta}{beta} threshold used.\n\nConclusionCpG sites with low variability within a tissue showed poor reproducibility between arrays. However, variance and thus reproducibility differs across different tissue types. Therefore, researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of platform or method used to assay methylation.