A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing

Abstract

The Illumina Infinium(R) MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are used for hypothesis generation or pilot studies, the natural conclusion is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system. However, BSAS correlated less well with EPIC array data when the magnitude of change via EPIC array was greater than 5%, suggesting that this lower specificity at larger differential methylation values is a consequence of PCR amplification that BSAS requires. However, our data suggests that BSAS does offer advantages that the EPIC array: BSAS amplifies a region of the genome (~500bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system.