Battle of epigenetic proportions: comparing Illumina’s EPIC methylation microarrays and TruSeq targeted bisulfite sequencing

ABSTRACT

DNA methylation microarrays have been the platform of choice for epigenome-wide association studies in epidemiology, but declining costs have rendered targeted bisulphite sequencing a feasible alternative. Nonetheless, the literature for researchers seeking guidance on which platform to choose is sparse. To fill this gap, we conducted a comparison study in which we processed cord blood samples from four newborns in duplicates using both the Illumina HumanMethylationEPIC BeadChip and the Illumina TruSeq Methyl Capture EPIC Kit, and evaluated both platforms in regard to coverage, reproducibility, and identification of differential methylation. We conclude that with current analytic goals microarrays still outperform bisulphite sequencing for precise quantification of DNA methylation.

KEYWORDS:

• DNA methylation
• EWAS
• microarray
• bisulphite sequencing
• comparison of experimental platforms

Acknowledgments

We would like to thank the staff of the Epigenomics Core Facility at Weill Cornell Medicine for running the TruSeq assay.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by National Institute of Environmental Health Sciences grants R00ES023450, R01ES020268, R01ES013744, R24ES028522, R01ES021357-04S1 and P30ES023515.