Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes

TLDR

Illumina Infinium DNA methylation BeadChips are the most widely used genome‑scale methylation assays, yet probe masking strategies are largely ad hoc and the newer EPIC array remains poorly characterized. This study aims to comprehensively characterize probes on the EPIC and HM450 microarrays. The authors assess probe mappability to the latest genome build, 3′ nested subsequence copy number, polymorphism effects, and identify a previously unrecognized color‑channel switch for Type I probes. They establish empirical exclusion criteria for underperforming probes, add 1,052 SNP probes to the EPIC array and demonstrate their use for ethnicity prediction, and introduce an out‑of‑band color‑channel application that repurposes 62,371 probes as internal bisulfite‑conversion controls.

Abstract

Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3΄ nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes. We show empirical evidence for exclusion criteria for underperforming probes, providing a sounder basis than current ad hoc criteria for exclusion. In addition, we describe novel probe uses, exemplified by the addition of a total of 1052 SNP probes to the existing 59 explicit SNP probes on the EPIC array and the use of these probes to predict ethnicity. Finally, we present an innovative out-of-band color channel application for the dual use of 62 371 probes as internal bisulfite conversion controls.