EPICv2 Re-annotated Manifest version 1.0
Creators: name: Mallabar-Rimmer, Bethan
name: Wells, Philippa
name: Franklin, Alice
name: Mill, Jonathan
name: Webster, Amy P
Publisher: name: Zenodo
Year: 2025
Subjects: subject: DNA Methylation
subject: EPICv2 manifest
subject: EPICv2
subject: Epigenetics
subject: Epigenomics

description: Citation:

When using this manifest, please cite the associated BioRxiv paper: https://www.biorxiv.org/content/10.1101/2025.03.12.642895v1 

Summary:

The Illumina Infinium MethylationEPIC v2.0 BeadChip (EPICv2 array) is a DNA methylation array released by Illumina for assessment of the human epigenome.(1) The CpG sites on the EPICv2 array are annotated with an open-source file provided by Illumina, the EPICv2 manifest.(2)

We have re-annotated the EPICv2 manifest using GENCODE Human release 47 (GENCODEv47) data (3) to label intragenic features, and a distance-based approach to label the regulatory genome.

This annotation is substantially more comprehensive than the original EPICv2 annotation provided by Illumina. For example, the original EPICv2 manifest identifies just 317,598 sites targeted by the EPICv2 array as mapping to a gene, whereas we have found that 700,392 EPICv2 array sites are located within a gene body according to publicly available GENCODE Human release 47 (GENCODEv47) data.

The original EPICv2 manifest annotates 202,631 sites as being within 1500bp of a transcription start site (TSS). Using a distance based approach, we label 267,183 sites in total as being within promoter distance of a gene (<1500bp upstream or <500bp downstream of the TSS), and 140,123 sites as being within enhancer distance (1501-5000bp upstream of the TSS, not including sites within a gene body).

We also include a column indicating whether a site is located in any promoter or enhancer, according to the GeneHancer database. (4) The re-annotated manifest additionally labels which sites are required for the Horvath DNA Methylation Age Calculator (5) and MethylDetectR (6) epigenetic clocks, to facilitate data preparation for these tools.

We hope this resource will facilitate more complete assessment of CpGs associated with gene bodies and regulatory regions during interpretation of epigenetic studies conducted using EPICv2.

Data access:

For most purposes, we recommend using either EPICv2_reannotated_manifest_v1.0.csv.zip or EPICv2_reannotated_manifest_v1.0.rds . These files contain our novel annotation of genes and distance-based regulatory features etc., and we have removed redundant columns from the original manifest which annotated the same features.

The other two files (EPICv2_reannotated_manifest_forcomparison_v1.0.csv.zip and EPICv2_reannotated_manifest_forcomparison_v1.0.rds) contain the novel annotation and original Illumina annotation, with no redundant columns removed. This allows for comparison between the original annotation and our re-annotation, and reproducibility of findings.

Further description of the re-annotated manifest and findings will be submitted to BioRxiv within the next two weeks (current date: 26/02/2025).

 

References:

(1) Illumina. Infinium MethylationEPIC v2.0 Kit [Internet]. 2025 [cited 2025 Feb 24]. Available from: https://emea.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html

(2) Illumina. Infinium MethylationEPIC v2.0 Product Files [Internet]. 2024 [cited 2025 Feb 24]. Available from: https://emea.support.illumina.com/downloads/infinium-methylationepic-v2-0-product-files.html

(3) Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, et al. GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Res. 2025 Jan 6;53(D1):D966–75. 

(4) Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, et al. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database. 2017 Jan 1;2017:bax028. 

(5) Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013 Dec 10;14(10):3156. 

(6) Hillary RF, Marioni RE. MethylDetectR: a software for methylation-based health profiling. Wellcome Open Res. 2020;5:283.