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Lookup NU author(s): Dr Anthony Watson, Dr Kirsten BrandtORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© The Author(s) 2024.The Illumina Methylation array platform has facilitated countless epigenetic studies on DNA methylation (DNAme) in health and disease, yet relatively few studies have so studied its reliability, i.e., the consistency of repeated measures. Here we investigate the reliability of both type I and type II Infinium probes. We propose a method for excluding unreliable probes based on dynamic thresholds for mean intensity (MI) and ‘unreliability’, estimated by probe-level simulation of the influence of technical noise on methylation β values using the background intensities of negative control probes. We validate our method in several datasets, including newly generated Illumina MethylationEPIC BeadChip v1.0 data from paired whole blood samples taken six weeks apart and technical replicates spanning multiple sample types. Our analysis revealed that specifically probes with low MI exhibit higher β value variability between repeated samples. MI was associated with the number of C-bases in the respective probe sequence and correlated negatively with unreliability scores. The unreliability scores were substantiated through validation in a new EPIC v1.0 (blood and cervix) and a publicly available 450k (blood) dataset, as they effectively captured the variability observed in β values between technical replicates. Finally, despite promising higher robustness, the newer version v2.0 of the MethylationEPIC BeadChip retained a substantial number of probes with poor unreliability scores. To enhance current pre-processing pipelines, we developed an R package to calculate MI and unreliability scores and provide guidance on establishing optimal dynamic score thresholds for a given dataset.
Author(s): Nazarenko T, Vavourakis CD, Jones A, Evans I, Schreiberhuber L, Kastner C, Ishaq-Parveen I, Redl E, Watson AW, Brandt K, Carter C, Zaikin A, Herzog CMS, Widschwendter M
Publication type: Article
Publication status: Published
Journal: Clinical Epigenetics
Year: 2024
Volume: 16
Issue: 1
Online publication date: 18/09/2024
Acceptance date: 31/08/2024
Date deposited: 02/10/2024
ISSN (print): 1868-7075
ISSN (electronic): 1868-7083
Publisher: BioMed Central Ltd
URL: https://doi.org/10.1186/s13148-024-01739-2
DOI: 10.1186/s13148-024-01739-2
Data Access Statement: The raw methylation data from the Repeatability set is available under controlled-access under the accession number EGAS00001007184 from the European Genome-phenome Archive (EGA), which is hosted by the EBI and the CRG. Raw DNA methylation data from the TACT study is not deposited to a public repository, because volunteers did not specifically consent to make data containing genetic information (that could identify individuals) publicly available. Preprocessed data with probes at SNP positions removed can be made available upon request from researchers in countries compliant with GDPR law only. The R code for calculation of the MI and unreliability scores is available in a GitHub repository (https://github.com/ChVav/epicMI) [20].
PubMed id: 39289706
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