SynthesisBMC research notes2021
An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies.
Synthesis in BMC research notes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A cell-type-resolved meta-analysis reveals glial DNA methylation changes associated with aging and Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Pooled it
- Differences in immune cell profiles around the time of islet autoimmunity seroconversion in children with and without type 1 diabetes.BMJ open diabetes research & care · 2026Article
- Longitudinal changes in epigenetic age acceleration prior to type 1 diabetes onset in the Diabetes Autoimmunity Study in the Young (DAISY).BMJ open diabetes research & care · 2026Article
- DNA Methylation Smoking Scores and Risk of Islet Autoimmunity and Type 1 Diabetes.Diabetes care · 2025Article
- Examining cellular heterogeneity in human DNA methylation studies: Overview and recommendations.STAR protocols · 2025Review
- Prediction of Multiple Degenerative Diseases Based on DNA Methylation in a Co-Physiology Mechanisms Perspective.International journal of molecular sciences · 2024Article
- A novel approach toward optimal workflow selection for DNA methylation biomarker discovery.BMC bioinformatics · 2024Article
- Longitudinal changes in DNA methylation during the onset of islet autoimmunity differentiate between reversion versus progression of islet autoimmunity.Frontiers in immunology · 2024Article
- Associations between blood leukocyte DNA methylation and sustained attention in mid-to-late childhood.Epigenomics · 2023Article
- A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data.Clinical epigenetics · 2023Article
- Epigenetic-based age acceleration in a representative sample of older Americans: Associations with aging-related morbidity and mortality.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes.Current genomics · 2023Article
- DNA Methylation NearPediatric diabetes · 2023Article
- Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies.Epigenetics · 2022Article
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Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
objectiveIllumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over time create challenges for data harmonization within and between studies, many of which obtained data from the older 450K and newer EPIC platforms. The pre-processing pipeline for DNA methylation is not trivial, and influences the downstream analyses. Incorporating different platforms adds a new level of technical variability that has not yet been taken into account by recommended pipelines. Our study evaluated the performance of various tools on different versions of platform data harmonization at each step of pre-processing pipeline, including quality control (QC), normalization, batch effect adjustment, and genomic inflation. We illustrate our novel approach using 450K and EPIC data from the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort.
resultsWe found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.