ArticleEpigenomics2018
Positional effects revealed in Illumina methylation array and the impact on analysis.
Article in Epigenomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies.BMC research notes · 2021Pooled it
- Blood DNA methylation and breast cancer risk: a prospective nested case-control study.EBioMedicine · 2026Article
- Parkinson's disease-associated alterations in DNA methylation and hydroxymethylation in human brain.NPJ Parkinson's disease · 2025Article
- A comprehensive guide to genomeZhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2025Review
- Serotonin Transporter (SLC6A4) and FK506-Binding Protein 5 (FKBP5) Genotype and Methylation Relationships with Response to Meditation in Veterans with PTSD.Molecular neurobiology · 2024Article
- Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain in PD-related genes, including PARK19 (DNAJC6) and PTPRN2 (IA-2β).Research square · 2024Article
- Differential Impact of Smoking on Methylome and Transcriptome in Crohn's Disease and Ulcerative Colitis.Inflammatory bowel diseases · 2024Article
- A higher dysregulation burden of brain DNA methylation in female patients implicated in the sex bias of Schizophrenia.Molecular psychiatry · 2023Article
- Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: the Framingham Heart Study.Scientific reports · 2023Article
- Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments.BMC bioinformatics · 2023Article
- A Higher Dysregulation Burden of Brain DNA Methylation in Female Patients Implicated in the Sex Bias of Schizophrenia.Research square · 2023Article
- Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts.Epigenetics · 2022Article
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- ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells.Database : the journal of biological databases and curation · 2022Article
- Evaluating the challenges and reproducibility of studies investigating DNA methylation signatures of psychological stress.Epigenomics · 2022Review
- Prenatal stress leads to deficits in brain development, mood related behaviors and gut microbiota in offspring.Neurobiology of stress · 2021Article
- Reduction in Epigenetic Age Acceleration Is Related to Empathy in Mothers with Neglectful Caregiving.Brain sciences · 2021Article
- SLC25A24 gene methylation and gray matter volume in females with and without conduct disorder: an exploratory epigenetic neuroimaging study.Translational psychiatry · 2021Article
- DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations.Molecular psychiatry · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
aimWe aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS &
methodsThree HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods.
resultsWe detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results.
conclusionPositional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.
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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.