ArticleBMC genomics2014
Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 11 of them syntheses 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.
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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
100 citing papers in PubMed, 11 syntheses or guidelines pooled it, 172 citations in OpenAlex.
- Associations of maternal night shift work during pregnancy with DNA methylation in offspring: a meta-analysis in the PACE consortium.Clinical epigenetics · 2025Pooled it
- Animal and plant protein intake during infancy and childhood DNA methylation: a meta-analysis in the NutriPROGRAM consortium.Epigenetics · 2024Pooled it
- Pooled it
- Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence.Molecular psychiatry · 2024Pooled it
- Pooled it
- A meta-analysis of epigenome-wide association studies on pregnancy vitamin B12 concentrations and offspring DNA methylation.Epigenetics · 2023Pooled it
- Maternal Mediterranean diet in pregnancy and newborn DNA methylation: a meta-analysis in the PACE Consortium.Epigenetics · 2022Pooled it
- DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies.Genome medicine · 2020Pooled it
- Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight.Nature communications · 2019Pooled it
- Maternal alcohol consumption and offspring DNA methylation: findings from six general population-based birth cohorts.Epigenomics · 2018Pooled it
- Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium.Human molecular genetics · 2017Pooled it
- Trial
- Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma.bioRxiv : the preprint server for biology · 2026Article
- Artificial Intelligence Design for Race-Based Prostate Cancer Stage Classification With Multilayer Perceptron: Feature Selection Optimization Approach.JMIR formative research · 2026Article
- MethylModes: computationally efficient detection of multimodal distributions in DNA methylation data.Bioinformatics (Oxford, England) · 2026Article
- Article
- fSuSiE enables fine-mapping of QTLs from genome-scale molecular profiles.bioRxiv : the preprint server for biology · 2025Article
- Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.Cell reports · 2025Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, certain genomic factors may compromise the ability to measure methylation using the array such as single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), repetitive DNA, and regions with reduced genomic complexity. Currently, there is no clear method or pipeline for determining which of the probes on the HM450K bead array should be retained for subsequent analysis in light of these issues.
resultsWe comprehensively assessed the effects of SNPs, INDELs, repeats and bisulfite induced reduced genomic complexity by comparing HM450K bead array results with whole genome bisulfite sequencing. We determined which CpG probes provided accurate or noisy signals. From this, we derived a set of high-quality probes that provide unadulterated measurements of DNA methylation.
conclusionsOur method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide. Additionally, we demonstrate the utility of our method through extraction of biologically relevant epigenetic changes in prostate cancer.
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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.