ReviewClinical epigenetics2016
Establishing an analytic pipeline for genome-wide DNA methylation.
Review in Clinical epigenetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 2 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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 2 syntheses or guidelines pooled it, 50 citations in OpenAlex.
- An epigenome-wide association study of early-onset major depression in monozygotic twins.Translational psychiatry · 2020Pooled it
- DNA methylation studies of depression with onset in the peripartum: A critical systematic review.Neuroscience and biobehavioral reviews · 2019Pooled it
- DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.Clinical epigenetics · 2025Review
- FBLN2 promoter hypermethylation: a negative prognostic biomarker and anti-PD-1 response predictor in clear cell renal cell carcinoma via high-throughput CpG Island screening.Clinical epigenetics · 2025Article
- Integrative Machine Learning Framework for Enhanced Subgroup Classification in Medulloblastoma.Healthcare (Basel, Switzerland) · 2025Article
- Defective X-chromosome inactivation and cancer risk in women.Communications biology · 2025Article
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- Article
- Study protocol for the Mindful Moms Study: A randomized controlled trial evaluating a mindful movement intervention for marginalized pregnant people experiencing depression.Contemporary clinical trials · 2023Article
- Cross-tissue correlations of genome-wide DNA methylation in Japanese live human brain and blood, saliva, and buccal epithelial tissues.Translational psychiatry · 2023Article
- Article
- Differential Methylation Analysis of Suicidal Ideation Severity in Schizophrenia with the Illumina MethylationEPIC Array.Healthcare (Basel, Switzerland) · 2022Article
- Differential DNA Methylation and Cardiometabolic Risk in African American Mother-Adolescent Dyads.Biological research for nursing · 2022Article
- Social epigenomics: are we at an impasse?Epigenomics · 2021Review
- Effect of DNA methylation on gene transcription is associated with the distribution of methylation sites across the genome in osteoarthritis.Experimental and therapeutic medicine · 2021Article
- DNA Methylation Markers from Negative Surgical Margins Can Predict Recurrence of Oral Squamous Cell Carcinoma.Cancers · 2021Article
- Epigenome-Wide Study of Posttraumatic Stress Disorder Symptom Severity in a Treatment-Seeking Adolescent Sample.Journal of traumatic stress · 2021Article
- Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease.Scientific reports · 2021Article
- Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth.Epigenetics · 2020Article
- Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer.Experimental & molecular medicine · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
The need for research investigating DNA methylation (DNAm) in clinical studies has increased, leading to the evolution of new analytic methods to improve accuracy and reproducibility of the interpretation of results from these studies. The purpose of this article is to provide clinical researchers with a summary of the major data processing steps routinely applied in clinical studies investigating genome-wide DNAm using the Illumina HumanMethylation 450K BeadChip. In most studies, the primary goal of employing DNAm analysis is to identify differential methylation at CpG sites among phenotypic groups. Experimental design considerations are crucial at the onset to minimize bias from factors related to sample processing and avoid confounding experimental variables with non-biological batch effects. Although there are currently no de facto standard methods for analyzing these data, we review the major steps in processing DNAm data recommended by several research studies. We describe several variations available for clinical researchers to process, analyze, and interpret DNAm data. These insights are applicable to most types of genome-wide DNAm array platforms and will be applicable for the next generation of DNAm array technologies (e.g., the 850K array). Selection of the DNAm analytic pipeline followed by investigators should be guided by the research question and supported by recently published methods.
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What OpenQuestion holds
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.