ArticleEpigenomics2012
MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples.
Article in Epigenomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 2 of them syntheses 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
50 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings.Molecular psychiatry · 2020Pooled it
- DNA methylation in peripheral tissue of schizophrenia and bipolar disorder: a systematic review.BMC genetics · 2016Pooled it
- Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome.Epigenetics · 2022Article
- Can epigenetics shine a light on the biological pathways underlying major mental disorders?Psychological medicine · 2022Review
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- DNA methylation of the KLK8 gene in depression symptomatology.Clinical epigenetics · 2021Article
- Review
- In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants.Plants (Basel, Switzerland) · 2021Review
- A methylation study of long-term depression risk.Molecular psychiatry · 2020Article
- MBD-seq - realities of a misunderstood method for high-quality methylome-wide association studies.Epigenetics · 2020Article
- Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences.Schizophrenia bulletin · 2020Article
- Novel genes exhibiting DNA methylation alterations in Korean patients with chronic lymphocytic leukaemia: a methyl-CpG-binding domain sequencing study.Scientific reports · 2020Article
- Progress toward liquid biopsies in pediatric solid tumors.Cancer metastasis reviews · 2019Review
- Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice.Aging cell · 2019Article
- Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes.PloS one · 2019Article
- A Whole Methylome Study of Ethanol Exposure in Brain and Blood: An Exploration of the Utility of Peripheral Blood as Proxy Tissue for Brain in Alcohol Methylation Studies.Alcoholism, clinical and experimental research · 2018Article
- Convergence of evidence from a methylome-wide CpG-SNP association study and GWAS of major depressive disorder.Translational psychiatry · 2018Article
- Epigenetic Aging in Major Depressive Disorder.The American journal of psychiatry · 2018Article
- Article
- Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray.PloS one · 2018Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
aimWe studied the use of methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) as a cost-effective screening tool for methylome-wide association studies (MWAS). MATERIALS &
methodsBecause MBD-seq has not yet been applied on a large scale, we first developed and tested a pipeline for data processing using 1500 schizophrenia cases and controls plus 75 technical replicates with an average of 68 million reads per sample. This involved the use of technical replicates to optimize quality control for multi- and duplicate-reads, an in silico experiment to identify CpGs in loci with alignment problems, CpG coverage calculations based on multiparametric estimates of the fragment size distribution, a two-stage adaptive algorithm to combine data from correlated adjacent CpG sites, principal component analyses to control for confounders and new software tailored to handle the large data set.
resultsWe replicated MWAS findings in independent samples using a different technology that provided single base resolution. In an MWAS of age-related methylation changes, one of our top findings was a previously reported robust association involving GRIA2. Our results also suggested that owing to the many confounding effects, a considerable challenge in MWAS is to identify those effects that are informative about disease processes.
conclusionThis study showed the potential of MBD-seq as a cost-effective tool in large-scale disease studies.
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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.