Evidence map›Paper›PMID 40098449›Full record

ArticleEpigenomics2025

Development and validation of a novel cell type estimation method for targeted bisulfite sequencing data.

F Berg, E Köper, A S Limberg, K Mattonet, B Budeus, R Kumsta, E M Hummel, D A Moser

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Epigenomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

8 authors.

F BergDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
E KöperDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
A S LimbergDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
K MattonetDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
B BudeusInstitute of Cell Biology, Medical Faculty, University of Duisburg-Essen, Essen, Germany.
R KumstaDepartment of Behavioural and Cognitive Sciences, Laboratory for Stress and Gene-Environment Interplay, University of Luxemburg, Esch-sur-Alzette, Luxemburg.
E M HummelDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
D A MoserDepartment of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

aimsEpidemiological studies of DNA methylation often use buccal swabs, which contain mixtures of cell types, but no low-cost methods exist for statistical correction in candidate gene studies using targeted bisulfite sequencing. This study aims to address this gap by estimating the proportion of buccal epithelial cells in swab and mouthwash samples. MATERIALS &

methodsWe applied a recently described and smoothly to implement method for estimating the proportion of buccal epithelial cells in buccal swab and mouthwash samples using targeted bisulfite sequencing. Additionally, we investigated the methylation of

resultsThe proposed estimation method showed strong correlation with the EpiDISH algorithm and effectively controlled for cellular heterogeneity. Over 90% of the variance in

conclusionOur findings provide a solution for controlling cellular heterogeneity in buccal swab and mouthwash DNA methylation studies. This method is particularly relevant for candidate gene studies in clinical settings, but future work should refine it for more detailed analyses of cell type proportions to improve precision.

Indexed as

DNA MethylationMouth MucosaSequence Analysis, DNAActininAlgorithmsEpithelial CellsFemaleHumansMaleSulfitesActininhydrogen sulfiteSulfitesacute stressbuccal swabscell type estimationscellular heterogeneityDNA methylationepigeneticsEWAStargeted bisulfite sequencing

Identifiers

PMID40098449
PMCPMC11980480

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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.