Evidence map›Paper›PMID 39951379›Full record

ReviewSTAR protocols2025

Examining cellular heterogeneity in human DNA methylation studies: Overview and recommendations.

Maggie Po-Yuan Fu, Sarah Martin Merrill, Keegan Korthauer, Michael Steffen Kobor

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in STAR protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Maggie Po-Yuan FuBC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Sarah Martin MerrillBC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Pyschiatry and Human Behavior, The Warren Alpert Medical School at Brown University, Providence, RI, USA.
Keegan KorthauerBC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada.
Michael Steffen KoborBC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC, Canada. Electronic address: michael.kobor@ubc.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Intersample cellular heterogeneity (ISCH) is one of the largest contributors to DNA methylation (DNAme) variability. It is imperative to account for ISCH to accurately interpret analysis results in epigenome-wide association studies. We compiled this primer based on the current literature to guide researchers through the process of estimating and accounting for ISCH in DNA methylation studies. This primer outlines the procedure of bioinformatic ISCH prediction, including using reference-based and reference-free algorithms. It then follows with descriptions of several methods to account for ISCH in downstream analyses, including robust linear regression and principal-component-analysis-based adjustments. Finally, we outlined three methods for estimating differential DNAme signals in a cell-type-specific manner. Throughout the primer, we provided statistical and biological justification for our recommendations, as well as R code examples for ease of implementation.

Indexed as

Computational BiologyDNA MethylationEpigenomicsAlgorithmsHumansGenomicsMolecular Biology

Identifiers

PMID39951379
PMCPMC11969412

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

None linked

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.