Evidence map›Paper›PMID 34565346›Full record

ArticleBMC bioinformatics2021

A targeted solution for estimating the cell-type composition of bulk samples.

Edwin J C G van den Oord, Lin Y Xie, Charles J Tran, Min Zhao, Karolina A Aberg

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

5 authors.

Edwin J C G van den OordCenter for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA.
Lin Y XieCenter for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA.
Charles J TranCenter for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA.
Min ZhaoCenter for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA.
Karolina A AbergCenter for Biomarker Research and Precision Medicine (BPM), School of Pharmacy, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Room 217, P.O. Box 980533, Richmond, VA, 23298, USA. kaaberg@vcu.edu.ORCID http://orcid.org/0000-0001-6103-5168

Funding

Developmental methylomics of childhood trauma and its health consequencesR01MH104576 · NIMH · VIRGINIA COMMONWEALTH UNIVERSITY · PI VAN DEN OORD, EDWIN · 2014 to 2018
$3.1M
Schizophrenia case-control study of neonatal and post onset methylomesR01MH109525 · NIMH · VIRGINIA COMMONWEALTH UNIVERSITY · PI ABERG, KAROLINA ANNA · 2017 to 2020
$2.3M
NIMH NIH HHS R01 MH104576NIMH NIH HHS R01MH104576NIMH NIH HHS R01 MH109525NIMH NIH HHS R01MH109525
6 · The paper itself

Abstract

backgroundTo avoid false-positive findings and detect cell-type specific associations in methylation and transcription investigations with bulk samples, it is critical to know the proportions of the major cell-types.

resultsWe present a novel approach that allows for precise estimation of cell-type proportions using only a few highly informative methylation markers. The most reliable estimates were obtained with 17 amplicons (34 CpGs) using the MuSiC estimator, for which the average correlations between the estimated and the true cell-type proportions were 0.889. Furthermore, the estimates were not significantly different from the true values (P = 0.95) indicating that the estimator is unbiased and the standard deviation of the estimates further indicate high precision. Moreover, the overall variability of the estimates as measured by the Root Mean Squared Error (RMSE), which is a function of both bias and precision, was low (mean RMSE = 0.038). Taken together, these results indicate that the approach produced reliable estimates that are both unbiased and highly precise.

conclusionThis cost-effective approach for estimating cell-type proportions in bulk samples allows for enhanced targeted analysis, which in turn will minimize the risk of reporting false-positive findings and allowing for detection of cell-type specific associations. The approach is applicable across platforms and can be extended to assess cell-type proportions for various tissues.

Indexed as

Cell-type proportionsDNA methylationReplication studiesStatistical deconvolutionTargeted analysisTranscription

Identifiers

PMID34565346
PMCPMC8474864

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.