Evidence map›Paper›PMID 42152147›Full record

ArticleClinical epigenetics2026

Development, characterization, and inter-laboratory validation of methylated human cell free DNA candidate reference materials.

Zhiyong He, Yves Konigshofer, Russell Garlick, Jayanthi Ramprakash, Madhumita Ramesh, Eric Hall, Adam Corner, Michelle Clarissa, Jocelyn H Wright, Victoria K Cannon and 13 more

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

Article in Clinical epigenetics, 2026. 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. Review
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

23 authors.

Zhiyong HeNational Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD, 20899, USA. Zhiyong.he@nist.gov.
Yves KonigshoferLGC Clinical Diagnostics Inc., Gaithersburg, MD, 20878, USA.
Russell GarlickLGC Clinical Diagnostics Inc., Gaithersburg, MD, 20878, USA.
Jayanthi RamprakashLGC Clinical Diagnostics Inc., Gaithersburg, MD, 20878, USA.
Madhumita RameshBio-Rad Laboratories, 1000 Alfred Nobel Dr., Hercules, CA, 94547, USA.
Eric HallBio-Rad Laboratories, 1000 Alfred Nobel Dr., Hercules, CA, 94547, USA.
Adam CornerBio-Rad Laboratories, 1000 Alfred Nobel Dr., Hercules, CA, 94547, USA.
Michelle ClarissaTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Jocelyn H WrightTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Victoria K CannonTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Ming YuTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
William M GradyTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Cecilia C S YeungTranslational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Zachary HeimerJBS Biosciences, 3805 Old Easton Rd, Doylestown, PA, 10892, USA.
Zhili WangJBS Biosciences, 3805 Old Easton Rd, Doylestown, PA, 10892, USA.
ShiPing ZouPillar Biosciences, 9 Strathmore Rd, Natick, MA, 01760, USA.
Shidong JiaPredicine, 3555 Arden Rd., Hayward, CA, 94545, USA.
Fang LiuPredicine, 3555 Arden Rd., Hayward, CA, 94545, USA.
Giancarlo BonoraPredicine, 3555 Arden Rd., Hayward, CA, 94545, USA.
Karol BomsztykUW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA.
Daniel MarUW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA.
Kenneth D ColeNational Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD, 20899, USA.
Hua-Jun HeNational Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD, 20899, USA. hua-jun.he@nist.gov.

Funding

Understanding adenoma progression: Interplay among tissue microenvironment, clonal architecture, and gut microbiomeU54CA274374 · NCI · FRED HUTCHINSON CANCER CENTER · PI Kristina A. Matkowskyj · 2022 to 2026
$10.7M
Translational Science of Gastrointestinal Cancer Initiation and ProgressionR50CA233042 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Ming Yu · 2018 to 2026
$2.4M
Influence of Pre-Analytical Factors in Globlastoma MGMT Promoter Methylation Biomarker AssayU01CA246503 · NCI · UNIVERSITY OF WASHINGTON · PI BOMSZTYK, KAROL, ROSTOMILY, ROBERT C · 2020 to 2024
$2.0M
NCI NIH HHS ACN20006NCI NIH HHS R50 CA233042NCI NIH HHS R50CA233042NCI NIH HHS U01 CA246503NCI NIH HHS U54 CA274374
6 · The paper itself

Abstract

backgroundAberrant DNA methylation biomarkers have demonstrated potential for early cancer detection, multicancer detection, and determining the tissue of origin. Due to their stability, frequency, and accessibility in bodily fluids, circulating cell-free DNA (cfDNA) methylation is a promising biomarker in liquid biopsy. A reliable and quantifiable analysis of cfDNA methylation status is critical to its application. However, there are current challenges and a lack of consensus on measurement methods. To address this, we developed two candidate methylated cfDNA reference materials (RMs).

methodsThe National Institute of Standards and Technology (NIST) RM consists of five components, formulated by mixing in vitro methylated cfDNA simulant at fractions of 0%, 5%, 25%, 50%, and 100% with native-state cfDNA simulant derived from the GM24385 cell line. The LGC Clinical Diagnostics (LGC) RM consists of two components: non-methylated cfDNA simulant derived from GM24385 genomic DNA and whole genome amplification and methylated cfDNA produced by in vitro methylation of amplified material. The candidate RMs were characterized, and the methylation status of three targets was confirmed by droplet digital PCR (ddPCR) assays. To test the utility of these RMs, six laboratories participated in an interlaboratory study, each using their own lab-developed assays and methods, which included methylation-specific qPCR, nanoplate digital PCR (dPCR), ddPCR, matrix methylated DNA immunoprecipitation-based assays, and whole-genome bisulfite sequencing.

resultsThe interlaboratory study results showed that the designed percentage of methylation was well correlated with the observed values across all participating labs, and good reproducibility was found for each individual method. However, slightly different methylation proportions associated with assay-specific biases were observed.

conclusionsThis study clearly demonstrates the value of candidate RMs as standards for evaluating assay performance, as well as for increasing confidence in reporting cfDNA methylation status for clinical applications.

Indexed as

Cell-Free Nucleic AcidsDNA MethylationBiomarkers, TumorHumansLiquid BiopsyReference StandardsReproducibility of ResultsBiomarkers, TumorCell-Free Nucleic AcidsCancer detectionCell free DNACharacterizationDNA methylationEpigeneticsInterlaboratory studyReference material

Identifiers

PMID42152147
PMCPMC13352979

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.