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

Zhiyong He¹, Yves Konigshofer², Russell Garlick²

¹National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD, 20899, USA. Zhiyong.he@nist.gov.

Clinical Epigenetics

|May 19, 2026

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Summary

Two new reference materials for cell-free DNA (cfDNA) methylation were developed to standardize measurements. An interlaboratory study showed these reference materials improve assay performance and confidence in cfDNA methylation analysis for cancer detection.

Area of Science:

Biomarker Discovery
Molecular Diagnostics
Genomics

Background:

Aberrant DNA methylation is key for early cancer detection and tissue of origin determination.
Circulating cell-free DNA (cfDNA) methylation is a promising liquid biopsy biomarker due to its stability and accessibility.
Standardized measurement methods for cfDNA methylation are lacking, hindering clinical application.

Purpose of the Study:

To develop and evaluate candidate reference materials (RMs) for quantifying cfDNA methylation.
To address the need for consensus and reliability in cfDNA methylation analysis.

Main Methods:

Two candidate cfDNA methylation RMs were developed: one by NIST and one by LGC Clinical Diagnostics.
RMs were characterized, and methylation status confirmed using droplet digital PCR (ddPCR).

Keywords:

Cancer detection Cell free DNA Characterization DNA methylation Epigenetics Interlaboratory study Reference material

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An interlaboratory study involving six labs assessed RM utility with diverse assays (qPCR, dPCR, bisulfite sequencing).

Main Results:

The interlaboratory study demonstrated good correlation between designed and observed methylation percentages across labs.
High reproducibility was observed for individual assay methods.
Assay-specific biases led to slight variations in methylation proportions.

Conclusions:

Candidate reference materials are valuable for evaluating assay performance in cfDNA methylation analysis.
These RMs enhance confidence in reporting cfDNA methylation status for clinical use.
Standardization through RMs is crucial for advancing liquid biopsy applications in oncology.