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Updated: Jul 9, 2026
08:25
Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients
Published on: September 9, 2020
A Pilot Study of Plasma Cell-Free DNA Fragmentomics in Gallbladder Cancer
Michael Daniels1, R Taylor Sundby2, Ling Su3
1National Cancer Institute, Division of Cancer Prevention, Cancer Prevention Fellowship Program, Shady Grove, MD, US; National Cancer Institute, Division of Cancer Epidemiology and Genetics, Infections and Immunoepidemiology Branch, Shady Grove, MD, US.
JHEP Reports : Innovation in Hepatology
|July 7, 2026
Summary
This study shows that circulating cell-free DNA (cfDNA) fragmentomics can distinguish gallbladder cancer (GBC) from benign conditions. These findings highlight cfDNA profiling as a promising noninvasive diagnostic tool for GBC.
Area of Science:
- Oncology
- Genomics
- Biomarkers
Background:
- Gallbladder cancer (GBC) is a lethal malignancy with limited diagnostic and prognostic biomarkers.
- Circulating cell-free DNA (cfDNA) fragmentomics offers a noninvasive approach for cancer detection and characterization.
- Current diagnostic methods for GBC are limited, necessitating novel noninvasive tools.
Purpose of the Study:
- To identify cfDNA-based features differentiating GBC from gallstones and healthy controls.
- To evaluate the utility of cfDNA fragmentomics for biological characterization of GBC.
- To assess the potential of cfDNA profiling as a noninvasive diagnostic tool for GBC.
Main Methods:
- cfDNA was extracted from archived plasma samples of 67 individuals across two case-control studies.
- Low-coverage whole genome sequencing was performed to analyze cfDNA fragmentomics.
- Computational packages were used to generate features and build a classification model, validated with external datasets.
Main Results:
- GBC patients exhibited significantly altered cfDNA features compared to controls (P<0.05).
- Key differentiating features included fragment lengths, end motifs, tumor fractions, copy number alterations, and transcription factor binding site accessibility.
- The cfDNA-based model achieved an AUC of 0.852 for discriminating GBC from non-cancerous conditions.
Conclusions:
- Archived plasma samples are suitable for cfDNA sequencing and fragmentomics analysis.
- cfDNA fragmentomics captures biologically relevant alterations in GBC, consistent with tissue genomics.
- cfDNA profiling holds promise as a noninvasive diagnostic tool for GBC and related hepatopancreatobiliary cancers.
