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Updated: Dec 15, 2025
Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients
Published on: September 9, 2020
Quantitative characterization of tumor cell-free DNA shortening
Juntang Guo1, Kefeng Ma1, Hua Bao2
1Department of Thoracic Surgery, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China.
Background:
Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer diagnosis and treatment monitoring; however, the underlying mechanism of shortened tumor cfDNA was still unknown, which potentially limits its further clinical application.
Results:
Using targeted sequencing of cfDNA in a large cohort of solid tumor patient, sequencing reads harboring tumor-specific somatic mutations were isolated to examine the exact size distribution of tumor cfDNA. For the majority of studied cases, 166 bp remained as the peak size of tumor cfDNA, with tumor cfDNA showing an increased proportion of short fragments (100-150 bp). Less than 1% of cfDNA samples were found to be peaked at 134/144 bp and independent of tumor cfDNA purity. Using whole-genome sequencing of cfDNA, we discovered a positive correlation between cfDNA shortening and the magnitude of chromatin inaccessibility, as measured by transcription, DNase I hypersensitivity, and histone modifications. Tumor cfDNA shortening occurred simultaneously at both 5' and 3' ends of the DNA wrapped around nucleosomes.
Conclusions:
Tumor cfDNA shortening exhibited two distinctive modes. Tumor cfDNA purity and chromatin inaccessibility were contributing factors but insufficient to trigger a global transition from 166 bp dominant to 134/144 bp dominant phenotype.
Insights
Shortened tumor cell-free DNA (cfDNA) is linked to chromatin inaccessibility, with most cases peaking at 166 bp. This finding advances understanding of cfDNA mechanisms for cancer diagnosis.
Area of Science:
- Molecular Biology
- Genomics
- Cancer Research
Background:
- Previous studies indicate tumor-derived cell-free DNA (cfDNA) is shorter than cfDNA from healthy cells.
- Shorter cfDNA fragments can enrich tumor cfDNA, aiding early cancer detection and monitoring.
- The mechanism behind tumor cfDNA shortening remains unclear, limiting clinical applications.
Purpose of the Study:
- To investigate the underlying mechanism of tumor cfDNA shortening.
- To analyze the size distribution of tumor cfDNA in a large cohort of cancer patients.
- To correlate cfDNA size with chromatin accessibility markers.
Main Methods:
- Targeted sequencing of cfDNA in solid tumor patients.
- Isolation of tumor-specific somatic mutation-harboring reads.
- Whole-genome sequencing of cfDNA.
- Analysis of chromatin inaccessibility using transcription, DNase I hypersensitivity, and histone modifications.
Main Results:
- The majority of tumor cfDNA samples peaked at 166 bp, with an increased proportion of short fragments (100-150 bp).
- A small subset (<1%) of cfDNA samples peaked at 134/144 bp, irrespective of tumor cfDNA purity.
- A positive correlation was observed between cfDNA shortening and chromatin inaccessibility.
- Tumor cfDNA shortening occurred at both 5' and 3' ends of nucleosome-bound DNA.
Conclusions:
- Tumor cfDNA shortening presents two distinct patterns.
- While tumor cfDNA purity and chromatin inaccessibility contribute, they do not fully explain the shift to 134/144 bp peaks.
