ArticleBMC genomics2020
Quantitative characterization of tumor cell-free DNA shortening.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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.
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.
Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- Article
- A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements.bioRxiv : the preprint server for biology · 2025Article
- GeneBits: ultra-sensitive tumour-informed ctDNA monitoring of treatment response and relapse in cancer patients.Journal of translational medicine · 2025Article
- Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA.Nucleic acids research · 2024Article
- Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment.Nature medicine · 2024Article
- Nucleosome reorganisation in breast cancer tissues.Clinical epigenetics · 2024Article
- Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids.Human genomics · 2023Article
- Circulating DNA fragmentomics and cancer screening.Cell genomics · 2023Review
- NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.Chromosoma · 2022Article
- Clinical application of liquid biopsy in cancer patients.BMC cancer · 2022Article
- Plasma Concentrations and Cancer-Associated Mutations in Cell-Free Circulating DNA of Treatment-Naive Follicular Lymphoma for Improved Non-Invasive Diagnosis and Prognosis.Frontiers in oncology · 2022Article
- Liquid biopsy approach to pancreatic cancer.World journal of gastrointestinal oncology · 2021Review
- Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology?Molecular diagnosis & therapy · 2021Review
- Recent Advancements in Nanoparticle-Based Optical Biosensors for Circulating Cancer Biomarkers.Materials (Basel, Switzerland) · 2021Review
- Molecular diagnosis of diffuse glioma using a chip-based digital PCR system to analyze IDH, TERT, and H3 mutations in the cerebrospinal fluid.Journal of neuro-oncology · 2021Article
- The Detection of Cancer Epigenetic Traces in Cell-Free DNA.Frontiers in oncology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundPrevious 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.
resultsUsing 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.
conclusionsTumor 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.