ArticlePloS one2017
Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 40 citations in OpenAlex.
- Investigation of the Presence of DNA in Human Blood Plasma Small Extracellular Vesicles.International journal of molecular sciences · 2023Article
- Novel insights into biomarkers of progression in Desmoid tumor.Frontiers in oncology · 2023Review
- Circulating cell free DNA and citrullinated histone H3 as useful biomarkers of NETosis in endometrial cancer.Journal of experimental & clinical cancer research : CR · 2022Article
- Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration.Life (Basel, Switzerland) · 2021Article
- Properties and Application of Cell-Free DNA as a Clinical Biomarker.International journal of molecular sciences · 2021Review
- Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects.Physiological reports · 2021Article
- Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine.Cancers · 2021Review
- Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling.Frontiers in neuroscience · 2021Article
- Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application.International journal of molecular sciences · 2020Review
- Quantitative characterization of tumor cell-free DNA shortening.BMC genomics · 2020Article
- Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA.Scientific reports · 2020Article
- Extracellular DNA in blood products and its potential effects on transfusion.Bioscience reports · 2020Review
- The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients.Precision clinical medicine · 2019Article
- Tumor-specific genetic aberrations in cell-free DNA of gastroesophageal cancer patients.Journal of gastroenterology · 2019Review
- Life and death of circulating cell-free DNA.Cancer biology & therapy · 2019Review
- Utility of cfDNA Fragmentation Patterns in Designing the Liquid Biopsy Profiling Panels to Improve Their Sensitivity.Frontiers in genetics · 2019Article
- Circulating cell-free nucleic acids: characteristics and applications.European journal of human genetics : EJHG · 2018Review
- Circulating tumor DNA (ctDNA) in the era of personalized cancer therapy.Journal of diabetes and metabolic disorders · 2018Review
- Proof of concept: prognostic value of the plasmatic concentration of circulating cell free DNA in desmoid tumors using ddPCR.Oncotarget · 2018Article
- A quarter century of EUS-FNA: Progress, milestones, and future directions.Endoscopic ultrasoundReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer. We analyzed the coverage spectrum of the human genome in our cfDNA samples. cfDNA exhibited no large regions with significant under-coverage, although we observed unbalanced coverage depth in cfDNA at transcription start sites and exon boundaries as a consequence of biased fragmentation due to ordered nucleosome positioning. We also analyzed the copy number variant status based on the whole-genome sequencing results and found high similarity between copy number profile constructed from tumor samples and cfDNA samples. Overall, we conclude that cfDNA comprises a good representation of the tumor genome in late stage gastric and lung cancer.
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.