ArticleJournal of clinical microbiology2018
Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods.
Article in Journal of clinical microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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.
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Who cites it
33 citing papers in PubMed.
- Cell-Free DNA Release Kinetics and Fragmentation Reflect Treatment Response and Resistance In Vitro.Cells · 2026Article
- Non-invasive diagnosis of invasive fungal disease with cell-free DNA PCR.Journal of clinical microbiology · 2026Review
- Inter-laboratory variability in cytomegalovirus DNA quantification: implications for standardization and clinical monitoring.Journal of clinical microbiology · 2025Article
- Droplet Digital PCR or Real-Time PCR as a Method for Quantifying SARS-CoV-2 RNA in Plasma-Is There a Difference?Viruses · 2025Article
- Dynamic profiling of Cell-free DNA fragmentation uncovers postprandial metabolic and immune alterations.Human genomics · 2025Article
- Molecular diagnosis of Cytomegalovirus infection: clinical performance of the Aptima transcription-mediated amplification assay toward conventional qPCR chemistry on whole blood samples.Journal of clinical microbiology · 2024Article
- Determination of DNA content as quality control in decellularized tissues: challenges and pitfalls.Regenerative biomaterials · 2024Article
- The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples.Frontiers in cell and developmental biology · 2024Review
- Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis.Frontiers in oncology · 2024Article
- Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood.Clinical epigenetics · 2023Article
- Evaluation of DNA Extraction Methods for Reliable Quantification ofBiosensors · 2023Article
- Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13.Nature communications · 2023Article
- Article
- Matrix Matters: Assessment of Commutability among BK Virus Assays and Standards.Journal of clinical microbiology · 2022Article
- Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations.International journal of environmental research and public health · 2022Review
- Accuracy of Pneumocystis jirovecii Plasma Cell-Free DNA PCR for Noninvasive Diagnosis of Pneumocystis Pneumonia.Journal of clinical microbiology · 2022Article
- Review
- Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Liquid biopsy enters the clinic - implementation issues and future challenges.Nature reviews. Clinical oncology · 2021Review
- Solid-phase silica-based extraction leads to underestimation of residual DNA in decellularized tissues.Xenotransplantation · 2021Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200 bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500 bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.
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