ArticleScientific reports2020
Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 19 citations in OpenAlex.
- Development and characterization of nucleosomal DNA-based reference materials for the epidermal growth factor receptor gene liquid biopsy.Analytical and bioanalytical chemistry · 2026Article
- Single-center experience using reflex-targeted next-generation sequencing at diagnosis of squamous cell lung carcinoma in daily practice.Virchows Archiv : an international journal of pathology · 2026Article
- Automation of customizable library preparation for next-generation sequencing into an open microfluidic platform.Scientific reports · 2024Article
- Multiomics Research: Principles and Challenges in Integrated Analysis.Biodesign research · 2024Review
- Identification of Somatic Mutations in Plasma Cell-Free DNA from Patients with Metastatic Oral Squamous Cell Carcinoma.International journal of molecular sciences · 2023Article
- Mutation profiles in circulating cell-free DNA predict acquired resistance to olaparib in high-grade serous ovarian carcinoma.Cancer science · 2022Article
- Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth.Nature biomedical engineering · 2022Article
- Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes.Veterinary research · 2021Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
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