ArticleGenomics, proteomics & bioinformatics2020
SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples.
Article in Genomics, proteomics & bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- RNA-binding protein gene NOP58 exhibits crucial prognostic and therapeutic value in Ewing sarcoma.Hereditas · 2025Article
- Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants.BMC genomics · 2024Article
- Sequencing by Binding rivals error-corrected Sequencing by Synthesis technology for accurate detection and quantification of minor (<0.1%) subpopulation variants.Research square · 2024Article
- Novel Markers for Liquid Biopsies in Cancer Management: Circulating Platelets and Extracellular Vesicles.Molecular cancer therapeutics · 2022Review
- OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.NAR genomics and bioinformatics · 2022Article
- Preparation of Duplex Sequencing Libraries for Archival Paraffin-Embedded Tissue Samples Using Single-Strand-Specific Nuclease P1.International journal of molecular sciences · 2022Article
- cfDNA Sequencing: Technological Approaches and Bioinformatic Issues.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Liquid Biopsy in Gastrointestinal Stromal Tumors: Ready for Prime Time?Current treatment options in oncology · 2021Review
- Next-generation sequencing methodologies to detect low-frequency mutations: "Catch me if you can".Mutation research. Reviews in mutation researchReview
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings. Duplex sequencing technology is the most commonly used approach in liquid biopsies. Unique molecular identifiers are attached to each double-stranded DNA template, followed by production of low-error consensus sequences to detect low frequency variants. However, high sequencing costs have hindered application of this approach in clinical practice. Here, we have developed an improved duplex sequencing approach called SinoDuplex, which utilizes a pool of adapters containing pre-defined barcode sequences to generate far fewer barcode combinations than with random sequences, and implemented a novel computational analysis algorithm to generate duplex consensus sequences more precisely. SinoDuplex increased the output of duplex sequencing technology, making it more cost-effective. We evaluated our approach using reference standard samples and cell-free DNA samples from lung cancer patients. Our results showed that SinoDuplex has high sensitivity and specificity in detecting very low allele frequency mutations. The source code for SinoDuplex is freely available at https://github.com/SinOncology/sinoduplex.
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