ArticleNature protocols2017
Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- The PEMDAC phase 2 study of pembrolizumab and entinostat in patients with metastatic uveal melanoma.Nature communications · 2021Trial
- Review
- DNA polymerase characteristics influence noise levels in sequencing of short tandem repeats.BMC genomics · 2026Article
- Detecting TP53 mutations in paired liquid and tissue biopsies from patients with high-grade serous ovarian carcinoma.International journal of cancer · 2026Article
- Long-term prognostic value of ctDNA in early breast cancer: insights from the neoadjuvant ABCSG-34 Trial.NPJ breast cancer · 2026Article
- Patient-specific sequencing panels enable sensitive circulating tumor DNA analysis in rhabdomyosarcoma independent of genetic profile.NPJ precision oncology · 2025Article
- High baseline PD-1+ CD8 T Cells and TIGIT+ CD8 T Cells in circulation associated with response to PD-1 blockade in patients with non-small cell lung cancer.Cancer immunology, immunotherapy : CII · 2025Article
- Navigating the Landscape of Liquid Biopsy in Colorectal Cancer: Current Insights and Future Directions.International journal of molecular sciences · 2025Review
- Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information.Communications biology · 2025Article
- Single-Tube, Switched Temperature Amplicon Barcoding for Multiplex Detection of Rare Mutations in Circulating Tumor DNA.The Journal of molecular diagnostics : JMD · 2025Article
- Digital sequencing is improved by using structured unique molecular identifiers.Genome biology · 2025Article
- Circulating tumor DNA in cholangiocarcinoma: current clinical applications and future perspectives.Frontiers in cell and developmental biology · 2025Review
- Circulating tumor DNA laboratory processes and clinical applications in nasopharyngeal carcinoma.Frontiers in oncology · 2025Review
- Liquid biopsy in cancer current: status, challenges and future prospects.Signal transduction and targeted therapy · 2024Review
- Personalized circulating tumor DNA analysis for sensitive disease monitoring and detection of relapse in neuroblastoma.Biomarker research · 2024Article
- Mechanistic basis of atypical TERT promoter mutations.Nature communications · 2024Article
- Long-Lasting Response to Lorlatinib in Patients with ALK-Driven Relapsed or Refractory Neuroblastoma Monitored with Circulating Tumor DNA Analysis.Cancer research communications · 2024Article
- Use of ctDNA in early breast cancer: analytical validity and clinical potential.NPJ breast cancer · 2024Review
- Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA.International journal of molecular sciences · 2024Article
- Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis.Communications biology · 2024Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols. Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing (SiMSen-seq) was developed to generate targeted barcoded libraries with minimal DNA input, flexible target selection and a very simple, short (∼4 h) library construction protocol. The protocol comprises a three-cycle barcoding PCR step followed directly by adaptor PCR to generate the library and then bead purification before sequencing. Thus, SiMSen-seq allows detection of variant alleles at <0.1% frequency with easy customization of library content (from 1 to 40+ PCR amplicons) and a protocol that can be implemented in any molecular biology laboratory. Here, we provide a detailed protocol for assay development and describe software to process the barcoded sequence reads.
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