ArticleNucleic acids research2019
High efficiency error suppression for accurate detection of low-frequency variants.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays.Annals of laboratory medicine · 2024Guideline
- Continuous versus Standard Palbociclib Treatment and Molecular Profiling of Solid Tissues and Liquid Biopsies in the CCTG MA.38 Trial in Advanced Breast Cancer.Cancer research communications · 2025Trial
- Identifying Mechanisms of Resistance by Circulating Tumor DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at Time of PARP Inhibitor Progression.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- HPV Serology and Circulating Viral DNA for Detection, Genotyping, and Measurement of Disease Burden in Oropharyngeal Cancer.International journal of cancer · 2026Article
- Methyltransferase-assisted single duplex sequencing for detecting circulating tumor DNA.EMBO molecular medicine · 2026Article
- Tumor-naïve ctDNA detection with deep learning-enhanced error suppression for sensitive mutation calling.Genome medicine · 2026Article
- Detection and classification of lymphoma from cell-free methylome data.NPJ precision oncology · 2026Article
- Optimization of a hybridization-based target enrichment protocol for precision oncology.Molecular biology reports · 2026Article
- Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications.iScience · 2025Article
- UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.Bioinformatics (Oxford, England) · 2025Article
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- Risk Assessment With Ultra-Low-Pass Whole-Genome Sequencing of Cell-Free DNA for Large B-Cell Lymphoma.JCO precision oncology · 2025Article
- Advancing Leukemia Management Through Liquid Biopsy: Insights into Biomarkers and Clinical Utility.Cancers · 2025Review
- A Review of Circulating Tumor DNA (ctDNA) and the Liquid Biopsy in Cancer Diagnosis, Screening, and Monitoring Treatment Response.Medical science monitor : international medical journal of experimental and clinical research · 2025Review
- Circulating tumor DNA to monitor treatment response in solid tumors and advance precision oncology.NPJ precision oncology · 2025Review
- A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers.Nucleic acids research · 2025Article
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- Article
- Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs.International journal of molecular sciences · 2024Article
- Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.BMC genomics · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to technical artefacts that can limit the accuracy for calling low-allele-frequency mutations. State-of-the-art methods to improve detection of low-frequency mutations often employ unique molecular identifiers (UMIs) for error suppression; however, these methods are highly inefficient as they depend on redundant sequencing to assemble consensus sequences. Here, we present a novel strategy to enhance the efficiency of UMI-based error suppression by retaining single reads (singletons) that can participate in consensus assembly. This 'Singleton Correction' methodology outperformed other UMI-based strategies in efficiency, leading to greater sensitivity with high specificity in a cell line dilution series. Significant benefits were seen with Singleton Correction at sequencing depths ≤16 000×. We validated the utility and generalizability of this approach in a cohort of >300 individuals whose peripheral blood DNA was subjected to hybrid capture sequencing at ∼5000× depth. Singleton Correction can be incorporated into existing UMI-based error suppression workflows to boost mutation detection accuracy, thus improving the cost-effectiveness and clinical impact of NGS.
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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.