ArticleNucleic acids research2012
Ultrasensitive detection of rare mutations using next-generation targeted resequencing.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
84 citing papers in PubMed, 1 synthesis or guideline pooled it, 134 citations in OpenAlex.
- A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.Briefings in bioinformatics · 2020Guideline
- Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.Scientific reports · 2015Trial
- Spatial and temporal description of antimalarial drug resistance markers in Ghana using targeted amplicon deep sequencing.Antimicrobial agents and chemotherapy · 2026Article
- MGDB: A Novel Bioinformatics Quality Control Tool for Clinical Next-Generation Sequencing.Cancer informatics · 2026Article
- Detection of mutations: from Ames test to duplex sequencing.Frontiers in molecular biosciences · 2026Review
- Viral oncogenes, viruses, and cancer: a third-generation sequencing perspective on viral integration into the human genome.Frontiers in oncology · 2023Review
- Methods to improve the accuracy of next-generation sequencing.Frontiers in bioengineering and biotechnology · 2023Review
- Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.Genome medicine · 2021Article
- Development of a new barcode-based, multiplex-PCR, next-generation-sequencing assay and data processing and analytical pipeline for multiplicity of infection detection of Plasmodium falciparum.Malaria journal · 2021Article
- Unraveling the Complexity of Imported Malaria Infections by Amplicon Deep Sequencing.Frontiers in cellular and infection microbiology · 2021Article
- Article
- Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019.PloS one · 2021Article
- Limited Practical Utility of Liquid Biopsy in the Treated Patients with Advanced Breast Cancer.Diagnostics (Basel, Switzerland) · 2020Article
- Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal.Malaria journal · 2020Article
- Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing.The Journal of biological chemistry · 2019Article
- Rare mutations in Pfmdr1 gene of Plasmodium falciparum detected in clinical isolates from patients treated with anti-malarial drug in Nigeria.Malaria journal · 2019Article
- FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue.G3 (Bethesda, Md.) · 2019Article
- Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes.Scientific reports · 2019Article
- Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.Trends in biotechnology · 2018Review
- INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance.Genome medicine · 2018Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
With next-generation DNA sequencing technologies, one can interrogate a specific genomic region of interest at very high depth of coverage and identify less prevalent, rare mutations in heterogeneous clinical samples. However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates. We demonstrate that we can robustly detect mutations at 0.1% fractional representation. This represents accurate detection of one mutant per every 1000 wild-type alleles. To achieve this sensitive level of mutation detection, we integrate a high accuracy indexing strategy and reference replication for estimating sequencing error variance. We employ a statistical model to estimate the error rate at each position of the reference and to quantify the fraction of variant base in the sample. Our method is highly specific (99%) and sensitive (100%) when applied to a known 0.1% sample fraction admixture of two synthetic DNA samples to validate our method. As a clinical application of this method, we analyzed nine clinical samples of H1N1 influenza A and detected an oseltamivir (antiviral therapy) resistance mutation in the H1N1 neuraminidase gene at a sample fraction of 0.18%.
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Registered trials
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.