ArticlePLoS computational biology2017
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- A set cover algorithm identifies minimal circulating tumour DNA sequencing targets for colorectal cancer detection.Scientific reports · 2025Article
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- Improved Quantification of Circulating Tumor DNA in Translocation-Associated Myxoid Liposarcoma by Simultaneous Detection of Breakpoints and Single Nucleotide Variants.Cancer medicine · 2025Article
- 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
- Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data.Scientific reports · 2023Article
- Accurate profiling of full-length Fv in highly homologous antibody libraries using UMI tagged short reads.Nucleic acids research · 2023Article
- Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2023Article
- Article
- Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma.JCO precision oncology · 2022Article
- An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency.NAR genomics and bioinformatics · 2022Article
- The Opportunities and Challenges of Molecular Tagging Next-Generation Sequencing in Liquid Biopsy.Molecular diagnosis & therapy · 2021Article
- Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA).Scientific reports · 2021Article
- Urinary Nucleic Acid in Tumor: Bioinformatics Approaches.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.BMC bioinformatics · 2020Article
- Family reunion via error correction: an efficient analysis of duplex sequencing data.BMC bioinformatics · 2020Article
- Review
- smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2019Article
- Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables.Computational and structural biotechnology journal · 2019Review
- Rare Event Detection Using Error-corrected DNA and RNA Sequencing.Journal of visualized experiments : JoVE · 2018Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
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