ArticleNature biotechnology2019
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07626073 (h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.), which is not on this map. Cited by 108 papers.
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h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.
Who cites it
108 citing papers in PubMed.
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
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- Investigating Bacillus anthracis genomic diversity and trait-specific lineages in an endemic area in northern Tanzania through a combination of traditional and culture-free sequencing approaches.PLoS neglected tropical diseases · 2026Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Optimisation and validation of capture mNGS for predicting antimicrobial resistance.EBioMedicine · 2026Article
- Review
- Best practices when benchmarking CATCH for the design of genome enrichment probes.Bioinformatics (Oxford, England) · 2026Article
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.Biomedicines · 2026Review
- Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes".Bioinformatics (Oxford, England) · 2026Article
- Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.Respiratory research · 2026Article
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Clinicopathologic Features of Genitourinary Malakoplakia and Analytical Utility of the MetaPath Assay.Infection and drug resistance · 2026Article
- teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.Microorganisms · 2025Article
- InvestigatingbioRxiv : the preprint server for biology · 2025Article
- Development and evaluation of a hybrid capture-based NGS panel for comprehensive detection of respiratory pathogens.Scientific reports · 2025Article
- Clinical application and impact of metagenomic next-generation sequencing for the diagnosis of infectious diseases in severely immunocompromised pediatric patients.BMC pediatrics · 2025Article
- GII.17 norovirus re-emerged in the 2020s as a result of dynamic and adaptive evolutionary processes.Nature communications · 2025Article
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
48 more citing papers are in PubMed but not listed here.
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48 authors.
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Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
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