publication . Article . Other literature type . 2019

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.

David Kang-Myung Yang; Christian Happi; Hayden C. Metsky; Lauren Paul; Irene Bosch; Thiago Moreno L. Souza; Damien Tully; Fernando Augusto Bozza;
Open Access
  • Published: 04 Feb 2019 Journal: Nature Biotechnology, volume 37, pages 160-168 (issn: 1087-0156, eissn: 1546-1696, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
  • Country: United Kingdom
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 w...
Subjects
free text keywords: Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering
Funded by
NIH| Genomic Center for Infectious Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19AI110818-02
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Design of a human monoclonal antibody-informed dengue vaccine
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI099210-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Host and Microbial Genetic Determinants of Febrile Illness in West Africa
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG007480-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
75 references, page 1 of 5

Houldcroft, CJ, Beale, MA, Breuer, J. Clinical and biological insights from viral genome sequencing. Nat. Rev. Microbiol.. 2017; 15: 183-192 [OpenAIRE] [PubMed] [DOI]

Worobey, M. 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature. 2016; 539: 98-101 [OpenAIRE] [PubMed] [DOI]

Andersen, KG. Clinical sequencing uncovers origins and evolution of Lassa virus. Cell. 2015; 162: 738-750 [OpenAIRE] [PubMed] [DOI]

Dudas, G. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017; 544: 309-315 [OpenAIRE] [PubMed] [DOI]

Bedford, T. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 2015; 523: 217-220 [OpenAIRE] [PubMed] [DOI]

Metsky, HC. Zika virus evolution and spread in the Americas. Nature. 2017; 546: 411-415 [OpenAIRE] [PubMed] [DOI]

Quick, J. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc.. 2017; 12: 1261-1276 [OpenAIRE] [PubMed] [DOI]

Barnes, KG. Evidence of Ebola virus replication and high concentration in semen of a patient during recovery. Clin. Infect. Dis.. 2017; 65: 1400-1403 [OpenAIRE] [PubMed] [DOI]

Henn, MR. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog.. 2012; 8: e1002529 [OpenAIRE] [PubMed] [DOI]

Li, JZ. Comparison of Illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. PLoS One. 2014; 9: e90485 [OpenAIRE] [PubMed] [DOI]

Depledge, DP. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One. 2011; 6: e27805 [OpenAIRE] [PubMed] [DOI]

Matranga, CB. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol.. 2014; 15: 519 [OpenAIRE] [PubMed] [DOI]

Bonsall, D. ve-SEQ: robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Res. 2015; 4: 1062 [OpenAIRE] [PubMed] [DOI]

Wang, D. Microarray-based detection and genotyping of viral pathogens. Proc. Natl Acad. Sci. USA. 2002; 99: 15687-15692 [OpenAIRE] [PubMed] [DOI]

Lapa, S. Species-level identification of orthopoxviruses with an oligonucleotide microchip. J. Clin. Microbiol.. 2002; 40: 753-757 [OpenAIRE] [PubMed] [DOI]

75 references, page 1 of 5
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 w...
Subjects
free text keywords: Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering
Funded by
NIH| Genomic Center for Infectious Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19AI110818-02
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Design of a human monoclonal antibody-informed dengue vaccine
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI099210-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Host and Microbial Genetic Determinants of Febrile Illness in West Africa
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG007480-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
75 references, page 1 of 5

Houldcroft, CJ, Beale, MA, Breuer, J. Clinical and biological insights from viral genome sequencing. Nat. Rev. Microbiol.. 2017; 15: 183-192 [OpenAIRE] [PubMed] [DOI]

Worobey, M. 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature. 2016; 539: 98-101 [OpenAIRE] [PubMed] [DOI]

Andersen, KG. Clinical sequencing uncovers origins and evolution of Lassa virus. Cell. 2015; 162: 738-750 [OpenAIRE] [PubMed] [DOI]

Dudas, G. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017; 544: 309-315 [OpenAIRE] [PubMed] [DOI]

Bedford, T. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 2015; 523: 217-220 [OpenAIRE] [PubMed] [DOI]

Metsky, HC. Zika virus evolution and spread in the Americas. Nature. 2017; 546: 411-415 [OpenAIRE] [PubMed] [DOI]

Quick, J. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc.. 2017; 12: 1261-1276 [OpenAIRE] [PubMed] [DOI]

Barnes, KG. Evidence of Ebola virus replication and high concentration in semen of a patient during recovery. Clin. Infect. Dis.. 2017; 65: 1400-1403 [OpenAIRE] [PubMed] [DOI]

Henn, MR. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog.. 2012; 8: e1002529 [OpenAIRE] [PubMed] [DOI]

Li, JZ. Comparison of Illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. PLoS One. 2014; 9: e90485 [OpenAIRE] [PubMed] [DOI]

Depledge, DP. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One. 2011; 6: e27805 [OpenAIRE] [PubMed] [DOI]

Matranga, CB. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol.. 2014; 15: 519 [OpenAIRE] [PubMed] [DOI]

Bonsall, D. ve-SEQ: robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Res. 2015; 4: 1062 [OpenAIRE] [PubMed] [DOI]

Wang, D. Microarray-based detection and genotyping of viral pathogens. Proc. Natl Acad. Sci. USA. 2002; 99: 15687-15692 [OpenAIRE] [PubMed] [DOI]

Lapa, S. Species-level identification of orthopoxviruses with an oligonucleotide microchip. J. Clin. Microbiol.. 2002; 40: 753-757 [OpenAIRE] [PubMed] [DOI]

75 references, page 1 of 5
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