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Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.
Metsky, Hayden C; Siddle, Katherine J; Gladden-Young, Adrianne; Qu, James; Yang, David K; Brehio, Patrick; Goldfarb, Andrew; Piantadosi, Anne; Wohl, Shirlee; Carter, Amber; Lin, Aaron E; Barnes, Kayla G; Tully, Damien C; Corleis, BjÓ§rn; Hennigan, Scott; Barbosa-Lima, Giselle; Vieira, Yasmine R; Paul, Lauren M; Tan, Amanda L; Garcia, Kimberly F; Parham, Leda A; Odia, Ikponmwosa; Eromon, Philomena; Folarin, Onikepe A; Goba, Augustine; Simon-Lorière, Etienne; Hensley, Lisa; Balmaseda, Angel; Harris, Eva; Kwon, Douglas S; Allen, Todd M; Runstadler, Jonathan A; Smole, Sandra; Bozza, Fernando A; Souza, Thiago M L; Isern, Sharon; Michael, Scott F; Lorenzana, Ivette; Gehrke, Lee; Bosch, Irene; Ebel, Gregory; Grant, Donald S; Happi, Christian T; Park, Daniel J; Gnirke, Andreas; Sabeti, Pardis C; Matranga, Christian B.
Affiliation
  • Metsky HC; Broad Institute of MIT and Harvard, Cambridge, MA, USA. hayden@mit.edu.
  • Siddle KJ; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA. hayden@mit.edu.
  • Gladden-Young A; Broad Institute of MIT and Harvard, Cambridge, MA, USA. kjsiddle@broadinstitute.org.
  • Qu J; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA. kjsiddle@broadinstitute.org.
  • Yang DK; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Brehio P; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Goldfarb A; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Piantadosi A; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Wohl S; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Carter A; Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
  • Lin AE; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Barnes KG; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Tully DC; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Corleis B; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Hennigan S; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Barbosa-Lima G; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Vieira YR; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Paul LM; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Tan AL; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Garcia KF; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
  • Parham LA; The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  • Odia I; The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  • Eromon P; Massachusetts Department of Public Health, Boston, MA, USA.
  • Folarin OA; Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil.
  • Goba A; Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil.
  • Simon-Lorière E; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
  • Hensley L; Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras.
  • Balmaseda A; Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras.
  • Harris E; Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.
  • Kwon DS; African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer's University, Ede, Nigeria.
  • Allen TM; African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer's University, Ede, Nigeria.
  • Runstadler JA; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria.
  • Smole S; Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone.
  • Souza TML; Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France.
  • Isern S; Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD, USA.
  • Michael SF; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua.
  • Lorenzana I; Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
  • Gehrke L; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Bosch I; The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  • Ebel G; The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  • Grant DS; Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA.
  • Happi CT; Massachusetts Department of Public Health, Boston, MA, USA.
  • Park DJ; Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil.
  • Gnirke A; Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil.
  • Sabeti PC; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
  • Matranga CB; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
Nat Biotechnol ; 37(2): 160-168, 2019 02.
Article in En | MEDLINE | ID: mdl-30718881
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Viral / Computational Biology / Metagenome / Metagenomics Limits: Animals / Humans Country/Region as subject: Africa Language: En Journal: Nat Biotechnol Journal subject: BIOTECNOLOGIA Year: 2019 Document type: Article Affiliation country:
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Viral / Computational Biology / Metagenome / Metagenomics Limits: Animals / Humans Country/Region as subject: Africa Language: En Journal: Nat Biotechnol Journal subject: BIOTECNOLOGIA Year: 2019 Document type: Article Affiliation country: