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DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing
Kim A. Lagerborg; Erica Normandin; Matthew R. Bauer; Gordon Adams; Katherine Figueroa; Christine Loreth; Adrianne Gladden-Young; Bennett Shaw; Leah Pearlman; Erica S. Shenoy; David Hooper; Virginia M. Pierce; Kimon C. Zachary; Daniel J. Park; Bronwyn L. MacInnis; Jacob E. Lemieux; Pardis C. Sabeti; Steven K. Reilly; Katherine J. Siddle.
Afiliación
  • Kim A. Lagerborg; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Erica Normandin; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Matthew R. Bauer; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Gordon Adams; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Katherine Figueroa; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Christine Loreth; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Adrianne Gladden-Young; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Bennett Shaw; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Leah Pearlman; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Erica S. Shenoy; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • David Hooper; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Virginia M. Pierce; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
  • Kimon C. Zachary; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Daniel J. Park; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Bronwyn L. MacInnis; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Jacob E. Lemieux; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Pardis C. Sabeti; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Steven K. Reilly; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
  • Katherine J. Siddle; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Preprint en En | PREPRINT-BIORXIV | ID: ppbiorxiv-435654
ABSTRACT
The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortiums amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.
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Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-BIORXIV Tipo de estudio: Diagnostic_studies / Experimental_studies / Prognostic_studies / Rct Idioma: En Año: 2021 Tipo del documento: Preprint
Texto completo
Añadir a Mi BVS
Imprimir
XML
Buscar en Google
Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-BIORXIV Tipo de estudio: Diagnostic_studies / Experimental_studies / Prognostic_studies / Rct Idioma: En Año: 2021 Tipo del documento: Preprint