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Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.
Bloom, Joshua S; Sathe, Laila; Munugala, Chetan; Jones, Eric M; Gasperini, Molly; Lubock, Nathan B; Yarza, Fauna; Thompson, Erin M; Kovary, Kyle M; Park, Jimin; Marquette, Dawn; Kay, Stephania; Lucas, Mark; Love, TreQuan; Sina Booeshaghi, A; Brandenberg, Oliver F; Guo, Longhua; Boocock, James; Hochman, Myles; Simpkins, Scott W; Lin, Isabella; LaPierre, Nathan; Hong, Duke; Zhang, Yi; Oland, Gabriel; Choe, Bianca Judy; Chandrasekaran, Sukantha; Hilt, Evann E; Butte, Manish J; Damoiseaux, Robert; Kravit, Clifford; Cooper, Aaron R; Yin, Yi; Pachter, Lior; Garner, Omai B; Flint, Jonathan; Eskin, Eleazar; Luo, Chongyuan; Kosuri, Sriram; Kruglyak, Leonid; Arboleda, Valerie A.
Afiliación
  • Bloom JS; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. jbloom@mednet.ucla.edu.
  • Sathe L; Howard Hughes Medical Institute, Chevy Chase, MD, USA. jbloom@mednet.ucla.edu.
  • Munugala C; Octant Inc., Emeryville, CA, USA. jbloom@mednet.ucla.edu.
  • Jones EM; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Gasperini M; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Lubock NB; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Yarza F; Octant Inc., Emeryville, CA, USA.
  • Thompson EM; Octant Inc., Emeryville, CA, USA.
  • Kovary KM; Octant Inc., Emeryville, CA, USA.
  • Park J; Octant Inc., Emeryville, CA, USA.
  • Marquette D; Octant Inc., Emeryville, CA, USA.
  • Kay S; Octant Inc., Emeryville, CA, USA.
  • Lucas M; Octant Inc., Emeryville, CA, USA.
  • Love T; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Sina Booeshaghi A; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Brandenberg OF; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Guo L; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Boocock J; Department of Mechanical Engineering, Caltech, Pasadena, CA, USA.
  • Hochman M; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Simpkins SW; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Lin I; Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • LaPierre N; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Hong D; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Zhang Y; Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Oland G; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Choe BJ; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Chandrasekaran S; Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Hilt EE; Octant Inc., Emeryville, CA, USA.
  • Butte MJ; Octant Inc., Emeryville, CA, USA.
  • Damoiseaux R; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Kravit C; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Cooper AR; Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA.
  • Yin Y; Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Pachter L; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Garner OB; Department of Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Flint J; Department of Emergency Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Eskin E; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Luo C; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Kosuri S; Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
  • Kruglyak L; Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, CA, USA.
  • Arboleda VA; California NanoSystems Institute, UCLA, Los Angeles, CA, USA.
Nat Biomed Eng ; 5(7): 657-665, 2021 07.
Article en En | MEDLINE | ID: mdl-34211145
Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Saliva / ARN Viral / SARS-CoV-2 Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Nat Biomed Eng Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Saliva / ARN Viral / SARS-CoV-2 Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Nat Biomed Eng Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido