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High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
John E Gorzynski; Hannah N De Jong; David Amar; Chris R Hughes; Alexander Ioannidis; Rob Bierman; Darren Liu; Yosuke Tanigawa; Amy Kistler; Jack Kamm; Jaehee Kim; Lorenzo Cappello; Norma F. Neff; Simone Rubinacci; Olivier Delaneau; Massa J. Shoura; Kinya Seo; Anna Kirillova; Archana Raja; Shirley Sutton; ChunHong Huang; Malaya Kumar Sahoo; Kalyan C. Mallempati; Gonzalo Montero-Martin; Kazutoyo Osoegawa; David Jimenez-Morales; Nathaniel Watson; Nathan Hammond; Ruchi Joshi; Marcelo Fernandez-Vina; Jeffrey W. Christle; Matthew T. Wheeler; Phil Febbo; Kyle Farh; Gary Schroth; F Desouza; Julia Palacios; Julia Salzman; Benjamin A. Pinsky; Manuel A Rivas; Carlos D. Bustamante; Euan A. Ashley; Victoria N. Parikh.
Affiliation
  • John E Gorzynski; Department of Genetics, Stanford University, Stanford CA
  • Hannah N De Jong; Department of Genetics, Stanford University, Stanford CA
  • David Amar; Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Chris R Hughes; Department of Genetics, Stanford University, Stanford CA
  • Alexander Ioannidis; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
  • Rob Bierman; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
  • Darren Liu; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
  • Yosuke Tanigawa; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
  • Amy Kistler; Chan Zuckerberg Biohub, San Francisco, CA
  • Jack Kamm; Chan Zuckerberg Biohub, San Francisco, CA
  • Jaehee Kim; Department of Biology, Stanford University, Stanford, CA
  • Lorenzo Cappello; Department of Statistics, Stanford University, Stanford, CA
  • Norma F. Neff; Chan Zuckerberg Biohub, San Francisco, CA
  • Simone Rubinacci; Swiss Institure of Bioinformatics
  • Olivier Delaneau; Swiss Institute of BioInformatics
  • Massa J. Shoura; Department of Genetics, Stanford University, Stanford, CA, Department of Pathology, Stanford University School of Medicine, Stanford, CA
  • Kinya Seo; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Anna Kirillova; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Archana Raja; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Shirley Sutton; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • ChunHong Huang; Department of Pathology, Stanford University School of Medicine, Stanford, CA
  • Malaya Kumar Sahoo; Department of Pathology, Stanford University School of Medicine, Stanford, CA
  • Kalyan C. Mallempati; Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA
  • Gonzalo Montero-Martin; Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA
  • Kazutoyo Osoegawa; Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA
  • David Jimenez-Morales; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Nathaniel Watson; Clinical Genomics Program, Stanford Medicine, Palo Alto, CA
  • Nathan Hammond; Clinical Genomics Program, Stanford Medicine, Palo Alto, CA
  • Ruchi Joshi; Clinical Genomics Program, Stanford Medicine, Palo Alto, CA
  • Marcelo Fernandez-Vina; Department of Statistics, Stanford University, Department of Pathology, Stanford University School of Medicine, Stanford, CA
  • Jeffrey W. Christle; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Matthew T. Wheeler; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
  • Phil Febbo; Illumina, San Dieg, CA
  • Kyle Farh; Illumina, San Diego, C
  • Gary Schroth; Illumina, Inc., San Diego, CA
  • F Desouza; Illumina, San Diego, CA
  • Julia Palacios; Biomedical Data Science, Stanford University, Stanford, CA, Department of Statistics, Stanford University
  • Julia Salzman; Biomedical Data Science, Stanford University, Stanford, CA
  • Benjamin A. Pinsky; Department of Pathology, Stanford University School of Medicine, Stanford, CA, Department of Medicine, Division of Infectious Diseases and Geographic Medicine,
  • Manuel A Rivas; Biomedical Data Science, Stanford University, Stanford, CA
  • Carlos D. Bustamante; Department of Genetics, Stanford University, Stanford CA, Biomedical Data Science, Stanford University, Stanford, CA
  • Euan A. Ashley; Department of Genetics, Stanford University, Stanford CA, Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, S
  • Victoria N. Parikh; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
Preprint in English | medRxiv | ID: ppmedrxiv-20163147
ABSTRACT
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.
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Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2020 Document type: Preprint
Fulltext
Add to My VHL
Print
XML
Search on Google
Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2020 Document type: Preprint