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FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

Author

Listed:
  • Heike Sichtig

    (U.S. Food and Drug Administration)

  • Timothy Minogue

    (U.S. Army Medical Research Institute of Infectious Diseases)

  • Yi Yan

    (U.S. Food and Drug Administration)

  • Christopher Stefan

    (U.S. Army Medical Research Institute of Infectious Diseases)

  • Adrienne Hall

    (U.S. Army Medical Research Institute of Infectious Diseases)

  • Luke Tallon

    (Institute for Genome Sciences at the University of Maryland)

  • Lisa Sadzewicz

    (Institute for Genome Sciences at the University of Maryland)

  • Suvarna Nadendla

    (Institute for Genome Sciences at the University of Maryland)

  • William Klimke

    (National Center for Biotechnology Information, National Library of Medicine)

  • Eneida Hatcher

    (National Center for Biotechnology Information, National Library of Medicine)

  • Martin Shumway

    (National Center for Biotechnology Information, National Library of Medicine)

  • Dayanara Lebron Aldea

    (Lawrence Livermore National Laboratory)

  • Jonathan Allen

    (Lawrence Livermore National Laboratory)

  • Jeffrey Koehler

    (U.S. Army Medical Research Institute of Infectious Diseases)

  • Tom Slezak

    (Lawrence Livermore National Laboratory)

  • Stephen Lovell

    (U.S. Food and Drug Administration)

  • Randal Schoepp

    (U.S. Army Medical Research Institute of Infectious Diseases)

  • Uwe Scherf

    (U.S. Food and Drug Administration)

Abstract

FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes as a public database for diagnostic purposes and demonstrate its utility on the example of two use cases. We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. In the second use case, we demonstrate the utility of FDA-ARGOS reference genomes for Ebola virus target sequence comparison as part of a composite validation strategy for ID-NGS diagnostic tests. The use of FDA-ARGOS as an in silico target sequence comparator tool combined with representative clinical testing could reduce the burden for completing ID-NGS clinical trials.

Suggested Citation

  • Heike Sichtig & Timothy Minogue & Yi Yan & Christopher Stefan & Adrienne Hall & Luke Tallon & Lisa Sadzewicz & Suvarna Nadendla & William Klimke & Eneida Hatcher & Martin Shumway & Dayanara Lebron Ald, 2019. "FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11306-6
    DOI: 10.1038/s41467-019-11306-6
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    Cited by:

    1. Jessica Karielle Tan & Venice Servellita & Doug Stryke & Emily Kelly & Jessica Streithorst & Nanami Sumimoto & Abiodun Foresythe & Hee Jae Huh & Jenny Nguyen & Miriam Oseguera & Noah Brazer & Jack Tan, 2024. "Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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