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

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

Authors:
ORCiD logo [1];  [2];  [1];  [2];  [2];  [3];  [3]; ORCiD logo [3];  [4];  [4]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [5];  [2];  [5];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States)
  2. U.S. Army Medical Research Inst. of Infectious Diseases, Frederick, MD (United States)
  3. Inst. for Genome Sciences at the Univ. of Maryland, Baltimore, MD (United States)
  4. National Library of Medicine (NLM), Bethesda, MD (United States). National Center for Biotechnology Information
  5. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1624176
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Science & Technology - Other Topics

Citation Formats

Sichtig, Heike, Minogue, Timothy, Yan, Yi, Stefan, Christopher, Hall, Adrienne, Tallon, Luke, Sadzewicz, Lisa, Nadendla, Suvarna, Klimke, William, Hatcher, Eneida, Shumway, Martin, Aldea, Dayanara Lebron, Allen, Jonathan, Koehler, Jeffrey, Slezak, Tom, Lovell, Stephen, Schoepp, Randal, and Scherf, Uwe. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. United States: N. p., 2019. Web. doi:10.1038/s41467-019-11306-6.
Sichtig, Heike, Minogue, Timothy, Yan, Yi, Stefan, Christopher, Hall, Adrienne, Tallon, Luke, Sadzewicz, Lisa, Nadendla, Suvarna, Klimke, William, Hatcher, Eneida, Shumway, Martin, Aldea, Dayanara Lebron, Allen, Jonathan, Koehler, Jeffrey, Slezak, Tom, Lovell, Stephen, Schoepp, Randal, & Scherf, Uwe. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. United States. doi:10.1038/s41467-019-11306-6.
Sichtig, Heike, Minogue, Timothy, Yan, Yi, Stefan, Christopher, Hall, Adrienne, Tallon, Luke, Sadzewicz, Lisa, Nadendla, Suvarna, Klimke, William, Hatcher, Eneida, Shumway, Martin, Aldea, Dayanara Lebron, Allen, Jonathan, Koehler, Jeffrey, Slezak, Tom, Lovell, Stephen, Schoepp, Randal, and Scherf, Uwe. Thu . "FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science". United States. doi:10.1038/s41467-019-11306-6. https://www.osti.gov/servlets/purl/1624176.
@article{osti_1624176,
title = {FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science},
author = {Sichtig, Heike and Minogue, Timothy and Yan, Yi and Stefan, Christopher and Hall, Adrienne and Tallon, Luke and Sadzewicz, Lisa and Nadendla, Suvarna and Klimke, William and Hatcher, Eneida and Shumway, Martin and Aldea, Dayanara Lebron and Allen, Jonathan and Koehler, Jeffrey and Slezak, Tom and Lovell, Stephen and Schoepp, Randal and Scherf, Uwe},
abstractNote = {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},
doi = {10.1038/s41467-019-11306-6},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {7}
}

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