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

Heike Sichtig (), Timothy Minogue (), Yi Yan, Christopher Stefan, Adrienne Hall, Luke Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, Dayanara Lebron Aldea, Jonathan Allen, Jeffrey Koehler, Tom Slezak, Stephen Lovell, Randal Schoepp and Uwe Scherf
Additional contact information
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

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-11306-6

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