April 21, 2020  |  

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

Authors: 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

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.

Journal: Nature communications
DOI: 10.1038/s41467-019-11306-6
Year: 2019

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