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

Area of Science:

• Genomics
• Bioinformatics
• Infectious Disease Diagnostics

Background:

• Emerging technologies like infectious disease next-generation sequencing (ID-NGS) require robust supporting tools.
• Public genomic databases often lack sufficient quality control for diagnostic applications.

Purpose of the Study:

• Introduce FDA-ARGOS, a quality-controlled reference genome database for diagnostic use.
• Demonstrate the utility of FDA-ARGOS in improving microbial identification and sequence comparison for ID-NGS.

Main Methods:

• Developed and quality-controlled a public reference genome database (FDA-ARGOS).
• Evaluated FDA-ARGOS using two use cases: microbial identification and Ebola virus target sequence comparison.
• Assessed performance against non-curated GenBank genomes.

Main Results:

• FDA-ARGOS enabled more accurate identification of Enterococcus avium from metagenomic samples compared to GenBank.
• Demonstrated the utility of FDA-ARGOS for Ebola virus target sequence comparison in ID-NGS validation.
• Provided quality control metrics and highlighted the need for genome quality gap filling.

Conclusions:

• FDA-ARGOS serves as a valuable resource for diagnostic purposes, enhancing the accuracy of ID-NGS.
• Utilizing FDA-ARGOS can streamline the validation of ID-NGS diagnostic tests, reducing clinical trial burdens.