FDA Releases Draft Guidance for NGS-Based Tests for Infectious Disease Diagnosis

The U.S. Food and Drug Administration (FDA) released a draft guidance mid-May to provide industry with recommendations for designing studies to establish the analytical and clinical performance characteristics of next generation sequencing- (NGS-) based tests for infectious disease diagnosis.

Generally, NGS-based tests for microbial identification and detection of antimicrobial resistance and virulence markers should be submitted to the FDA. for Class II premarket approval, although certain virus targets like hepatitis B and C, human papillomavirus, and HIV could raise classification to Class III status. The draft guidance includes tests with either targeted (e.g., panels) or agnostic sequencing approaches (e.g., direct genetic analysis from a multi-organism sample).

The need for regulatory oversight was stressed at the American Society for Microbiology’s 2015 colloquium on applications of NGS for clinical microbiology as participants noted culture-based methods are being replaced with molecular methods using nucleic acid amplification and hybridization technologies.

Yet, the FDA notes that NGS for infectious disease diagnosis differs from genetic testing in many ways that affects the design of regulatory approaches. For one, NGS-based tests have the potential to detect multiple infectious agents and/or resistance and virulence markers in a single human clinical specimen.

“The broad range of specimen types (e.g., urine, blood, cerebrospinal fluid (CSF), stool, sputum, etc.) and the large diversity of the infectious disease agents that can be present in the sample do not allow straightforward pre-analytical, biochemical, or bioinformatics processes,” the FDA writes in the draft guidance. “Each unique specimen type may require a different nucleic acid extraction procedure, a different library preparation protocol, and even a different bioinformatics algorithm to generate the final clinical result.”

Therefore, the FDA proposes using a “one system” approach for the evaluation of these diagnostics. This means the FDA will evaluate these devices as a complete system, including all component parts used from sample collection to final report of results. Components generally include specimen collection device, instruments, reagents, software (to generate the sequencing library or prepare the specimen for sequencing), the sequencing instruments (along with the associated reagents and data collection elements that generate the raw sequence reads), and the data analysis pipeline (assembly, annotation, variant calling).

Additionally, given the nature of infectious disease diagnosis, rapid results are needed for immediate treatment decisions and delayed or incorrect initial diagnoses can have fatal consequences. Since confirmatory re-testing is generally unfeasible due to the rapid nature results are put into action, the FDA proposes the use of regulatory-grade sequences as an alternative comparator method for clinical evaluation that relies heavily on public databases populated with regulatory-grade target sequences, such as the “FDA-ARGOS: FDA dAtabase for Regulatory Grade micrObial Sequences; BioProject 223 231221.”

The draft guidance, which is open for public comment through Aug. 11, details expected components of submissions, including:

• Benefit-risk analysis (addresses potential for and consequences of incorrect or missed identification; incorrect or missed antimicrobial resistance marker; incorrect detection of virulence; failure to differentiate colonization from infection; and missed identification of containment)
• Intended use (including nature of target-RNA, DNA, or both; specimen types; clinical syndrome; etc.)
• Test methodology
• Ancillary reagents
• Controls
• Interpreting test results and reports (describe the computational pipeline from raw sequencing data to final report and demonstrate lockdown of the bioinformatics pipeline)
• Device validation (pre-analytical factors, device performance metrics, analytical performance, instrumentation and software, and clinical evaluation)

Takeaway: FDA proposes one-system approach to review of NGS infectious disease testing.