In February of last year the FDA hosted a two-day workshop focused on technical and regulatory considerations related to the use of next generation sequencing (NGS) diagnostics in clinical practice.  This was a very forward-thinking move on the part of FDA, as clinical NGS is advancing rapidly and will soon become routine in the clinical laboratory.  The Genetic Testing Registry (GTR) currently lists 32,621 genetic tests, and 9,524 of them (or 29%) are NGS tests.

Last week FDA continued its support for clinical NGS diagnostic tests by releasing two draft guidances that clarify technical and scientific validity standards for NGS assays.

The first document describes how assay developers can use public databases of clinically validated genetic variants in support of their assay validation, and the guidelines that will be used to review and approve such databases.  The second document describes technical considerations for NGS tests, and focuses on tests for inherited disorders.  One must assume that a draft guidance for testing of somatic mutations will soon follow this germline-specific guidance document.

The database document is interesting in that it states FDA will only consider “curated databases using expert human interpretation” as meaningful for assay validation.  The Agency will also soon maintain a list of approved variant databases, which will interesting to evaluate.

The technical NGS document reads like most of the other product-related guidances that FDA has issued, with detailed discussion of technical and regulatory considerations.

An interesting omission from both documents is any reference to FDA’s plans to regulate lab-developed tests (LDTs). According to BiomarkerBase there are only 3 FDA-cleared or approved tests on the market that use sequencing, which is just 0.3% of all biomarker-based FDA tests.  There has been scant communication from FDA regarding timing on implementation of its LDT regulations, and given the rapid growth in NGS LDTs it seems like final guidance on LDT regulation should be forthcoming soon.