Safety Assessment of Genome Editing in Human Gene Therapy Products Using Next-Generation Sequencing; Draft Guidance for Industry

Dr. Kay C. Wiese, representing Simon Fraser University's Computational Biology Lab, proposes four specific quantitative reporting elements to be added to the draft guidance. The author argues for more rigorous disclosure of off-target nomination completeness, structural-variant detection floors, sequencing-depth adequacy, and bioinformatics reproducibility to address current qualitative gaps in the draft.

Diane Castillo, an independent scientist, argues that the proposed guidance is too permissive and fails to account for the stochastic and unpredictable nature of genome editing. She advocates for requiring single-cell long-read whole genome sequencing (scLRWGS) to detect large structural variants and off-target events that current short-read and targeted methods miss.

SeQure, a contract research organization, supports the draft guidance and suggests specific improvements regarding minimum sensitivity for off-target confirmation, the inclusion of optical genome mapping for structural variations, and the recommendation of insertion site analysis for certain payloads. They also advocate for high-throughput biochemical assays to account for human genetic variation and editor-specific nomination strategies.

The commenter provides specific technical feedback on the draft guidance, requesting clarification on FDA expectations for assurance levels when no off-target edits are detected. They also suggest that the guidance should include methods to normalize against chromosomal abnormalities that occur independently of genome editing methods.