FDA Issues Draft Guidance on Next-Generation Sequencing for Gene Therapy Safety Assessment
核心洞察
The FDA's Center for Biologics Evaluation and Research (搜索) has released draft guidance establishing standardized methods for using next-generation sequencing to assess safety risks in genome editing (搜索) therapies.
The guidance focuses on detecting off-target gene editing events and chromosomal translocations that could pose safety risks in both ex vivo and in vivo genome editing (搜索) products.
FDA Commissioner Marty Makary emphasized that genome editing (搜索) holds "extraordinary promise" for treating previously incurable genetic diseases (搜索) and represents the agency's forward approach to advancing therapeutic development.
The US Food and Drug Administration has released comprehensive draft guidance establishing standardized methods for using next-generation sequencing (NGS) technologies to assess safety risks associated with genome editing (搜索) therapies. The framework, developed by the Office of Therapeutic Products within the Center for Biologics Evaluation and Research (搜索) (CBER), aims to support sponsors developing both ex vivo and in vivo genome editing therapies seeking investigational new drug (IND) applications and biologics license applications.
Focus on Off-Target Editing Risks
The guidance places particular emphasis on how NGS methods can identify and account for potential safety risks associated with off-target gene editing events. According to the document, clinical development programs for genome edited products "should address both the risks associated with the gene therapy product itself as well as the additional risks associated with genome editing (搜索), including off-target editing and unintended changes to the genome for therapies targeting genetic diseases (搜索), including individualized therapies."
The FDA notes that gene editing at unintended sites or chromosomal translocations poses potential safety risks, as such edits may negatively impact normal cell function. To mitigate these risks, the agency advises sponsors to conduct complete analyses evaluating off-target editing risks and their effects on chromosomal integrity.
Sequencing Strategy Recommendations
The guidance provides detailed recommendations for sequencing strategies based on the type of genomic changes being assessed. For evaluating off-target sites that result in changes to short DNA stretches, the FDA recommends short-read sequencing-based methods. However, for longer sequence stretches, sponsors should implement long-read sequencing-based methods.
The document specifies that "sequencing should be performed using an adequate amount of the input material (genomic DNA, cell number, or RNA, as applicable) at a depth that allows detection of potential off-target editing events occurring at frequencies or edit rates that are usually lower than the on-target edit rate." Sponsors must provide in-house data, such as representative data from engineering NGS runs, and relevant information from peer-reviewed publications to support the adequacy and sensitivity of sequencing depth.
Genomic Integrity Assessment
For genome editing (搜索) techniques known to cause DNA double-strand breaks, as well as medium to large insertions or deletions that could affect genomic integrity, the FDA recommends sponsors perform "sensitive and quantitative" assessments of genomic integrity in edited cells using NGS. In these situations, sponsors should consider "choosing targeted sequencing and/or primer-based sequencing or other genome-wide NGS-based methods to detect low frequency translocation events and report chromosomal translocation rate(s) between on-target genomic site(s) where double strand break events occurred during genome editing."
Regulatory Context and Industry Impact
FDA Commissioner Marty Makary emphasized the significance of this guidance, stating that "genome editing (搜索) holds extraordinary promise for treating previously incurable genetic diseases (搜索), and today's announcement represents the FDA's forward approach to drive innovation and advance the development of genome editing therapies. This guidance provides sponsors with clear, scientifically-grounded recommendations for evaluating off-target editing risks using state-of-the-art sequencing technologies. We are serious about moving this ball forward."
The guidance builds upon previous regulatory frameworks, complementing the FDA's January 2024 guidance that addressed nonclinical, clinical, and chemistry, manufacturing, and controls considerations for human gene therapy products incorporating human genome editing (搜索).
Growing Industry Investment
The regulatory framework emerges amid significant industry investment in genome editing (搜索) technologies. Eli Lilly recently committed $1.12 billion to co-develop and commercialize gene editing therapies for hearing loss (搜索) with Seamless Therapeutics (搜索), and acquired gene editing medicines developer Verve Therapeutics for $1.3 billion. Verve is currently developing drugs designed to address drivers of atherosclerotic cardiovascular disease (搜索).
AstraZeneca has also invested in the modality through a $555 million deal with Algen Biotechnologies (搜索) for discovering novel therapeutic targets for immunological indications.
According to GlobalData, two-thirds of genome editors utilize CRISPR (搜索) technology, which gained significant attention following the milestone approval of Vertex Pharmaceuticals' CRISPR/Cas9-based sickle cell disease (搜索) gene therapy, Casgevy (exagamglogene autotemcel). However, the pipeline remains mostly early-stage, with development concentrated in high-impact areas including cancer (搜索) and rare diseases (搜索).
The FDA has opened the guidance for public comment until June 15, 2025, with submissions accepted through www.regulations.gov under docket number FDA-2026-D-1255.