Scientific Brief
SeQure DX™ Risk Assessment Services Align with FDA Guidance for Gene-Edited Human Gene Therapy Products
Since the development of CRISPR-Cas9 for targeted gene editing, the number of gene-edited cell therapies in development has significantly increased. With this rise came recognition of the need for industry-specific recommendations from international regulatory bodies. In 2024, the US Food and Drug Administration (FDA) released its first guidance for industry, "Human Gene Therapy Products Incorporating Human Genome Editing." The FDA outlines considerations for product development and non-clinical and clinical studies and provides directions on the information that should be included in any Investigational New Drug (IND) filing.
Design and screening of gene editing components
The FDA recommends that developers “optimize the [genome editing] components to reduce the potential for off-target genome modification,” noting that a “description of, and rationale for, the design and screening processes should be provided in the IND.” Our SeQure DX screening assays offer early insights into on- and off-target editing, providing unmatched precision in guide RNA design and selection. Addressing safety and regulatory expectations during guide design may reduce risks, streamline development and accelerate your path to the clinic.
Screening assays
Guide Profiler offers rapid, in silico screening of gRNA sequences against over 3,500 diverse genomes from the 1000 Genomes and HDGP initiatives, for identification of variants at the on-target site and candidate off-target editing (Figure 1). Guide Select couples in silico and multiplexed biochemical analysis for robust, cost-effective risk assessment (Figure 2). These screening tools support early-stage, variant-aware guide RNA design and selection, aligning with the FDA guidance.
Guide Profiler™ screening process
Figure 1: 1) Computational (in silico) search for sequence matches, 2) On-target variant analysis, 3) Off-target library size benchmarking, 4) Analysis of the biological impact of cutting at putative off-target loci and 5) Summary report outlining candidate guide RNA risk profiles.
Guide Select™ screening process
Figure 2: 1) In silico search for sequence matches with less than or equal to four differences, 2) Target oligos synthesized on DNA chip (~50– 240k), 3) Uniform ONE-seq™ library, 4) In vitro editing with multiplexed gRNAs, 5) Deep NGS sequencing and 6) Report detailing biological impacts and preview of off-target nomination.
Off-target risk assessment
The FDA emphasizes the need for sensitive, comprehensive, orthogonal assessment strategies to evaluate both on- and off-target editing events, genomic integrity, and associated biological impacts. Our suite of nomination and confirmation assays specifically aligns with these expectations, as illustrated in Figure 3.
Nomination assays
ONE-seq, DEUX-seq and GUIDE-seq provide high-sensitivity, orthogonal detection of candidate off-target sites across relevant human cell types. These assays address FDA recommendations for multi-method analysis and genome-wide, donor-inclusive evaluation.
Confirmation assays
Amplicon-seq and SAFER Detection verify editing activity at nominated sites and detect genomic rearrangements, including large deletions, inversions and translocations. Data generated with our confirmation assays answer the FDA’s call for genomic integrity assessments and evaluation of chromosomal abnormalities.
Figure 3: Enabling regulatory confidence. The SeQure DX assay portfolio aligns with the most recent FDA guidance for "Human Gene Therapy Products Incorporating Human Genome Editing." Our nomination and confirmation assays incorporate GLP principles and deliver data quality, reproducibility and sensitivity appropriate for regulatory submission. Our partners receive comprehensive data packages that include functional annotations of off-target events, supporting the FDA’s expectations for biological relevance and risk stratification.
About SeQure DX™
SeQure DX, a MaxCyte company, began with a mission to reduce the risk of cell therapy development and manufacturing, enabling safer therapies to reach patients faster. Our leading on- and off-target assessment assays empower precision medicine advancements across diverse viral and non-viral genome editing platforms.
Our comprehensive portfolio of regulatory-aligned screening, nomination and confirmation assays supports the rigorous analytical and safety standards required for genome editing safety assessments, from early discovery to pre clinical and IND-enabling studies.
