Comment from James Adams

To the Dockets Management Staff (HFA-305), I am writing to provide comments on the draft guidance regarding the safety assessment of genome editing in human gene therapy products. While I commend the FDA for providing a clear framework for the use of Next-Generation Sequencing (NGS) to detect off-target effects, I strongly recommend that the final guidance include Optical Genome Mapping (OGM) as a critical, complementary methodology for assessing genomic integrity. 1. Addressing the "Structural Variation Blind Spot" in NGS While NGS is the gold standard for detecting single-nucleotide variants and small indels, it is technically limited in its ability to detect large-scale structural variations (SVs) exceeding 500 base pairs, such as large translocations, inversions, and complex chromosomal rearrangements (e.g., chromothripsis). Genome editing, particularly CRISPR-Cas9, has been documented to cause unintended large-scale genomic alterations that NGS-based "short-read" methods often fail to span or resolve. 2. Superior Sensitivity for Loss of Genomic Integrity The current draft emphasizes "loss of genome integrity." Recent multicenter studies (e.g., Johns Hopkins and MD Anderson, April 2026) have demonstrated that OGM can identify pathogenic structural abnormalities in up to 30% of cases where traditional methods—including some NGS workflows—failed to detect them. By linearizing long DNA molecules, OGM provides the "big picture" of the genome necessary to ensure that gene-editing interventions have not introduced catastrophic structural changes. 3. Economic and Clinical Efficiency Including OGM in the safety assessment framework would align with the FDA’s goal of bringing individualized therapies to patients safely and efficiently. OGM serves as a faster, higher-resolution alternative to traditional karyotyping and FISH, which are currently used to monitor gross chromosomal stability but lack the resolution to detect cryptic rearrangements essential for modern gene therapy safety. Conclusion: To ensure the highest level of patient safety and a comprehensive assessment of "off-target" consequences, I urge the FDA to amend the final guidance to recommend Optical Genome Mapping alongside NGS. A dual-technology approach is necessary to capture the full spectrum of genomic alterations—from single-base changes to large-scale structural rearrangements—that may arise during the genome-editing process. I invite the FDA to review the findings published in Molecular Therapy — Methods & Clinical Development (Feb 2026), titled "Application of Optical Genome Mapping to Detect Genomic Alterations Introduced by Gene Editing Technologies." This study explicitly demonstrates that OGM can detect off-target rearrangements and variant allele fractions (VAFs) as low as 5%, outperforming sequencing-based methods in identifying complex and cryptic structural variants in edited human induced pluripotent stem cell (iPSC) lines. Sincerely, James Adams