Comment from Aleksandar Rajkovic

We commend the Food and Drug Administration (FDA) for providing a clear, science-driven framework for standardizing safety assessments of genome editing (GE) products. The emphasis on detecting low-frequency events and ensuring genomic integrity is vital for protecting patient safety. While Next-Generation Sequencing (NGS) is highly effective for identifying small insertion/deletion mutations (indels) and single nucleotide variants (SNVs), short-read and even some long-read sequencing technologies face technical limitations when resolving complex, large-scale structural variants (SVs). These include balanced translocations, large inversions, duplications, and high-order genomic rearrangements often caused by double-strand breaks (DSBs). To maximize regulatory safety standards, we respectfully request that the FDA explicitly include Optical Genome Mapping (OGM) in the final guidance document as a recommended orthogonal tool for the assessment of structural variants and chromosomal integrity. Our own experience has shown us that OGM is an important tool for assessing chromosomal integrity and we are aware of several papers describing this importance, including:We commend the Food and Drug Administration (FDA) for providing a clear, science-driven framework for standardizing safety assessments of genome editing (GE) products. The emphasis on detecting low-frequency events and ensuring genomic integrity is vital for protecting patient safety. While Next-Generation Sequencing (NGS) is highly effective for identifying small insertion/deletion mutations (indels) and single nucleotide variants (SNVs), short-read and even some long-read sequencing technologies face technical limitations when resolving complex, large-scale structural variants (SVs). These include balanced translocations, large inversions, duplications, and high-order genomic rearrangements often caused by double-strand breaks (DSBs). To maximize regulatory safety standards, we respectfully request that the FDA explicitly include Optical Genome Mapping (OGM) in the final guidance document as a recommended orthogonal tool for the assessment of structural variants and chromosomal integrity. Our own experience has shown us that OGM is an important tool for assessing chromosomal integrity and we are aware of several papers describing this importance, including: Cell line authentication using optical genome mapping https://pmc.ncbi.nlm.nih.gov/articles/PMC12257773/ Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research https://pmc.ncbi.nlm.nih.gov/articles/PMC10969360/ Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR-Cas9-mediated genome editing https://www.nature.com/articles/s41467-023-40901-x Unveiling Genomic Rearrangements in Engineered iPSC Lines by Optical Genome Mapping https://pubmed.ncbi.nlm.nih.gov/40654907/