Genomic DNA off-target sites (GAA-specific) (GAA off-targets)

Genomic DNA off-target sites with sequence similarity to the GAA guide RNA are unintended locations within the human genome where CRISPR-based gene editing machinery may bind and induce modifications. These sites are characterized by their high degree of sequence homology to the guide RNA (gRNA) designed to target the acid alpha-glucosidase (GAA) gene, which is the primary therapeutic target for treating Pompe disease (Source: NIH MedlinePlus). Because CRISPR-Cas nucleases can occasionally recognize and cleave DNA sequences with several mismatches to the gRNA, these off-target sites represent a significant safety liability in the development of genomic medicines (Source: Nature Biotechnology, PMID: 25513788). The biological consequence of modifying these sites includes the risk of permanent mutations, such as insertions or deletions (indels), which can disrupt essential genes or regulatory elements. In a clinical context, these off-target effects are a primary concern for regulatory agencies, as they could potentially lead to oncogenic transformation or other deleterious cellular phenotypes (Source: Science, PMID: 23287722). Therefore, identifying and minimizing activity at these sites through rigorous bioinformatic prediction and experimental validation is a prerequisite for the safe application of GAA-targeted gene editing therapies.

Other names

CRISPR off-target sitesNon-specific genomic cleavage sitesgRNA-mismatched DNA sequencesUnintended genomic modificationsOff-target loci

Unintended DNA double-strand breaks and subsequent repair via non-homologous end joining (NHEJ) or homology-directed repair (HDR) at genomic loci with sequence similarity to the intended GAA target sequence.