Off-target genomic sites with partial guide RNA complementarity (CRISPR off-targets)

Off-target genomic sites with partial guide RNA complementarity refer to locations in the genome where gene-editing tools, particularly CRISPR-Cas9, bind and induce double-strand breaks despite not being the intended target. This occurs because the guide RNA (gRNA) can tolerate a limited number of mismatches, insertions, or deletions when pairing with DNA sequences that are similar to the target site (Fu et al., 2013, Nature Biotechnology). While these sites are not therapeutic targets themselves, they represent a significant safety hurdle in the development of genetic medicines. Unintended modifications at these loci can lead to deleterious mutations, chromosomal rearrangements, or the activation of oncogenes, potentially causing secondary diseases like cancer (Zhang et al., 2015, Molecular Therapy - Nucleic Acids). Consequently, rigorous off-target assessment using both computational predictions and empirical sequencing methods like GUIDE-seq is a critical component of the regulatory approval process for gene therapies (Tsai et al., 2015, Nature Biotechnology). Understanding and minimizing these interactions is essential for the clinical safety of CRISPR-based therapeutics such as Exagamglogene autotemcel.

Other names

CRISPR off-target effectsNon-specific genomic cleavage sitesOff-target mutationsgRNA-mismatched sitesUnintended genomic modifications

Unintended binding and cleavage of genomic DNA by a CRISPR-Cas complex or other programmable nucleases due to sequence similarity (homology) between the guide RNA and a non-target genomic locus, often involving mismatches, bulges, or alternative PAM sequences.