Detection and quantification of unintended large on-target gene modifications due to CRISPR/Cas9 editing

CRISPR/Cas9 based gene editing typically functions by creating a DNA double-strand break (DSB) at the intended target locus in a cell. Recent reports showed the occurrence of unintended on-target large gene modifications by CRISPR/Cas9-induced DSB, including large deletions, insertions, and chromosomal rearrangements, in addition to small insertions and deletions. These on-target large gene modifications can have high frequencies, undetectable by standard short-range PCR based assays, leading to data misinterpretation, reduced efficacy, and potential safety concerns in therapeutic gene editing. Here, we summarize the recent advances in analyzing large on-target gene editing outcomes and their implications to clinical application, and discuss opportunities for future improvements.