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bioRxiv · 10.1101/480145

Base editing generates substantial off-target single nucleotide variants

Yang, H.·Li, Y.·Zuo, E.·Sun, Y.·Wei, W.·Yuan, T.·Ying, W.·Steinmetz, L. M.
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Abstract

Genome editing tools including CRISPR/Cas9 and base editors hold great promise for correcting pathogenic mutations. Unbiased genome-wide off-target effects of the editing in mammalian cells is required before clinical applications, but determination of the extent of off-target effects has been difficult due to the existence of single nucleotide polymorphisms (SNPs) in individuals. Here, we developed a method named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) to detect off-target mutations without interference of SNPs. We applied GOTI to both the CRISPR-Cas9 and base editing (BE3) systems by editing one blastomere of the two-cell mouse embryo and then compared whole genome sequences of progeny-cell populations at E14.5 stage. Sequence analysis of edited and non-edited cell progenies showed that undesired off-target single nucleotide variants (SNVs) are rare (average 10.5) in CRISPR-edited mouse embryos, with a frequency close to the spontaneous mutation rate. By contrast, BE3 editing induced over 20-fold higher SNVs (average 283), raising the concern of using base-editing approaches for biomedical application.

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Yang, H., Li, Y., Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Steinmetz, L. M.. 2018-11-27. Base editing generates substantial off-target single nucleotide variants. https://doi.org/10.1101/480145

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