Whole genome sequencing unveils that the frequency of spurious mutations is not substantially increased by CRISPR-Cas9 genome editing

Authors

• M Willi
• HE Smith
• C Wang
• C Liu
• L Hennighausen

Abstract

CRISPR-Cas9 genome editing is widely used and holds promise in personalized medicine for correcting human mutations and preventing diseases. However, recent studies have reported complex mutations on the target site of CRISPR-Cas9 treated mice. Thus, the safe application of this technology requires an additional understanding of potential off-target mutations, knowledge that currently does not exist and could be obtained by whole genome sequencing (WGS). We conducted WGS on 36 mice, 24 parents, six CRISPR-Cas9 edited, and six non-injected control pups, at a coverage of 60X. The single nucleotide polymorphisms (SNPs) and insertions and deletions (indels) analyses identified a similar number of mutations in each individual, with no evidence that those with a CRISPR-Cas9 edited genome carried more SNPs or indels. In order to extract de novo mutations, the SNPs and indels identified in the parents were subtracted from the progeny. Those results demonstrate that the number of de novo mutations is not significantly different between CRISPR-Cas9 mutated and control mice. Further characterization of SNPs and indels did not uncover differences in the properties of the de novo mutations identified in the progeny. Finally, we also did not identify mutations overlapping with predicted off-target sites. Our in-depth analysis of 36 WGS samples unveils that there is no evidence that CRISPR-Cas9 causes unintended mutations in vivo. Although we do not observe an increase in mutagenesis, our results do not rule out the occurrence of rare mutations at specific genomic loci or genomic rearrangement induced by CRISPR-Cas9 genome editing that could be problematic.

Scientific Focus Area: Genetics and Genomics

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