CRISPR off-target analysis in genetically engineered rats and mice

Nat Methods. 2018 Jul;15(7):512-514. doi: 10.1038/s41592-018-0011-5. Epub 2018 May 21.


Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that high-fidelity Cas9 versions reduced off-target mutation rates in vivo. Using whole-genome sequencing data from ten mouse embryos, treated with a single guide RNA (sgRNA), and from their genetic parents, we found 43 off-targets, 30 of which were predicted by an adapted version of GUIDE-seq.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Female
  • Genetic Engineering*
  • Genomics / methods*
  • Male
  • Mice
  • Multiplex Polymerase Chain Reaction / methods
  • RNA / genetics
  • Rats
  • Whole Genome Sequencing / methods


  • RNA