Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

Nat Biotechnol. 2015 Feb;33(2):175-8. doi: 10.1038/nbt.3127. Epub 2015 Jan 19.


The utility of CRISPR-Cas9 and TALENs for genome editing may be compromised by their off-target activity. We show that integrase-defective lentiviral vectors (IDLVs) can detect such off-target cleavage with a frequency as low as 1%. In the case of Cas9, we find frequent off-target sites with a one-base bulge or up to 13 mismatches between the single guide RNA (sgRNA) and its genomic target, which refines sgRNA design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems / genetics*
  • Genetic Vectors
  • Genome, Human
  • HEK293 Cells
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Integrases / genetics
  • Lentivirus / enzymology
  • Lentivirus / genetics*
  • RNA Editing / genetics*


  • Integrases