Genome-wide profiling of off-target effects.
Digenome-seq is an in vitro nuclease-digested whole-genome sequencing to profile genome-wide nuclease off-target effects in cells. This in vitro digest yields sequence reads with the same 5' ends at cleavage sites that can be computationally identified by Digenome program.
Citation info: Kim D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nature Methods 12, 237-243 (2015).
You can download a standalone program for digenome-seq here.
You can download a standalone program for edit distance calculator here(zip included).
After analyzing 964 sites cleaved in vitro by different 11 sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose an off-target scoring system of each target site for minimizing CRISPR-Cas9 off-target effects in the human genome. Please note that this off-target score is available for human genome with SpCas9 nucleases.
Citation info: Kim D. et al. Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Research doi:10.1101/gr.199588.115 (2016).
- Organism: Homo sapiens (GRCh38/hg38) — human
- SpCas9 nuclease from Steptococcus pyogenes (PAM is 5'-NGG-3')