@article{Kim01032016,
author = {Kim, Daesik and Kim, Sojung and Kim, Sunghyun and Park, Jeongbin and Kim, Jin-Soo}, 
title = {Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq},
volume = {26}, 
number = {3}, 
pages = {406-415}, 
year = {2016}, 
doi = {10.1101/gr.199588.115}, 
abstract ={We present multiplex Digenome-seq to profile genome-wide specificities of up to 11 CRISPR-Cas9 nucleases simultaneously, saving time and reducing cost. Cell-free human genomic DNA was digested using multiple sgRNAs combined with the Cas9 protein and then subjected to whole-genome sequencing. In vitro cleavage patterns, characteristic of on- and off-target sites, were computationally identified across the genome using a new DNA cleavage scoring system. We found that many false-positive, bulge-type off-target sites were cleaved by sgRNAs transcribed from an oligonucleotide duplex but not by those transcribed from a plasmid template. Multiplex Digenome-seq captured many bona fide off-target sites, missed by other genome-wide methods, at which indels were induced at frequencies <0.1%. After analyzing 964 sites cleaved in vitro by these sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose a guideline for the choice of target sites for minimizing CRISPR-Cas9 off-target effects in the human genome.}, 
URL = {http://genome.cshlp.org/content/26/3/406.abstract}, 
eprint = {http://genome.cshlp.org/content/26/3/406.full.pdf+html}, 
journal = {Genome Research} 
}