Paper Info
Title
CRISPRitz: rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing.
Abstract
Motivation: Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects. Results: To overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project).
Year
DOI
Venue
2020
10.1093/bioinformatics/btz867
BIOINFORMATICS
DocType
Volume
Issue
Journal
36
7
ISSN
Citations 
PageRank 
1367-4803
0
0.34
References 
Authors
0
5
Name
Order
Citations
PageRank
Samuele Cancellieri100.34
Matthew C Canver200.68
Nicola Bombieri331838.74
Rosalba Giugno400.34
Luca Pinello5497.71