COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

• Type of Material: Article
• Authors: Thomas J. Cradick, Georgia Institute of Technology; Peng Qiu, Georgia Institute of Technology; Ciaran M. Lee, Georgia Institute of Technology; Eli J. Fine, Georgia Institute of Technology; Gang Bao, Emory University
• Language: English
• Date: 2014-12-01
• Publisher: CELL PRESS
• Publication Version: Final Published Version
• Copyright Statement: © 2014 The American Society of Gene & Cell Therapy All rights reserved.
• License: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
• Final Published Version (URL): http://dx.doi.org/10.1038/mtna.2014.64
• Title of Journal or Parent Work: MOLECULAR THERAPY-NUCLEIC ACIDS
• Volume: 3
• Issue: 12
• Start Page: e214
• End Page: e214
• Grant/Funding Information: This work was supported by the National Institutes of Health through a Nanomedicine Development Center Award (PN2EY018244 to G.B.).
• Keywords: bulges; IMMUNE-SYSTEM; CAS9; DEFENSE; SEARCHES; BACTERIA; RISPR; NUCLEASES; Life Sciences & Biomedicine; Science & Technology; DNA CLEAVAGE; off-target; ADAPTIVE IMMUNITY; SPECIFICITY; Medicine, Research & Experimental; program; bioinformatics; Research & Experimental Medicine; specificity; DELETIONS
• Research Categories: Biology, Bioinformatics; Health Sciences, Immunology

Abstract

Precise genome editing using engineered nucleases can significantly facilitate biological studies and disease treatment. In particular, clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated (Cas) proteins are a potentially powerful tool for modifying a genome by targeted cleavage of DNA sequences complementary to designed guide strand RNAs. Although CRISPR/Cas systems can have on-target cleavage rates close to the transfection rates, they may also have relatively high off-target cleavage at similar genomic sites that contain one or more base pair mismatches, and insertions or deletions relative to the guide strand. We have developed a bioinformatics-based tool, COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu). Based on the user-supplied guide strand and input parameters, COSMID identifies potential off-target sites with the specified number of mismatched bases and insertions or deletions when compared with the guide strand. For each site, amplification primers optimal for the chosen application are also given as output. This ranked-list of potential off-target sites assists the choice and evaluation of intended target sites, thus helping the design of CRISPR/Cas systems with minimal off-target effects, as well as the identification and quantification of CRISPR/Cas induced off-target cleavage in cells.