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

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

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 t...

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Main Authors: Cradick, Thomas J, Qiu, Peng, Lee, Ciaran M, Fine, Eli J, Bao, Gang
Format: Online
Language:English
Published: Nature Publishing Group 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272406/
id pubmed-4272406
recordtype oai_dc
spelling pubmed-42724062014-12-29 COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites Cradick, Thomas J Qiu, Peng Lee, Ciaran M Fine, Eli J Bao, Gang Original Article 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. Nature Publishing Group 2014-12 2014-12-02 /pmc/articles/PMC4272406/ /pubmed/25462530 http://dx.doi.org/10.1038/mtna.2014.64 Text en Copyright © 2014 American Society of Gene & Cell Therapy http://creativecommons.org/licenses/by-nc-sa/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Cradick, Thomas J
Qiu, Peng
Lee, Ciaran M
Fine, Eli J
Bao, Gang
spellingShingle Cradick, Thomas J
Qiu, Peng
Lee, Ciaran M
Fine, Eli J
Bao, Gang
COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
author_facet Cradick, Thomas J
Qiu, Peng
Lee, Ciaran M
Fine, Eli J
Bao, Gang
author_sort Cradick, Thomas J
title COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
title_short COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
title_full COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
title_fullStr COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
title_full_unstemmed COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
title_sort cosmid: a web-based tool for identifying and validating crispr/cas off-target sites
description 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.
publisher Nature Publishing Group
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272406/
_version_ 1613169305080299520

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