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.
复制标题
DOI：
10.1038/mtna.2014.64
复制
发表时间：
2014-12-02
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
使用工程核酸酶进行精确的基因组编辑可以显著促进生物学研究和疾病治疗。特别是，聚集规律间隔短回文重复序列（CRISPR）与CRISPR相关（Cas）蛋白是一种潜在的强大工具，可以通过靶向切割与设计的引导链rna互补的DNA序列来修饰基因组。尽管CRISPR/Cas系统可以具有接近转染率的靶上切割率，但它们也可能在含有一个或多个碱基对错配的类似基因组位点上具有相对较高的靶外切割率，以及相对于引导链的插入或缺失。我们开发了一种基于生物信息学的工具COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and deletion)，用于搜索基因组中潜在的脱靶位点（http://crispr.bme.gatech.edu）。根据用户提供的引导链和输入参数，COSMID识别出潜在的脱靶位点，这些脱靶位点具有指定数量的不匹配碱基和插入或删除，并与引导链进行比较。对于每个位点，扩增引物的最佳选择的应用也给出了作为输出。这个潜在脱靶位点的排序列表有助于选择和评估预期的靶位，从而帮助设计具有最小脱靶效应的CRISPR/Cas系统，以及鉴定和量化CRISPR/Cas诱导的细胞脱靶切割。
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.
登录
查看更多内容
影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
影响因子：
17.3
作者：
Gaj, Thomas;Gersbach, Charles A.;Barbas, Carlos F., III
通讯作者：
Barbas, Carlos F., III
影响因子：
56.9
作者：
Jinek, Martin;Chylinski, Krzysztof;Charpentier, Emmanuelle
通讯作者：
Charpentier, Emmanuelle
DOI：
10.1007/978-1-60761-753-2_14
发表时间：
2010-01-01
期刊：
ENGINEERED ZINC FINGER PROTEINS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Cornu, Tatjana I.;Cathomen, Toni
通讯作者：
Cathomen, Toni
影响因子：
14.9
作者：
Fine EJ;Cradick TJ;Zhao CL;Lin Y;Bao G
通讯作者：
Bao G