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Brief Bioinform. 2018 Jul 20;19(4):721-724. doi: 10.1093/bib/bbx001.

Benchmarking CRISPR on-target sgRNA design.

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School of Life Sciences, Tongji University, China.
School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, China.
Dana-Farber Cancer Institute, Harvard School of Public Health, USA.
R&D Information, Innovation Center China, AstraZeneca, Shanghai, China.
College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China.


CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based gene editing has been widely implemented in various cell types and organisms. A major challenge in the effective application of the CRISPR system is the need to design highly efficient single-guide RNA (sgRNA) with minimal off-target cleavage. Several tools are available for sgRNA design, while limited tools were compared. In our opinion, benchmarking the performance of the available tools and indicating their applicable scenarios are important issues. Moreover, whether the reported sgRNA design rules are reproducible across different sgRNA libraries, cell types and organisms remains unclear. In our study, a systematic and unbiased benchmark of the sgRNA predicting efficacy was performed on nine representative on-target design tools, based on six benchmark data sets covering five different cell types. The benchmark study presented here provides novel quantitative insights into the available CRISPR tools.

[Indexed for MEDLINE]

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