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Improved design and analysis of CRISPR knockout screens.

ABSTRACT: Motivation:Genome-wide clustered, regularly interspaced, short palindromic repeat (CRISPR)-Cas9 screen has been widely used to interrogate gene functions. However, the rules to design better libraries beg further refinement. Results:We found single guide RNA (sgRNA) outliers are characterized by higher G-nucleotide counts, especially in regions distal from the PAM motif and are associated with stronger off-target activities. Furthermore, using non-targeting sgRNAs as negative controls lead to strong bias, which can be mitigated by using sgRNAs targeting multiple 'safe harbor' regions. Custom-designed screens confirmed our findings and further revealed that 19?nt sgRNAs consistently gave the best signal-to-noise ratio. Collectively, our analysis motivated the design of a new genome-wide CRISPR/Cas9 screen library and uncovered some intriguing properties of the CRISPR-Cas9 system. Availability and implementation:The MAGeCK workflow is available open source at https://bitbucket.org/liulab/mageck_nest under the MIT license. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Chen CH

PROVIDER: S-EPMC6247926 | BioStudies | 2018-01-01

REPOSITORIES: biostudies

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