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G3 (Bethesda). 2017 Aug 7;7(8):2719-2727. doi: 10.1534/g3.117.041277.

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens.

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Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada.
The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada.
Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030.
Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada.
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455.
Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada.
Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada


The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.


CRISPR/Cas9; cancer cell lines; core essential genes; genetic screens

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