evaluation and design of genome-wide crispr/spcas9 knockout screens

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ID: 260118
2017
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Abstract
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.
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hart2017g3:evaluation Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Traver Hart;Amy Hin Yan Tong;Katie Chan;Jolanda Van Leeuwen;Ashwin Seetharaman;Michael Aregger;Megha Chandrashekhar;Nicole Hustedt;Sahil Seth;Avery Noonan;Andrea Habsid;Olga Sizova;Lyudmila Nedyalkova;Ryan Climie;Leanne Tworzyanski;Keith Lawson;Maria Augusta Sartori;Sabriyeh Alibeh;David Tieu;Sanna Masud;Patricia Mero;Alexander Weiss;Kevin R. Brown;Matej Usaj;Maximilian Billmann;Mahfuzur Rahman;Michael Constanzo;Chad L. Myers;Brenda J. Andrews;Charles Boone;Daniel Durocher;Jason Moffat
Journal separation and purification technology
Year 2017
DOI
10.1534/g3.117.041277
URL
http://g3journal.org/lookup/doi/10.1534/g3.117.041277
Keywords
crispr/cas9 cancer cell linesgenetics

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