Munoz, Diana, Cassiani, Pamela, Li, Li, Billy, Eric, Wan, Jessica, Korn, Joshua, Jones, Michael, Golji, Javad, Ruddy, David, Yu, Kristine, Mcallister, Gregory, Hofmann, Francesco, Keen, Nicholas, Sellers, William, Schmelzle, Tobias, Stegmeier, Frank and Schlabach, Michael (2016) CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer discovery.

Abstract

The CRISPR/Cas9 system has emerged as a disruptive new tool to systematically probe gene function, but its performance and limitations have not yet been fully characterized. In this study, we compare the performance of CRISPR to RNAi-based screens for the identification of cancer dependencies by performing parallel deep-coverage shRNA and CRISPR screens targeting 2722 genes across several cancer cell line models. CRISPR-based dropout screens identified up to five times as many lethal genes compared to RNAi, indicating that RNAi-based screens have a higher rate of false-negatives. Using a CRISPR tiling array that encompasses all possible sgRNAs against the coding regions of a selected set of genes, we found that sgRNAs targeting essential domains provide the most robust dropout phenotypes. Surprisingly, we found that all highly amplified genes, including non-expressed genes, score as lethal by CRISPR, revealing an unanticipated class of false-positive hits in CRISPR-based screens. Collectively, these findings demonstrate the promise of CRISPR-based screens towards the systematic identification of cancer vulnerabilities but also reveal important limitations regarding false-positive hits especially in chromosomally unstable cancer lines.

Item Type:	Article
Date Deposited:	27 May 2016 23:45
Last Modified:	27 May 2016 23:45
URI:	https://oak.novartis.com/id/eprint/28324