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CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions

Munoz, Diana and Cassiani, Pamela and Li, Li and Billy, Eric and Wan, Jessica and Korn, Joshua and Jones, Michael and Golji, Javad and Ruddy, David and Yu, Kristine and Mcallister, Gregory and Hofmann, Francesco and Keen, Nicholas and Sellers, William and Schmelzle, Tobias and 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

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