Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic targets. As multiple large-scale screens become available, a formal assessment of the reproducibility of these experiments becomes necessary. We analyze data from recently published pan-cancer CRISPR-Cas9 screens performed at the Broad and Sanger Institutes. Despite significant differences in experimental protocols and reagents, we find that the screen results are highly concordant across multiple metrics with both common and specific dependencies jointly identified across the two studies. Furthermore, robust biomarkers of gene dependency found in one data set are recovered in the other. Through further analysis and replication experiments at each institute, we show that batch effects are driven principally by two key experimental parameters: the reagent library and the assay length. These results indicate that the Broad and Sanger CRISPR-Cas9 viability screens yield robust and reproducible findings.

CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated the two largest public independent CRISPR-Cas9 screens performed to date (at the Broad and Sanger institutes) by assessing, comparing, and selecting methods for correcting biases due to heterogeneous single-guide RNA efficiency, gene-independent responses to CRISPR-Cas9 targeting originated from copy number alterations, and experimental batch effects. Our integrated datasets recapitulate findings from the individual datasets, provide greater statistical power to cancer- and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. We provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets.

CRISPR-Cas9 viability screens are being increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers, and to assemble a comprehensive map of cancer genetic vulnerabilities that might be exploited therapeutically. Here, we integrated the two largest independent CRISPR-Cas9 screens performed to date (at Broad and Sanger institutes), by assessing and selecting methods for correcting technology-specific biases and batch effects arising from differences in the underlying experimental protocols. Our integrated datasets recapitulate findings from the individual ones, provide larger statistical power allowing novel cancer-and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. Finally, we provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets and assembling large cross-study cancer dependency maps.Cancer is a complex disease that can arise from multiple different genetic alterations.The alternative mechanisms by which cancer can evolve result in a large amount of heterogeneity between patients, with the vast majority of them still not benefiting from approved targeted therapies 1 . In order to identify and prioritize new potential therapeutic targets for precision cancer therapy, analyses of cancer vulnerabilities at a genome-wide scale and across large panels of in vitro cancer models are being increasingly performed 2-11 . This has been facilitated by recent advances in genome editing technologies allowing unprecedented precision and scale via CRISPR-Cas9 screens. To date, two large pan-cancer CRISPR-Cas9 screens have been independently performed by the Broad and Sanger institutes 2,12 . The two institutes have also joined forces in a collaborative endeavor with the aim of assembling a joint comprehensive map of all the intracellular genetic dependencies and vulnerabilities of cancer: the Cancer Dependency Map (DepMap) 13,14 .Despite the two generated datasets containing so far data from over 300 cell lines each, detecting all cancer dependencies has been estimated to require the analysis of thousands of cancer models 3 . Consequently, the integration of these two datasets will be key for the DepMap and other projects aiming at systematically probing cancer dependencies.This will provide a more comprehensive representation of heterogeneous cancer types as well as an increased sample size to support the use of statistical/machine-learning methods to identify molecular features associated with differential gene dependencies. This will form the basis for the development of effective new therapies with associated biomarkers for patient stratification 15 . Furthermore, designing robust standards and computational protocols for the integration of t...