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Design and analysis of CRISPR–Cas experiments

Abstract

A large and ever-expanding set of CRISPR–Cas systems now enables the rapid and flexible manipulation of genomes in both targeted and large-scale experiments. Numerous software tools and analytical methods have been developed for the design and analysis of CRISPR–Cas experiments, including resources to design optimal guide RNAs for various modes of manipulation and to analyze the results of such experiments. A major recent focus has been the development of comprehensive tools for use on data from large-scale CRISPR-based genetic screens. As this field continues to progress, a clear ongoing challenge is not only to innovate, but to actively maintain and improve existing tools so that researchers across disciplines can rely on a stable set of excellent computational resources for CRISPR–Cas experiments.

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Fig. 1: Sites in the human genome potentially able to be edited with CRISPR technology.
Fig. 2: Comparison of website tools for the selection of guide RNAs.
Fig. 3: Example workflow for analysis of large-scale pooled screens.

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Data availability

The data analyzed in Box 2 were accessed from the original publications.

Code availability

The code used to generate Fig. 1 and Box 2 is publicly available at https://github.com/ruth-hanna/software-tools-review.

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Acknowledgements

The authors thank M. Hegde for assistance with analysis and P. DeWeirdt for discussions.

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Correspondence to John G. Doench.

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J.G.D. is on the advisory board for Addgene and consults for Tango Therapeutics, Foghorn Therapeutics and Pfizer.

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Supplementary Table 1

The diversity of characterized Cas nucleases and their associated PAM sites that have been characterized for use in mammalian cells.

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Hanna, R.E., Doench, J.G. Design and analysis of CRISPR–Cas experiments. Nat Biotechnol 38, 813–823 (2020). https://doi.org/10.1038/s41587-020-0490-7

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