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CrispRVariants charts the mutation spectrum of genome engineering experiments

Nature Biotechnology volume 34, pages 701–702 (2016)Cite this article

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To the Editor:

CRISPR-Cas9 and related technologies enable the efficient alteration of genomic DNA at targeted positions and are widely used in applications ranging from individual gene knockouts to large-scale functional screening and therapeutic gene editing. Unlocking the full potential of these methods requires accurate evaluation of editing efficiencies. Here, we show that methodological decisions for analyzing sequencing data can substantially affect mutagenesis efficiency estimates. We provide a comprehensive R-based toolkit (CrispRVariants) and an accompanying web tool (CrispRVariantsLite) that resolve and localize individual mutant alleles with respect to the endonuclease cut site. CrispRVariants-enabled analyses of newly generated and existing genome editing data sets underscore how careful consideration of the full spectrum of variants resulting from genome engineering can not only inform effective guide RNA and amplicon design but also provide insights into the mutagenic process.

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Figure 1: The CrispRVariants plotVariants function summarizes variant types, locations and frequency across multiple clones from several injected animals.

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Acknowledgements

This work was supported by the Canton of Zürich, a Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNSF) professorship (PP00P3_139093), a Marie Curie Career Integration Grant from the European Commission, and a Schweizerische Herzstiftung grant to C.M.; European Research Council Starting Grant ANTIVIRNA (337284) and an SNSF Project Grant (31003A_149393) to M.J.; a European Commission 7th Framework Collaborative Project RADIANT grant (agreement number 305626) and an SNSF Project Grant (31003A_143883) to M.D.R.; a Universität Zürich (UZH) URPP Translational Cancer Research Seed Grant to A.B.; and a UZH Forschungskredit to C.H.

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Authors and Affiliations

  1. Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland

    Helen Lindsay, Alexa Burger, Berthin Biyong, Anastasia Felker, Christopher Hess, Jonas Zaugg, Elena Chiavacci, Christian Mosimann & Mark D Robinson

  2. SIB Swiss Insitute of Bioinformatics, University of Zurich, Zurich, Switzerland

    Helen Lindsay, Berthin Biyong & Mark D Robinson

  3. Institute of Biochemistry, University of Zurich, Zurich, Switzerland

    Carolin Anders & Martin Jinek

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  1. Helen Lindsay
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Correspondence to Helen Lindsay, Christian Mosimann or Mark D Robinson.

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Editor's note: This article has been peer reviewed.

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Lindsay, H., Burger, A., Biyong, B. et al. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat Biotechnol 34, 701–702 (2016). https://doi.org/10.1038/nbt.3628

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