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CRISPResso2 provides accurate and rapid genome editing sequence analysis

Nature Biotechnology volume 37, pages 224–226 (2019)Cite this article

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To the Editor — The field of genome editing is advancing rapidly1, most recently exemplified by the advent of base editors that enable changing single nucleotides in a predictable manner2,3,4. For the validation and characterization of genome editing experiments, targeted amplicon sequencing has become the gold standard5. Here we present a substantially updated version of our CRISPResso tool6 to facilitate the analysis of data that would be difficult to handle with existing tools6,7,8,9.

CRISPResso2 introduces five key innovations: first, comprehensive analysis of sequencing data from base editors; second, a batch mode for analyzing and comparing multiple editing experiments; third, allele-specific quantification of heterozygous or polymorphic references; fourth, a biologically informed alignment algorithm; and fifth, ultrafast processing time. We discuss each of these in turn below.

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Fig. 1: Novel features of CRISPResso2.

Code availability

CRISPResso2 is available online at http://crispresso2.pinellolab.org, where users can run up to four samples simultaneously. The command line version without any limitations and with additional tools is available as a Docker image at https://hub.docker.com/r/pinellolab/crispresso2/ (Supplementary Note 4). The source code is available as Supplementary Software and online at https://github.com/pinellolab/CRISPResso2.

Data availability

Fig. 1a–c shows data available as SRR3305546 (untreated), SRR3305543 (BE1), SRR3305544 (BE2) and SRR3305545 (BE3)2. Figure 1d shows data obtained from the authors of ref. 10.

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Acknowledgements

D.R.L. is supported by DARPA HR0011-17-2-0049; US NIH RM1 HG009490, R01 EB022376 and R35 GM118062; and the HHMI. J.K.J. is supported by DARPA HR0011-17-2-0042, NIH R35 GM118158 and NIH RM1 HG009490. D.E.B. is supported by the NIDDK (R03DK109232), NHLBI (DP2OD022716, P01HL32262), Burroughs Wellcome Fund, Doris Duke Charitable Foundation and St. Jude Children’s Research Hospital Collaborative Research Consortium. L.P. is supported by NHGRI (R00HG008399), DARPA HR0011-17-2-0042, and the Centers for Excellence in Genomic Science of the National Institutes of Health under award number RM1HG009490 through a New Collaborator Grant subaward.

Author information

Authors and Affiliations

  1. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Kendell Clement, Matthew C. Canver, Rick Farouni, Jonathan Y. Hsu, Daniel E. Bauer & Luca Pinello

  2. Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA

    Kendell Clement, Matthew C. Canver, Jason M. Gehrke, Rick Farouni, Jonathan Y. Hsu, J. Keith Joung & Luca Pinello

  3. Department of Pathology, Harvard Medical School, Boston, MA, USA

    Kendell Clement, Matthew C. Canver, Jason M. Gehrke, Rick Farouni, Jonathan Y. Hsu, J. Keith Joung & Luca Pinello

  4. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Holly Rees & David R. Liu

  5. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA

    Holly Rees & David R. Liu

  6. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA

    Holly Rees & David R. Liu

  7. Division of Hematology/Oncology, Boston Children’s Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

    Mitchel A. Cole & Daniel E. Bauer

  8. Department of Pediatrics, Harvard Medical School, Boston, MA, USA

    Daniel E. Bauer

  9. Harvard Stem Cell Institute, Cambridge, MA, USA

    Daniel E. Bauer

Authors
  1. Kendell Clement
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  2. Holly Rees
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  8. David R. Liu
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  9. J. Keith Joung
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  10. Daniel E. Bauer
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  11. Luca Pinello
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Contributions

K.C. and L.P. conceived the project, led the study and wrote the software. K.C. analyzed experimental data. All authors contributed input on measurement and visualization of genome editing outcomes and provided input on the manuscript.

Corresponding authors

Correspondence to Daniel E. Bauer or Luca Pinello.

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Competing interests

At the time of manuscript preparation, J.M.G. was a consultant for Beam Therapeutics, and now is employed by Beam Therapeutics. J.K.J. has financial interests in Beam Therapeutics, Editas Medicine, Endcadia, EpiLogic Therapeutics, Pairwise Plants, Poseida Therapeutics and Transposagen Biopharmaceuticals. J.K.J.’s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. J.K.J. is a member of the Board of Directors of the American Society of Gene and Cell Therapy. J.M.G. and J.K.J. are co-inventors on patents and patent applications that describe gene editing technologies. D.R.L. is a consultant and cofounder of Editas Medicine, Pairwise Plants and Beam Therapeutics, companies that use genome editing.

Additional information

Editor’s note: This article has been peer-reviewed.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15 and Supplementary Notes 1–4

Supplementary Software

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Clement, K., Rees, H., Canver, M.C. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol 37, 224–226 (2019). https://doi.org/10.1038/s41587-019-0032-3

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