Brief Communication | Published:

GuideScan software for improved single and paired CRISPR guide RNA design

Nature Biotechnology volume 35, pages 347349 (2017) | Download Citation

Abstract

We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We also show that the trie data structure of GuideScan enables the design of gRNAs that are more specific than those designed by existing tools.

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Acknowledgements

We thank members of the Ventura and the Leslie laboratories for comments and suggestions. We thank L. Fairchild and R. Pelossof for providing source code for the SplashRNA web server to serve as the backbone for the GuideScan website. This work was supported in part by NIH: grants P30-CA008748 (MSK Core), U01-HG007033 (C.S.L.), U01-HG007893 (C.S.L.), and by grants from the Geoffrey Beene Cancer Research Foundation (A.V.), the Uniting Against Lung Cancer Foundation (A.V.), the Cycle for Survival Foundation (A.V.), the Pershing Square Sohn Cancer Research Alliance (A.V.), and the Lung Cancer Research Foundation (J.A.V.). The GuideScan source code and all associated documentation are deposited at guidescan.com.

Author information

Author notes

    • Alexendar R Perez
    • , Yuri Pritykin
    •  & Joana A Vidigal

    These authors contributed equally to this work.

Affiliations

  1. Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Alexendar R Perez
    • , Yuri Pritykin
    • , Sagar Chhangawala
    • , Lee Zamparo
    •  & Christina S Leslie
  2. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Alexendar R Perez
    • , Joana A Vidigal
    •  & Andrea Ventura
  3. Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA.

    • Alexendar R Perez
    •  & Sagar Chhangawala

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Contributions

J.A.V., C.S.L., and A.V. conceived and supervised the project. Y.P. and A.R.P. developed the GuideScan algorithm with input from C.S.L.; A.R.P. and Y.P. implemented the GuideScan software package; A.R.P. performed the computational experiments; J.A.V. performed the wet-lab experiments; A.R.P. and S.C. implemented the web-server; L.Z. provided expertise in software development and helped improve the website user experience; J.A.V. drafted the manuscript with contributions from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Joana A Vidigal or Christina S Leslie or Andrea Ventura.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1,2 and Supplementary Note 1

Excel files

  1. 1.

    Supplementary Table 1

    Off-target reporting by competitor tools for a subset of promiscuous gRNAs.

  2. 2.

    Supplementary Table 2

    Number of gRNAs with off-targets with 0 or 1 mismatches.

  3. 3.

    Supplementary Table 3

    Genomic Coordinates used for tool comparison experiment.

  4. 4.

    Supplementary Table 4

    sequence of gRNAs and primers used in Fig. 2

Zip files

  1. 1.

    Supplementary Code

    Supplementary Code

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DOI

https://doi.org/10.1038/nbt.3804

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