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Genome Biol. 2019 Oct 23;20(1):218. doi: 10.1186/s13059-019-1839-4.

Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.

Author information

1
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
2
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
3
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.
4
University of Chinese Academy of Sciences, Beijing, 100049, China.
5
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
6
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. chenjia@shanghaitech.edu.cn.
7
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China. chenjia@shanghaitech.edu.cn.
8
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. liyang@picb.ac.cn.
9
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. liyang@picb.ac.cn.

Abstract

A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-to-T mutations. We further profile the accessibilities of 20 base editors to all possible pathogenic mutations in silico. Finally, we build the BEable-GPS (Base Editable prediction of Global Pathogenic SNVs) database for users to select proper base editors to model or correct disease-related mutations. The in vivo comparison and in silico profiling catalog the availability of base editors and their broad applications in biomedical studies.

KEYWORDS:

Base editing; Base editor; CRISPR/Cas; Cytidine deaminase; Pathogenic mutation

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