CRISPR-detector: fast and accurate detection, visualization, and annotation of genome-wide mutations induced by genome editing events

Lei Huang; Dan Wang; Haodong Chen; Jinnan Hu; Xuechen Dai; Chuan Liu; Anduo Li; Xuechun Shen; Chen Qi; Haixi Sun; Dengwei Zhang; Tong Chen; Yuan Jiang

doi:10.1016/j.jgg.2023.03.010

Volume 50 Issue 8

Aug. 2023

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Article Navigation > Journal of Genetics and Genomics > 2023 > 50(8): 563-572

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CRISPR-detector: fast and accurate detection, visualization, and annotation of genome-wide mutations induced by genome editing events

doi: 10.1016/j.jgg.2023.03.010

a College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
b BGI-Shenzhen, Shenzhen, Guangdong 518083, China;
c BNU-HKBU United International College, Zhuhai, Guangdong 519087, China;
d Sentieon Inc, San Jose, CA 94042, USA;
e School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China;
f National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China

Funds:

We would like to thank Dr. Hongxia Lan and Dr. Qianqian Gao for advising on our web server and providing sequencing data and colleagues at China National GeneBank (Shenzhen) and EHBIO Gene Technology (Beijing) for their guidance and help in constructing the web server. This work was supported by the Fundamental Research Funds for the Central Public Welfare Research Institutes (ZZ13-YQ-095 and ZZXT201708) and the Start-up Research Fund from BNU-HKBU United International College (UICR0700053-23).

Received Date: 2022-10-19
Revised Date: 2023-03-05
Accepted Date: 2023-03-08
Publish Date: 2023-03-30

Abstract

Abstract

The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing. To track on/off-target events with emerging new editing techniques, improved bioinformatic tools are indispensable. Existing tools suffer from limitations in speed and scalability, especially with whole-genome sequencing (WGS) data analysis. To address these limitations, we have developed a comprehensive tool called CRISPR-detector, a web-based and locally deployable pipeline for genome editing sequence analysis. The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline, with additional novel annotation and visualization modules designed to fit CRISPR applications. Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing. CRISPR-detector offers optimized scalability, enabling WGS data analysis beyond Browser Extensible Data file-defined regions, with improved accuracy due to haplotype-based variant calling to handle sequencing errors. In addition, the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users. These advantages facilitate rapid and efficient detection of mutations induced by genome editing events, especially for datasets generated from WGS. The web-based version of CRISPR-detector is available at https://db.cngb.org/crispr-detector, and the locally deployable version is available at https://github.com/hlcas/CRISPR-detector.
- Genome editing,
- On/off-target,
- Genetic background removal,
- Structural variation

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References(41)

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