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

作　　者：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 

机构地区：[1]College of Life Sciences,University of Chinese Academy of Sciences,Beijing 100049,China [2]BGI-Shenzhen,Shenzhen,Guangdong 518083,China [3]BNU-HKBU United International College,Zhuhai,Guangdong 519087,China [4]Sentieon Inc,San Jose,CA 94042,USA [5]School of Biology and Biological Engineering,South China University of Technology,Guangzhou,Guangdong 510006,China [6]National Resource Center for Chinese Materia Medica,China Academy of Chinese Medical Sciences,Beijing 100700,China

出　　处：《Journal of Genetics and Genomics》2023年第8期563-572,共10页遗传学报（英文版）

基　　金：supported by the Fundamental Research Funds for the Central Public Welfare Research Institutes(ZZ13-YQ-095 and ZZXT201708);the Start-up Research Fund from BNU-HKBU United International College(UICR0700053-23).

摘　　要：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.

关 键 词：Genome editing On/off-target Genetic background removal Structural variation 

分 类 号：R596[医药卫生—内科学] R440[医药卫生—临床医学]