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 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

作者机构：College of Life SciencesUniversity of Chinese Academy of SciencesBeijing 100049China BGI-ShenzhenShenzhenGuangdong 518083China BNU-HKBU United International CollegeZhuhaiGuangdong 519087China Sentieon IncSan JoseCA 94042USA School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouGuangdong 510006China National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China 

出 版 物：《Journal of Genetics and Genomics》 (遗传学报（英文版）)

年 卷 期：2023年第50卷第8期

页      面：563-572页

核心收录：

学科分类：100208[医学-临床检验诊断学] 1002[医学-临床医学] 100201[医学-内科学(含：心血管病、血液病、呼吸系病、消化系病、内分泌与代谢病、肾病、风湿病、传染病)] 10[医学] 

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) 

主　　题：Genome editing On/off-target Genetic background removal Structural variation 

摘      要：The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome *** track on/off-target events with emerging new editing techniques,improved bioinformatic tools are *** tools suffer from limitations in speed and scalability,especially with whole-genome sequencing(WGS)data *** address these limitations,we have developed a comprehensive tool called CRISPR-detector,a web-based and locally deployable pipeline for genome editing sequence *** core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline,with additional novel annotation and visualization modules designed to fit CRISPR ***-analysis of the treated and control samples is performed to remove existing background variants prior to genome ***-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 *** addition,the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by *** advantages facilitate rapid and efficient detection of mutations induced by genome editing events,especially for datasets generated from *** web-based version of CRISPR-detector is available at https://***/crispr-detector,and the locally deployable version is available at https://***/hlcas/CRISPR-detector.