海南医科大学学报2025，Vol.31Issue(18)：1408-1417,10.DOI:10.13210/j.cnki.jhmu.20250220.003
TransgeneR:基于测序数据发现基因组整合重组事件的一站式工具
TransgeneR:A one-stop tool for transgene integration and rearrangement discovery using sequencing data
摘要
Abstract
Objective:To build a sequencing data analysis tool to discover genome integration and rearrangement events that occur during the construction of transgenic animals,virus infection.Methods:A one-stop R analysis tool,TransgeneR was built,which uses sequencing data from transgenic animals or virus-infected samples to discover the integrated rearrangement events of ex-ogenous DNA through two rounds of sequence cleavage,as well as assembly and other analytical processes,incorporating infor-mation on position,orientation and cleavage site.The accuracy of integrated rearrangement event discovery was assessed in artifi-cially simulated genomes of MAPT transgenic mice as well as human tau(MAPT,0N4R)transgenic mice.Results:TransgeneR showed that it successfully discovered all the integration sites and rearrangement sites by using simulated animals,and that the number of rearrangement sites appeared to be related linearly with the cutting sequences number.TransgeneR discovered a single transgene integration site on chromosome 4[chr4:129387127(left side)and chr4:129387416(right side)]by using whole genome sequencing data from real transgenic animals.Conclusion:The systematic evaluation shows that TransgeneR is an effective tool to identify and study exogenous DNA integration and rearrangements events.关键词
全基因组测序/基因重组/转基因整合位点/DNA序列Key words
Whole genome sequencing/Genetic recombination/Transgene integration sites/DNA sequences分类
生物科学引用本文复制引用
李浩浩,孟国锋,谭红胜..TransgeneR:基于测序数据发现基因组整合重组事件的一站式工具[J].海南医科大学学报,2025,31(18):1408-1417,10.基金项目
This study was supported by Major Project of the"STAR"Program of Shanghai Jiao Tong University(20230101) （20230101）
Shanghai Science and Technology Commission Clinical Research Professional Technical Platform(23DZ2290600) 上海交通大学"交大之星"(STAR)计划重大项目(20230101) （23DZ2290600）
上海市科委临床研究专业技术平台(23DZ2290600) （23DZ2290600）
