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目的：构建一个测序数据分析工具，发现在转基因动物构建、病毒感染等过程中发生的基因组重组事件。方法：创建一站式R分析工具TransgeneR，基于转基因动物或者病毒感染样本的测序数据，通过两轮序列切割、组装等分析过程，结合位置、方向、切割位点等信息，发现外源DNA的整合重组事件。在人工模拟的MAPT转基因小鼠基因组以及人源tau(MAPT, 0N4R)转基因小鼠动物模型上，评价整合重组事件发现的准确性。结果：利用模拟动物，TransgeneR成功发现所有的整合和重组位点，而且重组位点的数量与切割序列的数量呈线性相关。利用真实转基因动物全基因组测序（whole genome sequencing, WGS）数据，TransgeneR发现4号染色体上有一个单一的转基因整合位点[chr4:129387127（左侧）和chr4:129387416（右侧）]。结论：系统性评价表明，TransgeneR是一个鉴定和研究外源DNA整合重组事件的有效工具。
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 exogenous DNA through two rounds of sequence cleavage, as well as assembly and other analytical processes, incorporating information on position, orientation and cleavage site. The accuracy of integrated rearrangement event discovery was assessed in artificially 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.
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基本信息:
DOI：10.13210/j.cnki.jhmu.20250220.003
中图分类号:Q811.4
引用信息:
[1]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.DOI:10.13210/j.cnki.jhmu.20250220.003.
基金信息:
上海交通大学“交大之星”（STAR）计划重大项目（20230101）; 上海市科委临床研究专业技术平台（23DZ2290600）~~
2025-02-20
2025-02-20
2025-02-20