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通过使用RetroInspector进行纳米孔测序,对人类基因组中的逆转移素变异进行高级分析

Javier Cuenca-Guardiola¹, Belén de la Morena-Barrio², Javier Corral²

¹Departamento de Informática y Sistemas, IMIB-Pascual Parrilla, CEIR Campus Mare Nostrum, Universidad de Murcia, 30100, Murcia, Spain.

Scientific reports

|April 25, 2025

概括

RetroInspector是使用纳米孔测序数据分析可转移元素 (TE) 的新管道. 这种工具可以改善TEs的检测,注释和基因定型,提高我们对遗传变异性和疾病的理解.

科学领域:

基因组学和生物信息学
分子生物学分子生物学
人类遗传学人类遗传学

背景情况:

可移植元素 (TE) 占人类基因组的很大一部分 (45%),有助于遗传变异性.
转基因与基因调节和各种疾病有关,但它们的检测和分析,特别是使用纳米孔测序,存在挑战.
现有的生物信息学工具需要改进,以便从纳米孔数据中全面分析人类TE插入和删除.

研究的目的:

介绍RetroInspector,一个用户友好和可配置的Snakemake管道用于对可转换元素 (TE) 的分析.
使用纳米孔测序数据实现TE的检测,注释,丰富和基因定型.
为研究遗传变异性和TE在人类健康和疾病中的作用的研究人员提供一个强大的工具.

主要方法:

RetroInspector使用来自样本的FASTQ文件和参考基因组进行TE识别和分析.
管道包含可配置参数,包括在变体过中支持读数的值.
它支持使用不同的参考基因组版本,并注释反转换特征.

主要成果:

RetroInspector成功地在三个纳米孔测序数据集中进行了TE的检测,注释,丰富和基因定型.
使用专有数据和公共数据进行的实验验证显示,管道的精度超过80%.
该工具允许对两个样本进行比较分析,并对与逆转换相关的特征进行注释.

结论:

RetroInspector提供了一种有效且易于使用的解决方案,用于从纳米孔测序数据中分析可转移元素.
该管道增强了对遗传变异的研究和TEs在人类基因组中的功能影响.
它经过验证的高精度和用户友好的配置使其成为基因组研究的宝贵工具.

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