基准测试小鼠污染删除协议在患者衍生异种移植的基因组分析
Mukund Bhandari1, Funan He1,2, Anna Rogojina1
1Greehey Children's Cancer Research Institute, San Antonio, TX, USA.
NPJ precision oncology
|April 17, 2025
概括
患者衍生异种移植 (PDX) 模型中的小鼠污染歪曲了基因组数据,膨胀了突变和基因表达. 像Xengsort这样的新计算工具有效地删除了鼠标读数,提高了用于癌症研究的PDX模型准确性.
科学领域:
- 基因组学就是基因组学.
- 癌症研究 癌症研究
- 生物信息学是一种生物信息学.
背景情况:
- 患者衍生异种移植 (PDX) 模型对于癌症研究至关重要.
- PDX模型的基因组和转录组分析通常被鼠标测序读取所污染.
研究的目的:
- 为了研究小鼠读污染对RNA测序 (RNAseq),全外基因组测序 (WES) 和PDX模型的全基因组测序 (WGS) 数据的影响.
- 为了对计算协议进行基准测试,以便从PDX数据中删除鼠标读取.
主要方法:
- 分析来自21个PDX模型的RNAseq,WES和WGS数据.
- 对12个用于移除鼠标读取的计算协议进行系统的基准测试.
- 使用黄金标准数据集进行评估.
主要成果:
- 鼠标阅读污染增加了免疫和 stromal 基因的表达,并膨胀了体质突变计数.
- 检测基因融合和副本数量的改变受到最小的影响.
- 伪对齐协议显示出卓越的性能和效率.
- Xengsort被确定为表现最好的工具.
结论:
- 删除鼠标读数对于PDX模型的精确基因组和转录组分析至关重要.
- 采用像Xengsort这样的先进工具是PDX基因组研究的建议.
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