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使用TCRβ CDR3序列建模T细胞克隆型谱的开放协议

Burcu Gurun^1,2, Wesley Horton³, Dhaarini Murugan⁴

¹Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. gurundem@ohsu.edu.

|June 26, 2023

概括

这项研究提出了一种负担得起的,开源的方法,用于使用下一代测序 (NGS) 进行T细胞受体谱的分析. 它纠正了批量测序中的放大偏差,为商业解决方案提供了具有成本效益的替代方案.

科学领域:

免疫学免疫学免疫学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

使用下一代测序 (NGS) 进行T细胞受体 (TCR) 谱系分析对于监测自适应性免疫系统动态至关重要.
基于基因组DNA的批量测序是具有成本效益的,但由于多个原始配对而受到变量的放大效率的影响.
这种变化引入了测量TCR曲目变化的偏差.

研究的目的:

开发一种具有成本效益和开源的方法,用于准确的TCR曲目概况.
在批量测序过程中解决和纠正多重目标放大固有的放大偏差.
提供一个可行的替代方案,以昂贵的商业解决方案,用于TCR曲目分析.

主要方法:

用于多重目标放大,使用了等等模原原料混合物.
实施单个统计规范化步骤,以纠正后序列化放大偏差.
开发的开放协议的结果与商业测序解决方案进行了比较.

主要成果:

拟议的统计规范化有效地纠正了放大偏差.
从开放协议和商业解决方案获得的批量克隆度指标之间观察到很高的一致性.
开发的方法证明了成本效益和效率.

结论:

开发的开源协议提供了一种廉价且准确的TCR曲目分析方法.
这种方法为商业解决方案提供了可靠的替代方案,提高了研究人员的可访问性.
规范化策略有效地减轻了基于NGS的TCR曲目批量测序中的偏差.

关键词:

放大偏差是一种放大偏差.在CDR3中,CDR3是指CDR3中的CDR3.克隆类型的计数数量.计数正常化计数正常化多重复合PCR是一种多重复合PCR.负二项式是一个负二项式.规范化规范化规范化合成TCR模板的使用情况合成模板合成模板 TCR 测序的测序方法

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