一个伪时间依赖的TWAS框架识别了沿细胞发育路径的疾病基因
medRxiv : the preprint server for health sciences
|November 24, 2025
概括
我们开发了伪时间依赖的转录组全相关性研究 (pt-TWAS) 来分析在连续细胞发育过程中对疾病风险的基因影响. 这种方法增强了统计能力,并确定了B细胞急性淋巴细胞白血病等疾病的因果细胞阶段.
科学领域:
- 遗传学和基因组学 遗传学和基因组学
- 计算生物学 计算生物学
- 系统生物学 系统生物学
背景情况:
- 全转录组关联研究 (TWAS) 整合基因表达和GWAS数据用于疾病风险解释.
- 大量组织表达数据提供了组织层面的洞察力,但单细胞数据允许更细微的细胞颗粒度.
- 现有的单细胞方法可能会错过连续的细胞过程,并错误地识别因果细胞阶段.
研究的目的:
- 开发一种新的TWAS框架,即伪时间依赖的TWAS (pt-TWAS),用于在更精细的细胞阶段分辨率下剖析基因疾病关联.
- 为了捕捉细胞发育路径沿着基因表达的持续动态变化.
- 通过将基因表达模式作为伪时间的连续函数来提高统计能力并识别因果细胞阶段.
主要方法:
- 开发了pt-TWAS框架,将基因表达模型作为伪时间的连续函数.
- 杆式表达量化特征位点 (eQTL) 信息跨细胞阶段,以提高统计能力.
- 构建和可视化基因效应曲线的同时置信波段,以识别因果细胞阶段.
主要成果:
- pt-TWAS在B细胞急性淋巴细胞白血病 (ALL) 中成功复制了已知的风险基因.
- 该方法精确确定了与ALL的基因效应相关的特定细胞阶段.
- pt-TWAS在分析离散细胞类型或细胞阶段的方法上证明了统计上的优势.
结论:
- pt-TWAS提供了一个强大的框架,用于使用单细胞数据对基因疾病关联进行精细分辨率分析.
- 该方法通过捕捉连续的细胞过程,准确地识别因果细胞阶段.
- pt-TWAS提高了对细胞水平疾病遗传贡献的理解.
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