从单细胞RNA-seq数据评估遗传祖先推断
Jianing Yao1,2,3, Steven Gazal1,2,4
1Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
bioRxiv : the preprint server for biology
|April 8, 2025
概括
从单细胞RNA测序 (scRNA-seq) 数据中推断供体遗传祖先对于减少偏见和理解人类遗传多样性至关重要. 这项研究验证了祖先推断的方法,揭示了当前scRNA-seq数据集中非欧洲祖先的明显不足.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 人口遗传学 人口遗传学
背景情况:
- 在单细胞RNA测序 (scRNA-seq) 中表征供体祖先对于数据集的一致性,偏差减少和识别祖先特定的监管机制至关重要.
- 在scRNA-seq研究中缺乏供体祖先信息,阻碍了对疾病相关性的全面分析和理解.
- 确保scRNA-seq数据集代表全球人类遗传多样性对于公平的研究成果至关重要.
研究的目的:
- 提出和评估一个评估方法的框架,从scRNA-seq数据中检测到的遗传多态度中推断遗传祖先.
- 为了证明像ADMIXTURE这样的既定工具的准确性,使用scRNA-seq数据推断祖先的推断,即使有有限的多态度和不完美的变异调用.
- 在现有的scRNA-seq数据集中推断捐赠者的遗传祖先,并突出人口代表性的潜在偏见.
主要方法:
- 开发了一个框架来评估使用scRNA-seq读取的遗传多态度的遗传祖先推断方法.
- 应用广泛使用的生物信息学工具,如ADMIXTURE,分析scRNA-seq数据以进行祖先估计.
- 在四个Human Cell Atlas scRNA-seq数据集中推断了196名捐赠者的遗传血统.
主要成果:
- 广泛使用的工具从scRNA-seq数据准确地推断出遗传祖先和混合物比例.
- 尽管有限的遗传多态度和scRNA-seq.固有的不完美的变异调用存在,但推断仍然强大.
- 对人类细胞图谱数据集的分析显示,欧洲血统的捐赠者数量不成比例.
结论:
- 使用现有的计算工具,从scRNA-seq数据推断遗传祖先是可行的和准确的.
- 目前的scRNA-seq数据集,包括来自人类细胞地图集的数据集,严重倾向于欧洲祖先.
- 敦促研究人员报告所有捐赠者的遗传血统,并优先生成更多多样化的scRNA-seq数据集,以提高代表性和减少偏见.
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