在HCHS/SOL中推断旧与新的本地祖先:一项比较研究
Xueying Chen1,2, Hao Wang3, Iris Broce4,5
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, United States.
Human molecular genetics
|June 9, 2025
概括
当地祖先推断 (LAI) 更新显示西班牙裔/拉丁裔人口的旧方法和新方法之间存在很高的一致性. 差异通常发生在具有挑战性的基因组区域,而不是由于软件或技术.
科学领域:
- 人口遗传学 人口遗传学
- 基因组祖先分析
- 生物信息学是一种生物信息学.
背景情况:
- 西班牙裔/拉丁裔人口表现出来自不同祖先群体的遗传混合物.
- 准确的当地祖先推断对于混合种群的遗传关联研究至关重要.
- 混合物映射依赖于在特定的基因组位置精确估计祖先的起源.
研究的目的:
- 评估更新的当地祖先推断 (LAI) 方法对西班牙裔/拉丁裔个体遗传分析的影响.
- 使用更新的参考面板,将传统的RFMix (LAI) 与较新的FLARE (LAI) 进行比较.
- 评估全球和本地祖先估计的一致性及其对混合物映射结果的影响.
主要方法:
- 使用了西班牙裔社区健康研究/拉丁裔研究 (HCHS/SOL) 数据集.
- 使用RFMix (旧) 和FLARE (新) 进行了本地祖先推断,并更新了参考面板.
- 推断方法之间的全球和本地祖先相关性比较.
- 分析了从两个推理方法中得出的混合映射关联.
主要成果:
- 新的和旧的LAI方法产生了非常相似的全球和本地祖先估计.
- 基于FLARE的添加剂映射结果与RFMix. 的结果非常一致.
- 在特定的基因组区域观察到较低的相关性 (Pearson R < 0.9).
- 协议较低的地区经常与ENCODE黑名单地区或基因集群有关.
结论:
- 更新的LAI方法与以前在混合种群中的方法在很大程度上一致.
- 基因组序列背景,特别是ENCODE黑名单地区,有助于降低推断协议.
- 推断稳定性更多地受到基因组区域特征的影响,而不是LAI软件或基因造型技术.
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