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在多个祖先的参考面板中,基因型归算的准确性和次要祖先的质量指标
Mingyang Shi1, Chizu Tanikawa2, Hans Markus Munter3
1Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
Briefings in bioinformatics
|January 15, 2024
概括
基因型归算质量指标可能会高估代表性不足的人口中的准确性. 模板切换率 (θ值) 在全基因组关联研究中显著影响归算准确性和质量评估.
科学领域:
- 遗传学 遗传学 是一个
- 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:
- 使用大型参考面板进行基因型归算可以加速全基因组关联研究 (GWAS).
- 对于代表人数不足的人群,最佳的参考小组组成 (大型多祖先与小人口特定) 仍然不清楚.
- 标准的归算质量指标可能不准确地反映不同人群中的归算准确性.
研究的目的:
- 为了评估基因型归算质量指标在代表性不足的东亚人口的准确性.
- 调查参考面板特征和隐藏的马尔科夫模型参数对归算准确性的影响.
- 为了确定祖先多样性和参考面板的大小对归算性能的影响.
主要方法:
- 通过使用Trans-Omics for Precision Medicine (TOPMed) 参考面板对18万名日本受试者的假定基因型.
- 差异组件分析以评估归算质量指标 (Rsq) 和剂量r2.
- 系统模拟变化的模板切换率 (θ值) 和参考面板组成.
主要成果:
- Rsq指标高估了剂量r2,特别是在边际质量的归算容器中,这表明系统偏差.
- 较低的θ值增加了归算的基因型确定性和Rsq,但剂量r2是不敏感的,导致偏差.
- 参考组的祖先多样性影响了θ值的估计,远方祖先提供了有限的额外变异.
结论:
- θ值显著影响归算剂量和归算质量指标的可靠性.
- 标准的归算质量指标对于评估代表性不足的人群中归算准确性可能不可靠.
- 仔细考虑参考小组组成和归算参数对于准确的遗传关联研究至关重要.
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