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DPImpute:超低覆盖全基因组测序的基因型推算框架及其在基因组选择中的应用

Weigang Zheng^1,2,3, Wenlong Ma^2,3, Zhilong Chen^2,3

¹Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

|February 27, 2025

概括

使用超低覆盖度测序,DPImpute准确地对整个基因组进行基因型测定. 这种方法显著提高了基因组选择准确性,采用最小的样本,推进育种计划和多样化的人口研究.

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.
计算生物学计算生物学

背景情况:

全基因组测序 (WGS) 对于理解基因型-表型联系至关重要.
高测序深度和大样本大小限制了WGS在基因组选择 (GS) 中的应用.
在GS中精确的表型预测需要高密度的基因型数据.

研究的目的:

开发一个具有成本效益和准确的归算管道,用于全基因组SNP基因型化.
为了在极低覆盖WGS (ulcWGS) 下使用有限的样本进行准确的基因型鉴定.
为了促进基因组选择和多样化的人口研究.

主要方法:

开发DPImpute (双相Impute),一个两步的归算管道.
应用DPImpute对具有极低覆盖率的WGS数据,具有较小的测试和参考群体.
在多祖先人类群体和单细胞数据中验证DPImpute.

主要成果:

在最小样本 (≤10个测试,≤100个参考) 和0.3X的测序深度下,获得了98.06%的SNP归算准确度.
在准确性方面超过了现有的归算方法.
在多祖先群体和单个血液/胚胎细胞中表现出高准确性.

结论:

DPImpute 能够实现精确且具有成本效益的基因定型,加速育种计划.
在人类和动物研究中,DPImpute是多样化的种群基因型定型的宝贵工具.
DPImpute 的网络服务器和 Docker 容器提高了研究人员的可访问性.

关键词:

繁殖模型繁殖模型对胚胎进行遗传查.基因组选择基因组选择基因类型的归算基因类型的归算一个单细胞基因型的基因型.

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