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一个高分辨率的哈普洛型解析参考面板,由中国卡杜里生物库研究构建

Canqing Yu^1,2,3, Xianmei Lan^4,5, Ye Tao⁵

¹Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China.

Nucleic acids research

|October 23, 2023

概括

一个新的CKB参考面板,建立在中度深度全基因组测序 (WGS) 数据的基础上,显著提高了大规模人口研究的基因型归算准确性. 本资源增强了对中国人群中复杂特征和疾病的遗传分析.

科学领域:

人口遗传学人口遗传学
基因组医学是基因组医学.
生物信息学是一种生物信息学.

背景情况:

精准医学需要高精度的个体基因型数据,但全基因组测序 (WGS) 对大型研究来说是成本高昂的.
准确的哈普洛型参考面板对于从微阵列等低密度数据中进行基因型归算至关重要.
现有的参考面板可能无法最佳地服务于特定人群的遗传多样性,例如中国人群.

研究的目的:

使用来自10,000名中国人的中等深度WGS数据构建一个高度准确的单 haplotype 参考面板.
评估与现有面板相比,用于基因型归算的新型CKB参考面板的性能.
为中国人口生成最大的全基因组归算数据集,并评估其在全基因组关联研究 (GWAS) 中的实用性.

主要方法:

在1万个样本上进行了中度深度全基因组测序 (WGS),以创建CKB参考面板.
使用CKB面板从微阵列数据集中计算基因型数据.
计算准确度和计算正确的变体数量与其他参考面板进行了比较.
使用CKB面板进行了100706个微阵列的大规模归算.
针对身高的全基因组关联研究 (GWAS) 在归算数据上进行.

主要成果:

与现有面板相比,CKB参考面板在基因型归算方面表现出优异的表现,显示出更高的准确性和更好的归算变体.
使用CKB面板对100706个微阵列进行了归算,结果是迄今为止中国人口中最大的全基因组归算数据集.
使用CKB输入的数据来测量高度的GWAS导致测试的单核酸多态 (SNP) 增加了三倍,显著SNP增加了两倍.

结论:

基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因基因
产生的大规模归算数据集是调查复杂特征和疾病的人口遗传研究的重要资源.
一个在线服务器提供基于CKB面板的免费基因型归算服务已经开发出来,促进了更广泛的研究应用.

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Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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