人类群体遗传结构的双标图模型及其应用

The PPG Biplot Model of Human Population Genetic Structure and Its Applications

提出了分析人类群体遗传结构的PPG双标图模型的基本原理及其应用。PPG双标图根据人类群体遗传学的基本原理,利用矩阵奇异值分解技术,将多维基因频率矩阵近似为一个能够用双标图表示的二维矩阵,从而实现了人类群体遗传结构的图形化和可视化直观分析。它与聚类分析、主成分分析、对应分析等传统多元统计分析方法相比,具有明显的优越性。PPG双标图通过其几何性质,反映了其丰富的群体遗传学含义;更重要的是,在基因频率矩阵前2项奇异值的累计贡献率足够大的前提下,利用双标图,以辅助线为补充,可以实现人类群体遗传结构的可视化直观定量分析:①比较各群体之间的遗传距离,划分群体类型;②比较各基因的变异性大小;③分析各基因之间的相关性;④比较某基因对各亚群体遗传结构的相对贡献;⑤比较任意2个亚群体遗传结构的差异;⑥分析任意2个基因的差异及其对各亚群体变异性的贡献;⑦分析群体与基因的交互作用及其对群体亚分的贡献。因此,PPG双标图值得在人类群体遗传结构分析中推广应用,但PPG双标图也存在一定的局限性。

This paper presents the principles and application of PPG biplot model to the field of human population genetics for analyzing the population genetic structure. The PPG biplot is created by using the technique of singular values decomposition （SVD）, and based on the theory of population subdivision model. It has some advantages over other conventional multivariate methods for analyzing the human population genetic structure, such as cluster analysis, principal components analysis, and correspondence analysis. Firstly, it is more genetic interpretative, at present study, based on the theory of human population genetics and the geometry of biplot, the genetic meanings of PPG biplot are defined and interpreted. Secondly, it shows graphical presentation of the gene frequency matrix, which greatly enhances our ability to understand the population genetic structure of the locus （loci）. The following genetic information can be graphically visualized： ①comparing the genetic distance between populations for population subdivision; ②comparing the genetic variation of different alleles; ③analyzing the correlation between alleles; ④comparing the relative contribution of a allele to the genetic structure of different populations; ⑤comparing the genetic structure variation of any two subpopulation; ⑥comparing the difference of any two alleles in different populations; ⑦analyzing the gone-population interaction and its contribution to population subdivision. As an example, the genetic structure of HLA-A locus for 26 Chinese Han populations was analyzed by using PPG biplot model. It indicated that the PPG biplot was an ideal tool for studying the human population genetic structure. However, the PPG biplot model also has some disadvantages.