Statistical Applications in Genetics and Molecular Biology Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
Statistical Applications in Genetics and Molecular Biology Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
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发表时间：
2011
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通讯作者：
Chaolong Wang;Zachary A. Szpiech;J. Degnan;M. Jakobsson;T. Pemberton;J. Hardy;A. Singleton;N. Rosenberg
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作者：
Chaolong Wang;Zachary A. Szpiech;J. Degnan;M. Jakobsson;T. Pemberton;J. Hardy;A. Singleton;N. Rosenberg
主成分分析（PCA）和多维标度（MDS）在人类群体遗传学的最新应用发现，“统计地图”的基础上的基因型在群体遗传样本往往类似于地理地图的基础采样位置。为了提供这些定性观测的正式测试，我们描述了一个Procrustes分析方法，用于定量评估种群遗传和地理地图的相似性。我们确认在两种情况下，一个使用来自欧洲的单核苷酸多态性（SNP）数据和一个使用SNP数据在世界范围内，一个可测量的高水平的一致性之间存在的统计地图的人口遗传变异和地理地图的采样位置。另外两个例子说明了普罗克鲁斯特方法在群体遗传学应用中的多功能性，验证了使用PCA和MDS的SNP分析的一致性，并表明全球拷贝数变异（CNV）的统计图与SNP变异的统计图雅阁，特别是当CNV分析仅限于具有最高质量数据的样本时。随着PCA和MDS统计地图越来越普遍地用于总结人口关系，我们的例子突出了潜在的普罗克鲁斯特为基础的定量比较，解释这些地图的结果。
Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that "statistical maps" based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide formal tests of these qualitative observations, we describe a Procrustes analysis approach for quantitatively assessing the similarity of population-genetic and geographic maps. We confirm in two scenarios, one using single-nucleotide polymorphism (SNP) data from Europe and one using SNP data worldwide, that a measurably high level of concordance exists between statistical maps of population-genetic variation and geographic maps of sampling locations. Two other examples illustrate the versatility of the Procrustes approach in population-genetic applications, verifying the concordance of SNP analyses using PCA and MDS, and showing that statistical maps of worldwide copy-number variants (CNVs) accord with statistical maps of SNP variation, especially when CNV analysis is limited to samples with the highest-quality data. As statistical maps with PCA and MDS have become increasingly common for use in summarizing population relationships, our examples highlight the potential of Procrustes-based quantitative comparisons for interpreting the results in these maps.