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首页> 外文期刊>BMC Medical Genomics >Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?
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Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

机译：资源约束下的人类祖先身份识别-一条染色体可以告诉我们关于人类生物地理祖先的哪些信息？

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While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge. We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods. We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs). Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.
机译：尽管使用基因组信息来进行大陆级血统比较简单，但是要区分具有密切关联的亚种群（例如，来自同一大陆）的个体仍然是一项艰巨的挑战。我们研究了在资源限制下根据基因组数据预测人类生物地理学的问题。尤其是，我们关注的情况是分析仅限于使用仅一个染色体的单核苷酸多态性（SNP）。我们提出了使用基于相关性和基于异常值的方法来构建此类祖先信息丰富的SNP面板的方法。我们使用来自1000个基因组计划第3期的数据，访问了仅由一条染色体组成的拟议SNP面板的性能。对于大陆一级的祖先分类，我们使用206个单核苷酸多态性（SNP）实现了96.75％的总体分类率。对于亚种群水平的祖先预测，我们实现了平均的成对二元分类率，如下所示：欧洲亚种群：76.6％（58个SNP）;非洲：87.02％（87个SNP）;东亚：73.30％（68个SNP）;南亚：81.14％（75个SNP）;美国：85.85％（68个SNP）。我们的结果表明，如果仔细分析一条染色体（特别是1号染色体），它可以容纳足够的信息来准确预测人类的生物地理谱系。这对于血统分析所需的计算资源以及此类分析的应用（例如在遗传疾病，法医和软生物特征学方面的研究）具有重要意义。

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