A different view on fine-scale population structure in Western African populations
A different view on fine-scale population structure in Western African populations
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DOI：
10.1007/s00439-019-02069-7
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发表时间：
2019-10-19
期刊：
影响因子：
5.3
通讯作者：
Van Steen, Kristel
中科院分区：
文献类型：
--
作者：
Chaichoompu, Kridsadakorn;Abegaz, Fentaw;Van Steen, Kristel
由于其悠久的遗传进化历史，非洲人表现出比世界上任何其他人口更多的遗传变异。它们的遗传多样性进一步有助于将非洲人细分为具有不同粒度的遗传相似性的个体群体。以一种计算高效和有意义的方式来检测细微尺度结构仍然具有挑战性。在这篇文章中，我们提出了一种新的概念验证工具，该工具以西非样本为样本，进行了精细的种群结构检测。这些样本包括来自25个种族群体的1396人(其中两个群体是非裔美国人后裔)。这一战略是基于最近开发的一种名为IPCAPS的工具。IPCAPS，即捕捉种群结构的迭代修剪，是一种遗传分裂聚类策略，它增强了迭代修剪PCA，对异常值具有健壮性，并且不需要单倍型的先验计算。我们的策略在喀麦隆、冈比亚、马里、美国西南部和巴巴多斯的样本中发现了12个组和6个组的精细结构。我们的发现有助于解释分析的西非样本中的进化过程，并在进行全基因组关联和相互作用研究时提高对精细结构解析的认识。
Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.