Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
Local Ancestry Inference in a Large US-Based Hispanic/Latino Study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
复制标题
DOI：
10.1534/g3.116.028779
复制
发表时间：
2016-06-01
期刊：
影响因子：
--
通讯作者：
Laurie CC
中科院分区：
文献类型：
--
作者：
Browning SR;Grinde K;Plantinga A;Gogarten SM;Stilp AM;Kaplan RC;Avilés-Santa ML;Browning BL;Laurie CC
我们使用RFMix方法在一项针对12，793名西班牙裔/拉丁裔个体的大型美国研究中估计了常染色体和X染色体上的本地血统，并通过孟德尔不一致率作为准确性的代表，比较了不同的参考面板和X染色体上的本地血统估计方法。我们开发了一种新的和直接的方法来执行祖先特定的PCA后，发现从现有的方法的结果中的人为行为。使用祖先特定的PCA，我们发现显着的人口结构内的非洲，欧洲和美洲印第安人的祖先在西班牙裔/拉丁美洲人的个人在我们的研究。在混合个体的非洲祖先组成部分中，祖父母来自中美洲的个体与祖父母来自加勒比海的个体以及参考约鲁巴人和Mandenka西非个体分开聚集。在欧洲部分，祖父母来自波多黎各的人与其他背景群体部分不同。在美洲印第安人祖先组成部分中，个人根据祖父母原籍国的不同分为多个不同的群体。因此，当地的祖先估计提供了进一步了解美国西班牙裔/拉丁裔人口的复杂的遗传结构，这必须在基因型-表型关联研究中得到适当的解释。它也为混合作图和祖先特异性等位基因频率估计提供了基础，这在识别疾病的危险因素中是有用的。
We estimated local ancestry on the autosomes and X chromosome in a large US-based study of 12,793 Hispanic/Latino individuals using the RFMix method, and we compared different reference panels and approaches to local ancestry estimation on the X chromosome by means of Mendelian inconsistency rates as a proxy for accuracy. We developed a novel and straightforward approach to performing ancestry-specific PCA after finding artifactual behavior in the results from an existing approach. Using the ancestry-specific PCA, we found significant population structure within African, European, and Amerindian ancestries in the Hispanic/Latino individuals in our study. In the African ancestral component of the admixed individuals, individuals whose grandparents were from Central America clustered separately from individuals whose grandparents were from the Caribbean, and also from reference Yoruba and Mandenka West African individuals. In the European component, individuals whose grandparents were from Puerto Rico diverged partially from other background groups. In the Amerindian ancestral component, individuals clustered into multiple different groups depending on the grandparental country of origin. Therefore, local ancestry estimation provides further insight into the complex genetic structure of US Hispanic/Latino populations, which must be properly accounted for in genotype-phenotype association studies. It also provides a basis for admixture mapping and ancestry-specific allele frequency estimation, which are useful in the identification of risk factors for disease.