BACKGROUND Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

中文翻译：

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在智利人中开发了一小部分SNP以推论祖先，以区分Aymara和Mapuche的组成部分。

背景技术当前南美人口的起源主要追溯到三个大陆祖先，即欧洲，美洲印第安人和非洲。由于人口分层，这些祖先相对比例的个体差异可能会与社会经济因素混淆。因此，血统是潜在的混杂变量，应在流行病学研究和公共卫生计划中加以考虑。但是，很少有研究评估当前智利人口的血统。这部分是由于通常用于估计祖先的基因组规模技术的高成本。在这项研究中，我们设计了一个SNP小小组，以准确评估迄今为止来自八个城市的智利混血儿种群（n = 3349）的最大样本中的血统。我们的小组还能够区分智利人的两个主要美洲印第安人成分：北部的Aymara和南部的Mapuche。结果选择了150个SNP类型的祖先信息标记（AIM），以最大程度地提高祖先的信息量和基因组覆盖率。其中，通过KASPar分析成功地对2843个样品进行了147种基因分型，平均缺失率为0.012，与微阵列数据的一致性为0.95。与AXIOM LAT1阵列获得的祖先相比，由AIM评估的祖先具有较高的相关性（欧洲为0.88，美洲为0.91，艾马拉为0.70，马普切为0.68）。该国的平均血统是0.53±0.14欧洲人，0.04±0.04非洲人和0.42±0.14美国印第安人，分为0.18±0.15艾马拉和0.25±0.13马普切。然而，从这些族裔的历史位置可以预期，马普切人的祖先在南部最高（40.03％），在北部的艾马拉（35.61％）。我们通过在线应用程序提供我们的结果，并演示在测试疾病的发生率与非遗传风险因素之间的关联时，如何将其用于调整血统。结论我们在许多不同的城市对当前智利人口进行了最广泛的抽样。祖先因纬度和人类发展而异。社区可以使用AIM专家组以较低的成本估算智利人和其他具有相似血统的人群的血统。我们通过在线应用程序提供我们的结果，并演示在测试疾病的发生率与非遗传风险因素之间的关联时，如何将其用于调整血统。结论我们在许多不同的城市对当前智利人口进行了最广泛的抽样。祖先因纬度和人类发展而异。社区可以使用AIM专家组，以低成本评估智利人和其他具有相似血统的人群的血统。我们通过在线应用程序提供我们的结果，并演示在测试疾病的发生率与非遗传风险因素之间的关联时，如何将其用于调整血统。结论我们在许多不同的城市对当前智利人口进行了最广泛的抽样。祖先因纬度和人类发展而异。社区可以使用AIM专家组以较低的成本估算智利人和其他具有相似血统的人群的血统。