Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components

Biological research: BR

article

Verdugo, Ricardo A.¹  Digman, Dayhana¹  Symon, Adriana¹  Asenjo, Soledad¹  López, Pamela¹  Blanco, Alejandro¹  Suazo, José³  Barozet, Emmanuelle⁴  Caba, Fresia⁵  Villalón, Marcelo⁶  Alvarado, Sergio⁶  Di Genova, Alex¹  Cáceres, Dante⁶  Salgado, Katherine⁵  Portales, Pilar⁷  Moreno-Estrada, Andrés⁸  Gignoux, Christopher R.⁹  Sandoval, Karla⁸  Bustamante, Carlos D.⁹  Eng, Celeste^1,10  Huntsman, Scott^1,10  Burchard, Esteban G.^1,11  Herrera, Luisa¹  Loira, Nicolás¹  Maass, Alejandro¹  Cifuentes, Lucía¹  Moraga, Mauricio¹  Acuña, Mónica¹  Berríos, Soledad¹  Llop, Elena¹  Valenzuela, Carlos Y.¹  Bustamante, M. Leonor¹ 

[1] Programa de Genética Humana del ICBM, Universidad de Chile;Departamento de Oncología Básico Clínica, Universidad de Chile;Instituto de Investigación en Ciencias Odontológicas, Universidad de Chile;Departamento de Sociología, Universidad de Chile;Universidad de Tarapacá;Instituto de Salud Poblacional “Escuela de Salud Pública”, Universidad de Chile;Corporación Municipal de Desarrollo Social;National Laboratory of Genomics for Biodiversity (LANGEBIO);Department of Genetics, Stanford University;Department of Medicine, University of California;Department of Bioengineering and Therapeutic Sciences, University of California;Departamento de Ingeniería Matemática, Universidad de Chile;Departamento de Psiquiatría, Universidad de Chile

关键词: Chile;    Admixture;    Ancestry;    Aymara;    Mapuche;    SNPs panel;   

DOI  :  10.1186/s40659-020-00284-5

来源: BioMed Central

【 摘 要 】

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. 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. 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.

【 授权许可】

Unknown