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

Autor: M. Acuña, Alex Di Genova, Katherine Salgado, Carlos Bustamante, Celeste Eng, Sergio Alvarado, Dante Cáceres, Nicolás Loira, Elena Llop, Soledad Asenjo, Ricardo A. Verdugo, Mauricio Moraga, Karla Sandoval, M. Leonor Bustamante, Emmanuelle Barozet, Fresia Caba, Soledad Berríos, Alejandro Toro Blanco, Andrés Moreno-Estrada, Esteban G. Burchard, Luisa Herrera, Scott Huntsman, Christopher R. Gignoux, Adriana Symon, Carlos Y Valenzuela, José Suazo, Pilar Portales, Alejandro Maass, Pamela López, Lucía Cifuentes, Marcelo Villalón, Dayhana Digman
Rok vydání: 2019
Předmět:
Zdroj: Biological Research
Biological Research v.53 2020
SciELO Chile
CONICYT Chile
instacron:CONICYT
Biological Research, Vol 53, Iss 1, Pp 1-11 (2020)
Biological research, vol 53, iss 1
Biological Research, Volume: 53, Article number: 15, Published: 24 APR 2020
ISSN: 0717-6287
Popis: 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.
Databáze: OpenAIRE
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