Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components
Abstract 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 stratif...
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| Lenguaje: | English |
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Sociedad de Biología de Chile
2020
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oai:scielo:S0716-976020200001002132020-06-25Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche componentsVerdugo,Ricardo A.Genova,Alex DiHerrera,LuisaMoraga,MauricioAcuña,MónicaBerríos,SoledadLlop,ElenaValenzuela,Carlos Y.Bustamante,M. LeonorDigman,DayhanaSymon,AdrianaAsenjo,SoledadLópez,PamelaBlanco,AlejandroSuazo,JoséBarozet,EmmanuelleCaba,FresiaVillalón,MarceloAlvarado,SergioCáceres,DanteSalgado,KatherinePortales,PilarMoreno-Estrada,AndrésGignoux,Christopher R.Sandoval,KarlaBustamante,Carlos D.Eng,CelesteHuntsman,ScottBurchard,Esteban G.Loira,NicolásMaass,AlejandroCifuentes,Lucía Chile Admixture Ancestry Aymara Mapuche SNPs panel Abstract 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.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.53 20202020-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602020000100213en10.1186/s40659-020-00284-5 |
| institution |
Scielo Chile |
| collection |
Scielo Chile |
| language |
English |
| topic |
Chile Admixture Ancestry Aymara Mapuche SNPs panel |
| spellingShingle |
Chile Admixture Ancestry Aymara Mapuche SNPs panel Verdugo,Ricardo A. Genova,Alex Di Herrera,Luisa Moraga,Mauricio Acuña,Mónica Berríos,Soledad Llop,Elena Valenzuela,Carlos Y. Bustamante,M. Leonor Digman,Dayhana Symon,Adriana Asenjo,Soledad López,Pamela Blanco,Alejandro Suazo,José Barozet,Emmanuelle Caba,Fresia Villalón,Marcelo Alvarado,Sergio Cáceres,Dante Salgado,Katherine Portales,Pilar Moreno-Estrada,Andrés Gignoux,Christopher R. Sandoval,Karla Bustamante,Carlos D. Eng,Celeste Huntsman,Scott Burchard,Esteban G. Loira,Nicolás Maass,Alejandro Cifuentes,Lucía Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| description |
Abstract 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. |
| author |
Verdugo,Ricardo A. Genova,Alex Di Herrera,Luisa Moraga,Mauricio Acuña,Mónica Berríos,Soledad Llop,Elena Valenzuela,Carlos Y. Bustamante,M. Leonor Digman,Dayhana Symon,Adriana Asenjo,Soledad López,Pamela Blanco,Alejandro Suazo,José Barozet,Emmanuelle Caba,Fresia Villalón,Marcelo Alvarado,Sergio Cáceres,Dante Salgado,Katherine Portales,Pilar Moreno-Estrada,Andrés Gignoux,Christopher R. Sandoval,Karla Bustamante,Carlos D. Eng,Celeste Huntsman,Scott Burchard,Esteban G. Loira,Nicolás Maass,Alejandro Cifuentes,Lucía |
| author_facet |
Verdugo,Ricardo A. Genova,Alex Di Herrera,Luisa Moraga,Mauricio Acuña,Mónica Berríos,Soledad Llop,Elena Valenzuela,Carlos Y. Bustamante,M. Leonor Digman,Dayhana Symon,Adriana Asenjo,Soledad López,Pamela Blanco,Alejandro Suazo,José Barozet,Emmanuelle Caba,Fresia Villalón,Marcelo Alvarado,Sergio Cáceres,Dante Salgado,Katherine Portales,Pilar Moreno-Estrada,Andrés Gignoux,Christopher R. Sandoval,Karla Bustamante,Carlos D. Eng,Celeste Huntsman,Scott Burchard,Esteban G. Loira,Nicolás Maass,Alejandro Cifuentes,Lucía |
| author_sort |
Verdugo,Ricardo A. |
| title |
Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| title_short |
Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| title_full |
Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| title_fullStr |
Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| title_full_unstemmed |
Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components |
| title_sort |
development of a small panel of snps to infer ancestry in chileans that distinguishes aymara and mapuche components |
| publisher |
Sociedad de Biología de Chile |
| publishDate |
2020 |
| url |
http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602020000100213 |
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