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 stratific...
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| Format: | Article |
| Language: | English |
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BMC
2020-04-01
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| Series: | Biological Research |
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| Online Access: | http://link.springer.com/article/10.1186/s40659-020-00284-5 |
| _version_ | 1828747866016841728 |
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| author | Ricardo A. Verdugo Alex Di Genova Luisa Herrera Mauricio Moraga Mónica Acuña Soledad Berríos Elena Llop Carlos Y. Valenzuela M. Leonor Bustamante Dayhana Digman Adriana Symon Soledad Asenjo Pamela López Alejandro Blanco José Suazo Emmanuelle Barozet Fresia Caba Marcelo Villalón Sergio Alvarado Dante Cáceres Katherine Salgado Pilar Portales Andrés Moreno-Estrada Christopher R. Gignoux Karla Sandoval Carlos D. Bustamante Celeste Eng Scott Huntsman Esteban G. Burchard Nicolás Loira Alejandro Maass Lucía Cifuentes |
| author_facet | Ricardo A. Verdugo Alex Di Genova Luisa Herrera Mauricio Moraga Mónica Acuña Soledad Berríos Elena Llop Carlos Y. Valenzuela M. Leonor Bustamante Dayhana Digman Adriana Symon Soledad Asenjo Pamela López Alejandro Blanco José Suazo Emmanuelle Barozet Fresia Caba Marcelo Villalón Sergio Alvarado Dante Cáceres Katherine Salgado Pilar Portales Andrés Moreno-Estrada Christopher R. Gignoux Karla Sandoval Carlos D. Bustamante Celeste Eng Scott Huntsman Esteban G. Burchard Nicolás Loira Alejandro Maass Lucía Cifuentes |
| author_sort | Ricardo A. Verdugo |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-14T04:50:01Z |
| format | Article |
| id | doaj.art-2ce97e1e592a4a30aefdab2ba01db8cd |
| institution | Directory Open Access Journal |
| issn | 0717-6287 |
| language | English |
| last_indexed | 2024-04-14T04:50:01Z |
| publishDate | 2020-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Biological Research |
| spelling | doaj.art-2ce97e1e592a4a30aefdab2ba01db8cd2022-12-22T02:11:19ZengBMCBiological Research0717-62872020-04-0153111110.1186/s40659-020-00284-5Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche componentsRicardo A. Verdugo0Alex Di Genova1Luisa Herrera2Mauricio Moraga3Mónica Acuña4Soledad Berríos5Elena Llop6Carlos Y. Valenzuela7M. Leonor Bustamante8Dayhana Digman9Adriana Symon10Soledad Asenjo11Pamela López12Alejandro Blanco13José Suazo14Emmanuelle Barozet15Fresia Caba16Marcelo Villalón17Sergio Alvarado18Dante Cáceres19Katherine Salgado20Pilar Portales21Andrés Moreno-Estrada22Christopher R. Gignoux23Karla Sandoval24Carlos D. Bustamante25Celeste Eng26Scott Huntsman27Esteban G. Burchard28Nicolás Loira29Alejandro Maass30Lucía Cifuentes31Programa de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChileMathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChileInstituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de ChileDepartamento de Sociología, Facultad de Ciencias Sociales, Universidad de Chile, Centro de Estudios de Conflicto y Cohesión, SocialFacultad de Ciencias de la Salud, Universidad de TarapacáInstituto de Salud Poblacional “Escuela de Salud Pública”, Universidad de ChileInstituto de Salud Poblacional “Escuela de Salud Pública”, Universidad de ChileInstituto de Salud Poblacional “Escuela de Salud Pública”, Universidad de ChileFacultad de Ciencias de la Salud, Universidad de TarapacáCorporación Municipal de Desarrollo SocialNational Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAVDepartment of Genetics, Stanford UniversityNational Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAVDepartment of Genetics, Stanford UniversityDepartment of Medicine, University of CaliforniaDepartment of Medicine, University of CaliforniaDepartment of Bioengineering and Therapeutic Sciences, University of CaliforniaMathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de ChileMathomics, Centro de Modelamiento Matemático y Centro para la Regulación del Genoma, Facultad de Ciencias Físicas y Matemáticas, Universidad de ChilePrograma de Genética Humana del ICBM, Facultad de Medicina, Universidad de ChileAbstract 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.http://link.springer.com/article/10.1186/s40659-020-00284-5ChileAdmixtureAncestryAymaraMapucheSNPs panel |
| spellingShingle | Ricardo A. Verdugo Alex Di Genova Luisa Herrera Mauricio Moraga Mónica Acuña Soledad Berríos Elena Llop Carlos Y. Valenzuela M. Leonor Bustamante Dayhana Digman Adriana Symon Soledad Asenjo Pamela López Alejandro Blanco José Suazo Emmanuelle Barozet Fresia Caba Marcelo Villalón Sergio Alvarado Dante Cáceres Katherine Salgado Pilar Portales Andrés Moreno-Estrada Christopher R. Gignoux Karla Sandoval Carlos D. Bustamante Celeste Eng Scott Huntsman Esteban G. Burchard Nicolás Loira Alejandro Maass Lucía Cifuentes Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components Biological Research Chile Admixture Ancestry Aymara Mapuche SNPs panel |
| title | 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_short | 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 |
| topic | Chile Admixture Ancestry Aymara Mapuche SNPs panel |
| url | http://link.springer.com/article/10.1186/s40659-020-00284-5 |
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