Article
A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set
Registro en:
SANTOS, H. C. et al. A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set. European Journal of Human Genetics, v. 24, p. 725–731, 2016.
1018-4813
10.1038/ejhg.2015.187
Autor
Santos, Hadassa Campos
Horimoto, Andréa Roseli Vancan Russo
Santos, Eduardo Martín Tarazona
Soares, Fernanda Rodrigues
Barreto, Maurício Lima
Horta, Bernardo Lessa
Costa, Maria Fernanda Furtado de Lima
Gouveia, Mateus Henrique
Machado, Moara
Silva, Thiago Magalhães da
Sanches, José Maurício
Esteban, Nubia
Magalhães, Wagner Carlos Santos
Rodrigues, Maíra Ribeiro
Kehdy, Fernanda de Souza Gomes
Pereira, Alexandre da Costa
The Brazilian EPIGEN Project Consortium
Resumen
Barreto, Mauricio Lima “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”. Department of Science and Technology (DECIT/ SCTIE) and National Fund for Scientific and
Technological Development (FNDCT), Ministry of Health, Brazil; Funding of Studies and Projects (FINEP), Ministry of Science and Technology, Brazil; Coordination of Improvement of Higher Education Personnel (CAPES), Ministry of Education, Brazil. HCS is supported by a grant from the São Paulo Research Foundation (FAPESP). The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.