A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set

Abstract

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 timeefficient 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.

Association of the genetic ancestry with resistant hypertension in the ReHOT (Resistant Hypertension Optimal Treatment) randomized study

“…In this method, each chip had enough arrays to obtain the 192 genotypes of 15 individuals at the same time and a further negative control reaction to evaluate the quality of genotyping. 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 21 .…”

“…The analysis of GA was performed using the Admixture program 24 , which is a tool for estimating the maximum likelihood of individual ancestors of data sets of multilocus SNP genotypes. The ancestry proportions were estimated for our samples using the panel of AIMs and samples from HapMap, HGDP and 1000 Genomes projects as reference for European, African and Native American populations 21 .…”

Avaliações farmacometabolômicas e de ancestralidade genética em pacientes hipertensos de um estudo clínico randomizado

“…A escolha do painel utilizado para a análise da AG dos indivíduos foi baseada do artigo de Santos H.C. e colaboradores 63…”

Variantes nos genes OCA2 e HERC2 associadas a fenótipos clássicos de pigmentação e estruturas secundárias presentes na íris em amostra miscigenada da população brasileira

“…-Kurtz et al, 2007;Pimenta et al, 2006;Santos et al, 2009;Lins et al, 2011;Parra et al, 2003;Pena et al, 2011). Em contrapartida, outros estudos indicam que a cor da pele auto-declarada seria consistente com a contribuição ancestral dominante ou relativa (Blanton et al, 2008;Cardena et al, 2013;Manta et al, 2013;Muniz et al, 2008;Pena et al, 2009;Queiroz et al, 2013;Santos et al, 2010 (Ferreira et al, 2006;Muniz et al, 2008 De uma forma geral, a ancestralidade europeia predomina em todas as regiões do país, atingindo suas maiores estimativas nas regiões sudeste e principalmente na região sul, com 79% e 85% respectivamente (Santos et al, 2015). Existem localidades que desviam deste padrão.…”

“…Existem localidades que desviam deste padrão. Na região norte do país a contribuição ameríndia chega a 52% (Guerreiro et al, 1993), e na região nordeste pode-se observar cerca de 50% de contribuição africana em algumas populações (Santos et al, 2015).…”