Genetic composition of Brazilian population samples based on a set of twenty‐eight ancestry informative SNPs

Abstract

Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry-informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of F(st) among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations.

Relação entre a etnia auto-declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro.

“…Although these data corroborate with previous studies in relation of major contribution of genomic ancestry 2,20 , it is possible to observe that there were differences between our data and these studies because we found a slightly larger percentage of African genomic ancestry and a slightly lower percentage of European genomic ancestry in the black and brown individuals. These differences could be mainly due to the socio-economic bias that exists in the Brazilian population.…”

“…This emphasizes the fact that in a population where there is a high degree of admixture and where superfi cial physical traits can vary with age and environmental factors, only the self-declaration of ethnicity is not a good method for ethnic classifi cation 6,20 .…”

“…According to the IBGE, the Brazil is composed of 48.2% of individuals self-declared as white and in the Southeast is 56.7% 19 . Various genetics studies with different Brazilian sub-populations had demonstrated the discrepancy between the self-declaration information and the individual's genetic background 4,20 , including this one. These facts demonstrate the existence of problems in the methodology used for the acquisition of information on ethnicity in the Brazilian population, resulting in a major diffi culty in using these data in epidemiological studies.…”

Polymorphism analysis of the CTLA-4 gene in paracoccidioidomycosis patients

“…Sixteen ancestry informative markers with large differences in allelic frequency were previously selected to estimate genetic admixture (Moreno Lima et al 2007). Genotype data from three ethnic parental populations were used to adjust inference in admixed population: Sub-Saharan African (120 individuals), Amerindian (69 individuals) and European-American (78 individuals) (Smith et al 2004, Lins et al 2010a). The evaluation of population structure was performed using the Structure 2.1 software by means of Bayesian inference (Pritchard et al 2000).…”

“…Genotypes were determined using GeneScan Analysis Software, version 3.7 (Applied Biosystems) and Genotyper version 3.7 (Applied Biosystems). A detailed, optimized multiplex, singlebase extension protocol, with reagent concentrations and PCR thermocycling conditions, was described elsewhere (Lins et al , 2010a.…”