Research Article: Genomic Ancestry, Self-Reported “Color” and Quantitative Measures of Skin Pigmentation in Brazilian Admixed Siblings

Date Published: November 2, 2011

Publisher: Public Library of Science

Author(s): Tailce K. M. Leite, Rômulo M. C. Fonseca, Nanci M. de França, Esteban J. Parra, Rinaldo W. Pereira, Tom R. Gaunt.


A current concern in genetic epidemiology studies in admixed populations is that population stratification can lead to spurious results. The Brazilian census classifies individuals according to self-reported “color”, but several studies have demonstrated that stratifying according to “color” is not a useful strategy to control for population structure, due to the dissociation between self-reported “color” and genomic ancestry. We report the results of a study in a group of Brazilian siblings in which we measured skin pigmentation using a reflectometer, and estimated genomic ancestry using 21 Ancestry Informative Markers (AIMs). Self-reported “color”, according to the Brazilian census, was also available for each participant. This made it possible to evaluate the relationship between self-reported “color” and skin pigmentation, self-reported “color” and genomic ancestry, and skin pigmentation and genomic ancestry. We observed that, although there were significant differences between the three “color” groups in genomic ancestry and skin pigmentation, there was considerable dispersion within each group and substantial overlap between groups. We also saw that there was no good agreement between the “color” categories reported by each member of the sibling pair: 30 out of 86 sibling pairs reported different “color”, and in some cases, the sibling reporting the darker “color” category had lighter skin pigmentation. Socioeconomic status was significantly associated with self-reported “color” and genomic ancestry in this sample. This and other studies show that subjective classifications based on self-reported “color”, such as the one that is used in the Brazilian census, are inadequate to describe the population structure present in recently admixed populations. Finally, we observed that one of the AIMs included in the panel (rs1426654), which is located in the known pigmentation gene SLC24A5, was strongly associated with skin pigmentation in this sample.

Partial Text

Population structure can be a source of confounding in genetic epidemiology studies. Typically, the effect of population stratification is to inflate the rate of false positives in case-control or quantitative trait studies. This is particularly the case in populations that are the result of recent admixture between continental groups [1]. The Brazilian population is primarily the result of admixture between European, African and Native American groups [2]–[5]. The Brazilian census classifies individuals according to “color” or “race”, and includes the following categories: “Branca” (i.e. “white”), “Parda” (i.e. “brown”), “Preta” (i.e. “black”), “Amarela” (i.e. “yellow”) and “Indígena” (i.e. “indigenous”). However, several studies have demonstrated that stratifying according to “color” is not a useful strategy to control for population structure, due to the dissociation between self-reported “color” and genomic ancestry [6]–[11]. The best strategy to identify, and control for, population stratification in association studies in recently admixed groups is to use AIMs, which are genetic markers showing large frequency differences between the parental populations, to estimate individual ancestry proportions and to include them as covariates in the statistical analysis [1], [12].

The study was approved by the Research Ethics Committee in the Catholic University of Brasília (CEP/UCB N° 078/2006) and written informed consent was obtained from each volunteer or responsible in cases of participants with less than 18 years of age.

Table 2 shows the main characteristics of the sample. The average age was 15.6 years, the average melanin index was 36.5, and the average European, West African and Native American contributions were 69%, 21% and 10%, respectively. For the variable “color”, 31.4% of the participants reported to be “white”, 60.5% reported to be “brown” and 8.1% reported to be “black”.

In this manuscript, we studied the relationship between self-reported “color”, quantitative measures of skin pigmentation, and genomic ancestry in a sample of full siblings from Brasilia. With respect to previous research in Brazil, this study is novel in that we measured skin pigmentation objectively using reflectometry and we sampled full siblings, which allowed us to evaluate the agreement of self-reported “color” and melanin index in each pair of siblings. Using a panel of 21 AIMs, we estimated that this sample has a European contribution of 69%, an African contribution of 21% and a Native American contribution of 10% (Table 2). These relative contributions are quite similar to those that have been reported in previous studies using AIMs in Brazil. For example, Lins et al. [4], estimated parental contributions in samples from different geopolitical regions in Brazil, and reported that European ancestry ranged from 69% to 88%, African ancestry from 7% to 19%, and Native American ancestry from 5% to 12%. Pena et al. [8] evaluated genetic ancestry in North, Northeast, Southeast and South regions of Brazil and reported similar figures, with the European contribution ranging from 60.1% to 79.5%, the African contribution from 10.3% to 29.3% and the Native American contributions from 7.3% to 18.55%. Using the program ADMIXMAP, we also obtained an estimate of the number of generations since admixture, which was approximately 9 generations, approximately 270 years ago, assuming 30 years per generation according to Helgason [32], which is quite consistent with historical data. However, it is important to mention that this estimate is based on a limited number of AIMs, so it has to be interpreted with caution.