Latin America
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NEW Brazilian study 2019 with 15,105 Sample
NEW Brazilian study 2019 with 15,105 Sample
https://journals.plos.org/plosone/ar...0216653#sec012
Context-dependence of race self-classification: Results from a highly mixed and unequal middle-income country
Materials and methods
Participants
The Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) is a multi-centre prospective cohort study designed primarily to identify risk factors and the natural history of diabetes and cardiovascular disease (CVD) [25,26]. The cohort comprises 15,105 active or retired employees of universities or research institutions located in six Brazilian capitals (Salvador, Vitória, Belo Horizonte, Rio de Janeiro, São Paulo, Porto Alegre) who were 35–74 years of age at baseline (2008–2010). ELSA-Brasil was performed in accordance with relevant guidelines and regulations, and all participants from ELSA-Brasil gave written informed consent to participate in the study. ELSA-Brasil was approved by the Ethics Committees of the Hospital das Clínicas de Porto Alegre, Hospital Universitário da Universidade de São Paulo, Fundação Oswaldo Cruz, Universidade Federal de Minas Gerais, Universidade Federal da Bahia, and Universidade Federal do Espírito Santo.
Among the 15,105 ELSA-Brasil participants, 9,834 (65%) were genotyped. Proportions varied between 25% in Porto Alegre and 91% in São Paulo. Of these, 116 (1,2%) did not have valid values for race/colour and were therefore excluded from the analysis. Among participants who self-declared as white, 65% were genotyped. Among participants who self-declared as black, brown, of Asian descent (mostly individuals with East Asian ancestors) and indigenous, this proportion was 62%, 65%, 75% and 66%, respectively.
The comparison between genotyped participants, who were included in this study, and non-genotyped participants can be found in the S1 Table. Given the study objectives and the small number of participants who self-declared as being of Asian descent (N = 281) or indigenous (104), these two groups were also excluded. Thus, the final sample included 9,333 participants. When compared with excluded participants, the study population had a higher proportion of white and brown participants and lower educational and income levels.
Questionnaires: The main predictor variables were sex, age in years (continuous), self-declared skin race/colour (white, black, brown, indigenous and of Asian descent; “brancos”, “pretos”, “pardos”, “indígenas” and “amarelos”), formal educational level achieved (until secondary education or university), per capita income and current residential address.
Global genetic ancestry determination
Purified DNA was obtained from peripheral blood from ELSA’s participants using the QIAamp DNA Mini-kit®. Samples were genotyped using a 192 AIM panel shown to be able to capture main continental ancestry components in the Brazilian population [30]. Genotyping was performed with the QuantstudioTM platform. Briefly, a multiplex TaqMan reaction was conducted in each sample for the 192 SNP panel according to manufacturer instructions. Each genotyping run carried 2 control genotypes (samples sequenced for all 192 variant alleles) and one negative control. Fluorescent results were analyzed in the QuantStudioTM and genotyped using the TaqMan_Genotyper, version 1.3 (Life Technologies, Foster City, CA, EUA) using the ‘autocalling’ tool for genotype assignment. Genotyping experiments were considered valid only with a call rate above 80% and with 100% of concordance for genotyping assignment for control samples.
Analysis of genomic ancestry was conducted using the ADMIXTURE program [31]. ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. Specifically, Admixture uses a block relaxation approach to alternately update allele frequency and ancestry fraction. ADMIXTURE estimates parameter standard errors using bootstrapping. As the contributions of differential ancestral genomes have previously been described by our group, as well as others, we used a supervised approach for ancestry determination. We used 200 bootstrap replicates (default) and k = 3 (number of populations assumed for the analysis). All ADMIXTURE analyses were repeated 4 times with different random seed numbers and in all cases, results were highly correlated.
We assumed as reference ancestral populations individuals from the Human Genome Diversity Project (HGDP): Pima, Maya as Amerindians and from the HapMap project, Africans: YRI (Yoruba in Ibadan, Nigeria), LWK (Luhya in Webuye, Kenya), ASW (Americans of African Ancestry in SW, USA); European: CEU (Utah Residents with Northern and Western European ancestry) and TSI (Tuscan in Italy). Ancestry variables are analysed as ancestry fractions (continuous).
Results
Participants’ characteristics
Most participants in this study have high educational levels (50.8% had a university degree) and self-declared as white (54.6%), whereas 29.4% and 16% self-declared as brown and black, respectively (Table 1). The study population also consisted of younger individuals and marginally more women (53.8%). Only in Salvador did most participants self-declare as brown or black. Median income was US$ 362 (monthly per capita income in United States dollars (USD), conversion rate: 2 Brazilian reais = 1USD). Median proportion of African, European and Amerindian ancestry was 20%, 70% and 10%, respectively. Only participants in Salvador presented a higher proportion (40%) of African ancestry and only those in Porto Alegre presented a higher proportion (80%) of European ancestry. In the census tracts where participants reside, 32.9% of inhabitants self-declared as brown or black. This proportion varied between 75.1% in Salvador and 11.9% in Porto Alegre.
In ELSA-Brasil, among those who self-declared as black or brown, the proportion of African ancestry was 56.4% and 26.5%, respectively (Fig 1). Among those who self-declared as brown, the proportion of African ancestry varied between 20% in Porto Alegre and 32.8% in Salvador. Among this group, the proportion of European ancestry was 58.9%, varying between 58.1% in Salvador and 67.9% in Belo Horizonte. Medians of African, European and Amerindian proportions according to research centres and self-declared race/colour can be found in S2 Table.
Here i made some modifications so its easier to understand
Average results per region and color.
Ancestry boxplots
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Originally Posted by Bolsonaro2018
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