Colonialism, ethnogenesis, and biogeographic ancestry in the US Southwest

OBJECTIVE

Differences between self-perceived biogeographic ancestry and estimates derived from DNA are potentially informative about the formation of ethnic identities in different sociohistorical contexts. Here, we compared self-estimates and DNA-estimates in New Mexico, where notions of shared ancestry and ethnic identity have been shaped by centuries of migration and admixture.

MATERIALS AND METHODS

We asked 507 New Mexicans of Spanish-speaking descent (NMS) to list their ethnic identity and to estimate their percentages of European and Native American ancestry. We then compared self-estimates to estimates derived from 291,917 single nucleotide polymorphisms (SNPs), and we examined how differences between the estimates varied by ethnic identity.

RESULTS

Most NMS (94%) predicted that they had non-zero percentages of European and Native American ancestry. Self-estimates and SNP-estimates were positively correlated (rEuropean  = 0.38, rNative-American  = 0.36, p < 0.001). The correlations belie systematic patterns of underestimation and overestimation based on ethnic identity. NMS with ancestral ties to 20th century immigrants, who identified as Mexican or Mexican American, often underestimated their European ancestry (self-estimate < SNP-estimate) and overestimated their Native American ancestry. The pattern was reversed for NMS who emphasized deep connections to colonial New Mexico and identified as Spanish or Spanish American.

DISCUSSION

While NMS accurately predicted that they had European and Native American ancestry, they predicted ancestry percentages with only moderate accuracy. Differences between self-estimated and SNP-estimated ancestry were associated with ethnic identities that were shaped by migration to the region over the past 400 years. We connect ethnic identities and patterns of ancestry estimation to resistance to colonial hegemony and discuss the implications of our results for the construction of ethnic identities, now and in the past.

Racial and regional inequalities of dental pain in adolescents: Brazilian National Survey of School Health (PeNSE), 2009 to 2015

The aim of the study is: (a) investigate the racial inequalities as one specific dimension that affects dental pain in Brazilian adolescents; and (b) investigate the regional variations of dental pain. This cross-sectional study used data from Brazilian National Survey of School Health (PeNSE), carried out with adolescents in 2009, 2012 and 2015. Dental pain was evaluated through the question: "Did you have dental pain in the last six months?". The main exposures were race and Brazilian regions, used to evaluate inequalities related to the outcome. Sex, age, school type and maternal education were used as covariables. The statistical significance of the trends in dental pain was tested using linear regression. The analysis was conducted in Stata 13.0 statistical package using the svy command. The standard prevalence of dental pain was 18.8%, 21.1% and 23.7%, showing an increasing trend over time (p < 0.001). We observed absolute inequalities in dental pain related to race and regions. A higher prevalence was found in non-white girls of public schools and in the Northern Region. The indexes of inequalities increased in the group of black girls, related to an increase of dental pain predominantly in girls whose mothers had lower educational level. It was observed that the prevalence of dental pain in Brazilian adolescents increased over time as well as its inequalities, which remained in marginalized populations and linked to Brazilian regions.

The impact of socioeconomic and phenotypic traits on self-perception of ethnicity in Latin America

Self-perception of ethnicity is a complex social trait shaped by both, biological and non-biological factors. We developed a comprehensive analysis of ethnic self-perception (ESP) on a large sample of Latin American mestizos from five countries, differing in age, socio-economic and education context, external phenotypic attributes and genetic background. We measured the correlation of ESP against genomic ancestry, and the influence of physical appearance, socio-economic context, and education on the distortion observed between both. Here we show that genomic ancestry is correlated to aspects of physical appearance, which in turn affect the individual ethnic self-perceived ancestry. Also, we observe that, besides the significant correlation among genomic ancestry and ESP, specific physical or socio-economic attributes have a strong impact on self-perception. In addition, the distortion among ESP and genomic ancestry differs across age ranks/countries, probably suggesting the underlying effect of past public policies regarding identity. Our results indicate that individuals' own ideas about its origins should be taken with caution, especially in aspects of modern life, including access to work, social policies, and public health key decisions such as drug administration, therapy design, and clinical trials, among others.

Fostering Responsible Research on Ancient DNA

Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.

Perspectivas, motivaciones e intereses en la búsqueda de ancestrías genéticas en Buenos Aires, Argentina

Este artículo propone una aproximación etnográfica al estudio de las perspectivas, motivaciones e intereses de los individuos participantes en el proyecto “Ancestría genética e identidad”. Basados en un corpus de entrevistas y en un marco teórico que utiliza los conceptos de genealogía y pedigrí, indagamos la significación que el dato genético adquiere en la recreación de las historias e identidades personales y familiares, así como el modo en que el test de ancestría genética se articula y entra en negociación con otras experiencias y registros de tipo oral o escrito. En el marco de las investigaciones desarrolladas en este campo, también señalamos la importancia de considerar los contextos sociales, jurídicos y políticos para comprender el impacto de estas nuevas tecnologías.

A systematic scoping review of the genetic ancestry of the Brazilian population

The genetic background of the Brazilian population is mainly characterized by three parental populations: European, African, and Native American. The aim of this study was to overview the genetic ancestry estimates for different Brazilian geographic regions and analyze factors involved in these estimates. In this systematic scoping review were included 51 studies, comprehending 81 populations of 19 states from five regions of Brazil. To reduce the potential of bias from studies with different sampling methods, we calculated the mean genetic ancestry weighted by the number of individuals. The weighted mean proportions of European, African, and Native American ancestries were 68.1%, 19.6%, and 11.6%, respectively. At the regional level, the highest European contribution occurred in the South, while the highest African and Native American contributions occurred in the Northeastern and Northern regions, respectively. Among states in the Northeast region, Bahia and Ceará showed significant differences, suggesting distinct demographic histories. This review contributes for a broader understanding of the Brazilian ancestry and indicates that the ancestry estimates are influenced by the type of molecular marker and the sampling method.

Context-dependence of race self-classification: Results from a highly mixed and unequal middle-income country

Ethnic-racial classification criteria are widely recognized to vary according to historical, cultural and political contexts. In Brazil, the strong influence of individual socio-economic factors on race/colour self-classification is well known. With the expansion of genomic technologies, the use of genomic ancestry has been suggested as a substitute for classification procedures such as self-declaring race, as if they represented the same concept. We investigated the association between genomic ancestry, the racial composition of census tracts and individual socioeconomic factors and self-declared race/colour in a cohort of 15,105 Brazilians. Results show that the probability of self-declaring as black or brown increases according to the proportion of African ancestry and varies widely among cities. In Porto Alegre, where most of the population is white, with every 10% increase in the proportion of African ancestry, the odds of self-declaring as black increased 14 times (95%CI 6.08-32.81). In Salvador, where most of the population is black or brown, that increase was of 3.98 times (95%CI 2.96-5.35). The racial composition of the area of residence was also associated with the probability of self-declaring as black or brown. Every 10% increase in the proportion of black and brown inhabitants in the residential census tract increased the odds of self-declaring as black by 1.33 times (95%CI 1.24-1.42). Ancestry alone does not explain self-declared race/colour. An emphasis on multiple situational contexts (both individual and collective) provides a more comprehensive framework for the study of the predictors of self-declared race/colour, a highly relevant construct in many different scenarios, such as public policy, sociology and medicine.

Association between serotonin 2C receptor gene (HTR2C) polymorphisms and psychopathological symptoms in children and adolescents

Serotonin 2C receptors (5HT2C) are involved in serotonin-driven dynamic equilibrium adjustments responsible for homeostatic stability in brain structures that modulate behavior and emotions. Single nucleotide polymorphisms (SNPs) from the serotonin 2C receptor gene (HTR2C) have been associated with several neurological and mental disorders, including abnormalities in cognitive and emotional processes. The aim of this study was to evaluate the association between the rs6318 SNP of the HTR2C gene and behavioral characteristics exhibited by children and adolescents based on the Child Behavior Checklist (CBCL/6-18) inventory. Eighty-five psychiatric outpatients between 8 and 18 years of age underwent genotyping of the rs6318 SNP. The CBCL/6-18 scale was administered to their caregivers. The chi-squared test was used to assess differences in the frequency of C and G alleles of the rs6318 SNP relative to the grouped CBCL/6-18 scores; significance level was 5%. The presence of the G allele of rs6318 was found to be associated with characteristics of aggressive behavior and social problems, and aggressive behavior was found to be associated with heterozygosis in females. These findings contribute to the identification of mental and behavioral phenotypes associated with gene expression.

Self-reported color-race and genomic ancestry in an admixed population: A contribution of a nationwide survey in patients with type 1 diabetes in Brazil

AIMS

The development of type 1 diabetes (T1D) and its chronic complications may have a genetic background. The primary objective of our study was to characterize the relationship between self-reported color-race and genomic ancestry (GA) in patients with T1D. As secondary objective, we aimed to characterize GA of patients with T1D from different urban geographical regions of Brazil, compared to healthy Brazilian controls from the same regions.

METHODS

This was a cross-sectional, nationwide survey conducted in 14 public clinics from 10 Brazilian cities. Global and individual GA were inferred using a panel of 46 ancestry informative markers (AIMs) in 1698 T1D patients. Ancestry percentage was compared with published data of Brazilian healthy controls (n = 936) for the same AIMs.

RESULTS

A higher median individual European ancestry was observed in T1D patients in comparison to controls 67.8 [31.2] vs. 56.3 [25.7]%, respectively (median [IQR]; p < 0.001). As for self-reported color-race in T1D group, 923 (54.3%) participants reported to be White, 610 (35.9%) Brown, 132 (7.8%) Black, 18 (1.1%) Asian and 15 (0.9%) Indigenous. European GA prevailed in those who self-reported as White (74.6%) and Brown (61.1%) and constituted 39.1% in Black self-reported patients.

CONCLUSIONS

Our study showed that T1D patients presented a higher percentage of European GA than the healthy population. Additionally, European GA was found in a considerable percentage of T1D patients who self-reported as non-White. Further studies are necessary to establish the influence of GA in the development of T1D as well its related chronic complications in admixed populations.

Association Between ABCB1 Polymorphism and Stable Warfarin Dose Requirements in Brazilian Patients

The ideal dose of the oral anticoagulant warfarin varies widely among patients, mainly due to genetic factors. Genetic variations that impact warfarin pharmacokinetics and the vitamin K cycle are plausible candidates for being associated with warfarin dose requirements. Therefore, the aim of this study was to assess whether polymorphisms in the ABCB1 and CYP4F2 genes were associated with stable warfarin dose requirements in Brazilian patients. This retrospective study included samples from 309 individuals. Genotyping of ABCB1 c.3435C>T and CYP4F2 c.1297G>A were performed by polymerase chain reaction followed by melting curve analysis (HRM-PCR) and TaqMan® genotyping assay, respectively. Stable doses were adjusted in a linear multiple regression model for age, gender, body mass index, self-reported race, use of amiodarone, CYP2C9 (^*2 and ^*3), VKORC1 c.1639G>A, and ABCB1 c.3435C>T or CYP4F2 c.1297G>A. By performing a univariate analysis of variance, we found that the warfarin patients who carry ABCB1 c.3435T variant alleles (CT and TT genotypes) need fewer warfarin stable doses in comparison with the individuals that are CC wild-type: 2.5 (p = 0.003) and 4.3 (p < 0.001) mg/week less, respectively, for the overall group of patients on stable anticoagulation therapeutics (n = 309); and 5.5 (p = 0.006) and 10.2 (p < 0.001) mg/week less, respectively, for the self-declared non-white stable subgroup (n = 76). No statistically significant differences in dose requirements were observed according to CYP4F2 genotypes. In conclusion, our results suggest ABCB1 c.3435C>T variant may influence warfarin dose requirements in Brazilian patients, when associated with other genotypic, demographic and clinical factors.

Polymorphisms in SIGLEC1 contribute to susceptibility to pulmonary active tuberculosis possibly through the modulation of IL-1ß

Siglec-1/CD169 is a sialoadhesin expressed by macrophages thought to function in cell-to-cell interactions. In the lung, the expression of Siglec-1 is specific for alveolar macrophages and single nucleotide polymorphisms (SNPs) in SIGLEC1 have been recently associated with asthma severity. Taking in account the role of alveolar macrophages in the control of M. tuberculosis and the poor literature about the contribution of SIGLEC1 genetics in M. tuberculosis susceptibility and development of pulmonary active TB, selected SNPs in SIGLEC1 were analysed in a case/control cohort from a TB endemic area of Brazil Amazon. Our findings evidenced for the first time the novel association between SIGLEC1 rs3859664 SNP and active pulmonary TB. Intriguingly, carriers of the polymorphism produced less IL-1ß than non-carriers, suggesting the possible involvement of Siglec-1 signalling pathway with inflammasome complex.

To Be or Not to Be (Black or Multiracial or White)

Culture shapes the meaning of race and, consequently, who is placed into which racial categories. Three experiments conducted in the United States and Brazil illustrated the cultural nature of racial categorization. In Experiment 1, a target’s racial ancestry influenced Americans’ categorizations but had no impact on Brazilians’ categorizations. Experiment 2 showed cultural differences in the reliance on two phenotypic cues to race; Brazilians’ categorizations were more strongly determined by skin tone than were Americans’ categorizations, and Americans’ categorizations were more strongly determined by other facial features compared to Brazilians' categorizations. Experiment 3 demonstrated cultural differences in the motivated use of racial categories. When the racial hierarchy was threatened, only Americans more strictly enforced the Black–White racial boundary. Cultural forces shape the conceptual, perceptual, and ideological construal of racial categories.

HABP2 p.G534E variant in patients with family history of thyroid and breast cancer

Familial Papillary Thyroid Carcinoma (PTC) has been described as a hereditary predisposition cancer syndrome associated with mutations in candidate genes including HABP2. Two of 20 probands from families with history of PTC and breast carcinoma (BC) were evaluated by whole exome sequencing (WES) revealing HABP2 p.G534E. Sanger sequencing was used to confirm the involvement of this variant in three families (F1: 7 relatives; F2: 3 and F3: 3). The proband and his sister (with no malignant tumor so far) from F1 were homozygous for the variant whereas one relative with PTC from F2 was negative for the variant. Although the proband of the F3 with PTC was HABP2 wild type, three relatives presented the variant. Five of 170 healthy Brazilian individuals with no family history of BC or PTC and three of 50 sporadic PTC presented the p.G534E. These findings suggested no association of this variant with our familial PTC cases. Genes potentially associated with deregulation of the extracellular matrix organization pathway (CTSB, TNXB, COL4A3, COL16A1, COL24A1, COL5A2, NID1, LOXL2, MMP11, TRIM24 and MUSK) and DNA repair function (NBN and MSH2) were detected by WES, suggesting that other cancer-associated genes have pathogenic effects in the risk of familial PTC development.

Surnames and ancestry in Brazil

This paper presents a method for classifying the ancestry of Brazilian surnames based on historical sources. The information obtained forms the basis for applying fuzzy matching and machine learning classification algorithms to more than 46 million workers in 5 categories: Iberian, Italian, Japanese, German and East European. The vast majority (96.7%) of the single surnames were identified using a fuzzy matching and the rest using a method proposed by Cavnar and Trenkle (1994). A comparison of the results of the procedures with data on foreigners in the 1920 Census and with the geographic distribution of non-Iberian surnames underscores the accuracy of the procedure. The study shows that surname ancestry is associated with significant differences in wages and schooling.

Hemoglobinas variantes na área médica e no discurso cotidiano: um olhar sobre raça, nação e genética no Brasil contemporâneo

Resumo Este artigo analisa a relação entre discursos médicos e noções cotidianas sobre raça, população e nação. Para isso, tomo como estudo de caso a comparação entre o uso dessas categorias na produção de artigos acadêmicos de dois renomados hematologistas brasileiros sobre a presença de hemoglobinas variantes patológicas no Brasil e a compreensão que famílias de pacientes diagnosticados com doença falciforme têm dessas mesmas questões. A comparação permite mostrar não só como os discursos da medicina influenciam o modo como questões relacionadas a raça e hereditariedade são compreendidas pelo público mais amplo, mas também a impossibilidade de separar em ambos casos, tanto na produção médica quanto nas falas dos pacientes, as noções sobre raça e hereditariedade de ideias mais amplas sobre o passado e o futuro da nação.

Genotyping and differential expression analysis of inflammasome genes in sporadic malignant melanoma reveal novel contribution of CARD8, IL1B and IL18 in melanoma susceptibility and progression

Sporadic melanoma malignancy is correlated with constitutive secretion of IL-1β in transformed melanocytes suggesting the involvement of inflammasome in melanoma. Common variants in inflammasome genes are known to affect IL-1β expression. To investigate the contribution of inflammasome genetics in melanoma development and progression and to identify a potential prognostic marker, the distribution of selected inflammasome SNPs was analysed in a Brazilian case/control cohort of sporadic malignant melanoma (SMM) and then the expression of inflammasome components was evaluated in melanoma biopsies. Allele and gene-specific Taqman assays were implied for genotyping of case/control DNA samples and for relative expression analysis in skin biopsies respectively. CARD8 rs6509365 was found to be significantly more common in healthy volunteers than in SMM patients suggesting a protection effect of this variant towards melanoma development. Accordingly, CARD8 expression was found to be reduced in nevus compared to melanoma biopsies. Upon stratification, NLRP1 rs11651270 and CARD8 rs2043211 were found associated with nodular melanoma; IL1B rs1143643 to a lower value of Breslow index; IL18 rs5744256 to melanoma development in sun sensitive individuals. As expected, IL1B expression was up-regulated in tumour biopsies especially in metastatic samples, whereas IL18 was down-regulated compared to nevus. Our results demonstrated for the first time the contribution of inflammasome genes CARD8, IL1B and IL18 in SMM.

Low C4, C4A and C4B gene copy numbers are stronger risk factors for juvenile-onset than for adult-onset systemic lupus erythematosus

OBJECTIVE

Complete deficiency of Complement C4 component is a strong genetic risk factor for SLE. C4 is encoded by two different genes, C4A and C4B, which show considerable gene copy number (GCN) variation. This study investigates the association of total C4, C4A and C4B GCN with JSLE.

METHODS

Ninety JSLE patients, 170 adult-onset SLE (aSLE) patients and 200 healthy individuals were evaluated for C4A and C4B GCN by quantitative real-time PCR.

RESULTS

JSLE patients had lower GCN for C4A (mean = 1.7; 95% CI: 1.5, 1.9) and C4B (mean = 1.5; 95% CI: 1.3, 1.6) compared with healthy individuals (mean C4A = 2.3; 95% CI: 2.2, 2.5, P < 0.001; C4B = 2.0; 95% CI: 1.8, 2.1; P < 0.001) or with aSLE patients (mean C4A = 1.9; 95% CI: 1.8, 2.1, P = 0.006; mean C4B = 1.8; 95% CI: 1.7, 1.9, P < 0.001). Low total C4 GCN (<4 copies) was more frequent in JSLE than in healthy individuals (59% vs 28%; P < 0.001). The same was observed for low C4A (⩽1 copy) (52% vs 18%; P < 0.001) and for low C4B (60% vs 31%; P < 0.001). JSLE had a stronger association with low total C4 (OR = 3.68, 95% CI: 2.19, 6.20), C4A (OR = 4.98, 95% CI: 2.88, 8.62) and C4B (OR = 3.26; 95% CI: 1.95, 5.47) than aSLE (C4 OR = 2.03; 95% CI: 1.32, 3.13; C4A OR = 2.36; 95% CI: 1.46, 3.81; C4B OR = 1.13; 95% CI: 0.73, 1.74). In addition, pericarditis in JSLE patients was associated with low C4 (OR = 4.13; 95% CI: 1.02, 16.68; P = 0.047) and low C4A (OR = 5.54; 95% CI: 1.37, 22.32; P = 0.016).

CONCLUSION

Low total C4, C4A and C4B GCN were associated with a stronger risk for developing JSLE than aSLE. Additionally, low total C4 and C4A GCN are risk factors for pericarditis in JSLE.

Genetics against race: Science, politics and affirmative action in Brazil

This article analyses interrelations between genetic ancestry research, political conflict and social identity. It focuses on the debate on race-based affirmative action policies, which have been implemented in Brazil since the turn of the century. Genetic evidence of high levels of admixture in the Brazilian population has become a key element of arguments that question the validity of the category of race for the development of public policies. In response, members of Brazil's black movement have dismissed the relevance of genetics by arguing, first, that in Brazil race functions as a social--rather than a biological--category, and, second, that racial classification and discrimination in this country are based on appearance, rather than on genotype. This article highlights the importance of power relations and political interests in shaping public engagements with genetic research and their social consequences.

Explaining the visible and the invisible: Public knowledge of genetics, ancestry, physical appearance and race in Colombia

Using data from focus groups conducted in Colombia, we explore how educated lay audiences faced with scenarios about ancestry and genetics draw on widespread and dominant notions of nation, race and belonging in Colombia to ascribe ancestry to collectivities and to themselves as individuals. People from a life sciences background tend to deploy idioms of race and genetics more readily than people from a humanities and race-critical background. When they considered individuals, people tempered or domesticated the more mechanistic explanations about racialized physical appearance, ancestry and genetics that were apparent at the collective level. Ideas of the latency and manifestation of invisible traits were an aspect of this domestication. People ceded ultimate authority to genetic science, but deployed it to work alongside what they already knew. Notions of genetic essentialism co-exist with the strategic use of genetic ancestry in ways that both fix and unfix race. Our data indicate the importance of attending to the different epistemological stances through which people define authoritative knowledge and to the importance of distinguishing the scale of resolution at which the question of diversity is being posed.

Genomic research, publics and experts in Latin America: Nation, race and body

The articles in this issue highlight contributions that studies of Latin America can make to wider debates about the effects of genomic science on public ideas about race and nation. We argue that current ideas about the power of genomics to transfigure and transform existing ways of thinking about human diversity are often overstated. If a range of social contexts are examined, the effects are uneven. Our data show that genomic knowledge can unsettle and reinforce ideas of nation and race; it can be both banal and highly politicized. In this introduction, we outline concepts of genetic knowledge in society; theories of genetics, nation and race; approaches to public understandings of science; and the Latin American contexts of transnational ideas of nation and race.

Building the genomic nation: 'Homo Brasilis' and the 'Genoma Mexicano' in comparative cultural perspective

This article explores the relationship between genetic research, nationalism and the construction of collective social identities in Latin America. It makes a comparative analysis of two research projects--the 'Genoma Mexicano' and the 'Homo Brasilis'--both of which sought to establish national and genetic profiles. Both have reproduced and strengthened the idea of their respective nations of focus, incorporating biological elements into debates on social identities. Also, both have placed the unifying figure of the mestizo/mestiço at the heart of national identity constructions, and in so doing have displaced alternative identity categories, such as those based on race. However, having been developed in different national contexts, these projects have had distinct scientific and social trajectories: in Mexico, the genomic mestizo is mobilized mainly in relation to health, while in Brazil the key arena is that of race. We show the importance of the nation as a frame for mobilizing genetic data in public policy debates, and demonstrate how race comes in and out of focus in different Latin American national contexts of genomic research, while never completely disappearing.

Evaluation of a high throughput method for the detection of mutations associated with thrombosis and hereditary hemochromatosis in Brazilian blood donors

Background

The aim of this study was to evaluate the OpenArray platform for genetic testing of blood donors and to assess the genotype frequencies of nucleotide-polymorphisms (SNPs) associated with venous thrombosis (G1691A and G20210A), hyperhomocysteinemia (C677T, A1298C), and hereditary hemochromatosis (C282Y, H63D and S65C) in blood donors from Sao Paulo, Brazil.

Methods

We examined 400 blood donor samples collected from October to November 2011. The SNPs were detected using OpenArray technology. The blood samples were also examined using a real-time PCR–FRET system to compare the results and determine the accuracy of the OpenArray method.

Results

We observed 100% agreement in all assays tested, except HFE C282Y, which showed 99.75% agreement. The HFE C282Y assay was further confirmed through direct sequencing, and the results showed that OpenArray analysis was accurate. The calculated frequencies of each SNP were FV G1691A 98.8% (G/G), 1.2% (G/A); FII G2021A 99.5% (G/G), 0.5% (G/A); MTHFR C677T 45.5% (C/C), 44.8% (C/T), 9.8% (T/T); MTHFR A1298C 60.3% (A/A), 33.6% (A/C), 6.1% (C/C); HFE C282Y 96%(G/G), 4%(G/A), HFE H63D 78.1%(C/C), 20.3% (C/G), 1.6% (G/G); and HFE S65C 98.1% (A/A), 1.9% (A/T).

Conclusion

Taken together, these results describe the frequencies of SNPs associated with diseases and are important to enhance our current knowledge of the genetic profiles of Brazilian blood donors, although a larger study is needed for a more accurate determination of the frequency of the alleles. Furthermore, the OpenArray platform showed a high concordance rate with standard FRET RT-PCR.

Pharmacogenomics, human genetic diversity and the incorporation and rejection of color/race in Brazil

Public funding for research on the action of drugs in countries like the United States requires that racial classification of research subjects should be considered when defining the composition of the samples as well as in data analysis, sometimes resulting in interpretations that Whites and Blacks differ in their pharmacogenetic profiles. In Brazil, pharmacogenomic results have led to very different interpretations when compared with those obtained in the United States. This is explained as deriving from the genomic heterogeneity of the Brazilian population. This article argues that in the evolving field of pharmacogenomics research in Brazil there is simultaneously both an incorporation and rejection of the US informed race-genes paradigm. We suggest that this must be understood in relation to continuities with national and transnational history of genetic research in Brazil, a differently situated politics of Brazilian public health and the ongoing valorization of miscegenation or race mixture by Brazilian geneticists as a resource for transnational genetic research. Our data derive from anthropological investigation conducted in INCA (Brazilian National Cancer Institute), in Rio de Janeiro, with a focus on the drug warfarin. The criticism of Brazilian scientists regarding the uses of racial categorization includes a revision of mathematical algorithms for drug dosage widely used in clinical procedures around the world. Our analysis reveals how the incorporation of ideas of racial purity and admixture, as it relates to the efficacy of drugs, touches on issues related to the possibility of application of pharmaceutical technologies on a global scale.

Does ethnic ancestry play a role in smoking?

The higher proportion of smokers among Black people in Brazil has been attributed to socioeconomic disparities, but genetic factors could also contribute for this finding. This study aimed at investigating associations between smoking status with genetically defined ethnic ancestry and socioeconomic features in Brazilians. Blood samples were collected from 448 volunteers (66.7% male; age: 37.1 ± 11.4 years) classified as current smokers (CS: 60.9%), former smokers (FS: 8.9%) and never smokers (NS: 30.1%). Individual interethnic admixtures were determined using a 48 insertion-deletion polymorphisms ancestry-informative-marker panel. CS showed a lower amount of European ancestry than NS (0.837 ± 0.243 X 0.883 ± 0.194, p ≤ 0.05) and FS (0.837 ± 0.243 X 0.864 ± 0.230, p ≤ 0.05), and a higher proportion of African Sub-Saharan ancestry than FS (0.128 ± 0.222 X 0.07 ± 0.174, p ≤ 0.05) and NS (0.128 ± 0.222 X 0.085 ± 0.178, p ≤ 0.05). NS reported a higher number of years in school than CS (11.2 ± 3.7 X 8.9 ± 3.8, p ≤ 0.001). CS were less common in economic Class A (30%) and more common in Class B (56.8%). In multivariate analysis, only lower number of school years and lower economic class were associated with higher chances for CS. The use of genetic molecular markers for characterizing ethnic background confirmed that socioeconomic disparities are the main determinants of higher smoking rates among Blacks in Brazil.

The colour of the human skin: fruitful science, unsuitable wordings

A review of the various facets of the colour of human skin is proposed. It aims first at illustrating the paradoxical association of the remarkable recent scientific advances that characterize changes in the skin colour, with some totally inappropriate or outdated phrasings used in its communication. As a second objective, it aims at proposing an alternative to these wordings. The latter would combine six shade types, defined by Individual Type Angle (ITA) values, a coloured reference chart and associated colour adjectives, highly corresponding to the six Phototypes previously defined by Fitzpatrick. Such alternative would overcome most references to both ethnic- and ethical-related issues.

The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

The degree of admixture in Brazil between historically isolated populations is complex and geographically variable. Studies differ as to what the genetic and phenotypic consequences of this mixing have been. In Northeastern Brazil, we enrolled 522 residents of Salvador and 620 of Fortaleza whose distributions of self-declared color were comparable to those in the national census. Using the program Structure and principal components analysis there was a clear correlation between biogeographic ancestry and categories of skin color. This correlation with African ancestry was stronger in Salvador (r=0.585; P<0.001) than in Fortaleza (r=0.236; P<0.001). In Fortaleza, although self-declared blacks had a greater proportion of European ancestry, they had more African ancestry than the other categories. When the populations were analyzed without pseudoancestors, as in some studies, the relationship of 'race' to genetic ancestry tended to diffuse or disappear. The inclusion of different African populations also influenced ancestry estimates. The percentage of unlinked ancestry informative markers in linkage disequilibrium, a measure of population structure, was 3-5 times higher in both Brazilian populations than expected by chance. We propose that certain methods, ascertainment bias and population history of the specific populations surveyed can result in failure to demonstrate a correlation between skin color and genetic ancestry. Population structure in Brazil has important implications for genetic studies, but genetic ancestry is irrelevant for how individuals are treated in society, their health, their income or their inclusion. These track more closely with perceived skin color than genetic ancestry.

On slaves and genes: "origins" and "processes" in genetic studies of the Brazilian population

In this article I examine how contemporary geneticists investigating the history and configuration of the Brazilian population engage with other academic disciplines. To do so I use as a case study some articles published by geneticists researching the presence of hemoglobin S variants in Brazil, in which there is a clear pretension to contribute to the analysis of issues such as slavery or Brazil's ethnic identity. By contrasting these studies with contemporary works from history and the social science, the explanatory centrality of "origin" in the genetic studies analyzed is problematized, as is the lack of interaction with the epistemological characteristics of other areas of knowledge.

Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

Latin America has a history of extensive mixing between Native Americans and people arriving from Europe and Africa. As a result, individuals in the region have a highly heterogeneous genetic background and show great variation in physical appearance. Latin America offers an excellent opportunity to examine the genetic basis of the differentiation in physical appearance between Africans, Europeans and Native Americans. The region is also an advantageous setting in which to examine the interplay of genetic, physical and social factors in relation to ethnic/racial self-perception. Here we present the most extensive analysis of genetic ancestry, physical diversity and self-perception of ancestry yet conducted in Latin America. We find significant geographic variation in ancestry across the region, this variation being consistent with demographic history and census information. We show that genetic ancestry impacts many aspects of physical appearance. We observe that self-perception is highly influenced by physical appearance, and that variation in physical appearance biases self-perception of ancestry relative to genetically estimated ancestry.

Nine things to remember about human genome diversity

Understanding how and why humans are biologically different is indispensable to get oriented in the ever-growing body of genomic data. Here we discuss the evidence based on which we can confidently state that humans are the least genetically variable primate, both when individuals and when populations are compared, and that each individual genome can be regarded as a mosaic of fragments of different origins. Each population is somewhat different from any other population, and there are geographical patterns in that variation. These patterns clearly indicate an African origin for our species, and keep a record of the main demographic changes accompanying the peopling of the whole planet. However, only a minimal fraction of alleles, and a small fraction of combinations of alleles along the chromosome, is restricted to a single geographical region (and even less so to a single population), and diversity between members of the same population is very large. The small genomic differences between populations and the extensive allele sharing across continents explain why historical attempts to identify, once and for good, major biological groups in humans have always failed. Nevertheless, racial categorization is all but gone, especially in clinical studies. We argue that racial labels may not only obscure important differences between patients but also that they have become positively useless now that cheap and reliable methods for genotyping are making it possible to pursue the development of truly personalized medicine.

The Nature/Culture of Genetic Facts

This review aims to explore the relationship between anthropology and genetics, an intellectual zone that has been occupied in different ways over the past century. One way to think about it is to contrast a classical “anthropological genetics” ( Roberts 1965 ), that is to say, a genetics that presumably informs anthropological issues or questions, with a “genomic anthropology” ( Pálsson 2008 ), that is to say, an anthropology that complements and relativizes modern genomics (on the model of, say, medical anthropology and legal anthropology). 1 This review argues that a principal contribution of anthropology to the study of human heredity lies in the ontology of genetic facts. For anthropology, genetic facts are not natural, with meanings inscribed on them, but are instead natural/cultural: The natural facts have cultural information (values, ideologies, meanings) integrated into them, not layered on them. To understand genetic facts involves confronting their production, which has classically been restricted to questions of methodology but which may be conceptualized more broadly. This review is not intended as a critique of the field of anthropological genetics, but as a reformulation of its central objects of study. I argue for reconceptualizing the ontology of scientific facts in anthropological genetics, not as (value-neutral) biological facts situated in a cultural context, but instead as inherently biocultural facts.

Ancestry, Temporality, and Potentiality: Engaging Cancer Genetics in Southern Brazil

In this paper I examine the variety of ways potential is articulated, entailed, and produced in how the field of cancer genetics is being constituted as a domain of transnational research and an emerging site of health-care intervention in southern Brazil. Drawing on analysis of fieldwork in Brazilian cancer-genetics clinics, I explore how different expressions of potential come to inform dynamically the pursuit of prevention, care, and research as diversely scaled investments for those working and living with cancer-genetics knowledge and technologies. It illustrates how specific temporalities help to constitute and "abductively" frame the meaning of these different potentials particularly as this relates to a focus on ancestry. Colonial histories of migration, the embodied effects of dietary habits, or the moral failings of near and distant ancestors as well as promissory futures and the contingency of lived lives become at different times templates for identifying, materializing, and transforming how the potential of cancer genetics in Brazil is articulated. Potential is also expressed through an idiom of "choice" in different efforts to situate participation in cancer-genetics research as prevention or to negotiate access to basic public health. I explore how these expressions of cancer genetics as potential powerfully yet unevenly work to sustain knowledge practices as well as propel patients and their families into fledgling domains of clinical practice and scientific research. At the same time there is always an "excess of meaning" in these endeavors that make visible lines of fracture and disjuncture in collective efforts to make future histories of and from the pursuit of cancer genetics in southern Brazil.

Biological races in humans

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.

Ancestry analysis reveals a predominant Native American component with moderate European admixture in Bolivians

We have genotyped 46 Ancestry Informative Markers (AIMs) in two of the most populated areas in Bolivia, namely, La Paz (Andean region; n=105), and Chuquisaca (Sub-Andean region; n=73). Using different analytical tools, we inferred admixture proportions of these two American communities by comparing the genetic profiles with those publicly available from the CEPH (Centre d'Etude du Polymorphisme Humain) panel representing three main continental groups (Africa, Europe, and America). By way of simulations, we first evaluated the minimum sample size needed in order to obtain accurate estimates of ancestry proportions. The results indicated that sample sizes above 30 individuals could be large enough to estimate main continental ancestry proportions using the 46 AIMs panel. With the exception of a few individuals, the results also indicated that Bolivians showed a predominantly Native American ancestry with variable levels of European admixture. The proportions of ancestry were statistically different in La Paz and Chuquisaca: the Native American component was 86% and 77% (Mann-Whitney U-test: un-adjusted P-value=2.1×10(-5)), while the European ancestry was 13% and 21% (Mann-Whitney U-test: un-adjusted P-value=3.6×10(-5)), respectively. The African ancestry in Bolivians captured by the AIMs analyzed in the present study was below 2%. The inferred ancestry of Bolivians fits well with previous studies undertaken on haplotype data, indicating a major proportion of Native American lineages. The genetic differences observed in these two groups suggest that forensic genetic analysis should be better performed based on local databases built in the main Bolivian areas.

Association of ethnicity and survival in peritoneal dialysis: a cohort study of incident patients in Brazil

BACKGROUND

There are no available epidemiologic studies about the impact of ethnicity on outcomes of patients treated with peritoneal dialysis (PD) in South America. This study aims to assess the effect of ethnicity on the mortality of incident PD patients in Brazil.

STUDY DESIGN

Prospective observational cohort study of incident patients treated with PD.

SETTINGS & PARTICIPANTS

Patients 18 years or older who started PD therapy between December 2004 and October 2007 in 114 Brazilian dialysis centers.

PREDICTORS

Self-reported ethnicity defined by the Brazilian Institute of Geography and Statistics as black and brown versus white patients and baseline demographic, socioeconomic, clinical, and laboratory data were collected at baseline.

OUTCOME

Mortality, using cumulative mortality curves in which kidney transplantation and transfer to hemodialysis therapy were treated as competing end points. Multivariate Cox proportional hazards analysis was used to adjust for gradually more potential explanatory variables, censored for kidney transplantation and transfer to hemodialysis therapy. Analyses were performed for all patients, as well as stratified for elderly (aged ≥65 years) and nonelderly patients.

RESULTS

1,370 patients were white, 516 were brown, and 273 were black. The competing-risk model showed higher mortality in white patients compared with black and brown patients. With white patients as the reference, Cox proportional hazards analysis showed a crude HR for mortality of 0.77 (95% CI, 0.56-1.05) for black and 0.74 (95% CI, 0.59-0.94) for brown patients. After adjusting for potential explanatory factors, HRs were 0.67 (95% CI, 0.48-0.95) and 0.77 (95% CI, 0.43-1.01), respectively. The same results were observed in elderly and nonelderly patients.

LIMITATIONS

Ethnicity was self-determined and some misclassification might have occurred.

CONCLUSIONS

Black and brown Brazilian incident PD patients have a lower mortality risk compared with white patients.

Primary immunodeficiency diseases in different age groups: a report on 1,008 cases from a single Brazilian reference center

Primary immunodeficiencies (PIDs) represent a large group of diseases that affect all age groups. Although PIDs have been recognized as rare diseases, there is epidemiological evidence suggesting that their real prevalence has been underestimated. We performed an evaluation of a series of 1,008 infants, children, adolescents and adults with well-defined PIDs from a single Brazilian center, regarding age at diagnosis, gender and PID category according to the International Union of Immunological Societies classification. Antibody deficiencies were the most common category in the whole series (61 %) for all age groups, with the exception of <2-year-old patients (only 15 %). In the >30-year-old group, antibody deficiencies comprised 84 % of the diagnoses, mostly consisting of common variable immunodeficiency, IgA deficiency and IgM deficiency. Combined immunodeficiencies represented the most frequent category in <2-years-old patients. Most congenital defects of phagocytes were identified in patients <5 -years of age, as were the diseases of immune dysregulation, with the exception of APECED. DiGeorge syndrome and ataxia-telangiectasia were the most frequent entities in the category of well-defined syndromes, which were mostly identified in patients <10-years of age. Males represented three-quarters and two-thirds of <2 -years-old and 2-5-years -old patients, respectively, whereas females predominated among the >30-year-old patients. Our data indicated that some PIDs were only detected at early ages, likely because affected patients do not survive long. In addition, our data pointed out that different strategies should be used to search for PIDs in infants and young children as compared to older patients.

The admixture structure and genetic variation of the archipelago of Cape Verde and its implications for admixture mapping studies

Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.

Sex determination by linear measurements of palatal bones and skull base

Genetically determined sexual dimorphism is not restricted to reproductive organs. All body structures show sexual differences which emerge during puberty and persist lifelong. The aim of this study is to obtain a reliable method for sex determination through the analysis of linear measurements of palate bones and skull base. One hundred skulls of both sexes, 50 from males and 50 from females, aged between 22 and 55 years, from the São Gonçalo Cemetery of Cuiabá, capital of Mato Grosso state, Brazil, were analyzed. Distances between the incisive foramen, right and left greater palatine foramens and the basion were measured with a digital caliper. Finally, data were tabulated and statistically analyzed. Measurements showed significant sexual dimorphism, except the distance between the right and the left greater palatine foramens. The superior expression of sex dimorphism corresponded to the distance from the basion to the incisive foramen. The authors obtained two mathematical models for sex determination, with a reliability rate of 63% and 65% respectively.

Making sense of skin color in clinical care

The background of this article is that assessment and quantification of skin color is important to health care; color is one indicator of overall health and is linked to oxygenation, tissue perfusion, nutritional status, and injury. The purpose is to describe how skin color varies across racial/ethnic groups so that the information can be applied to clinical practice. The method used is cross-sectional, descriptive design (n = 257). We recorded self-defined race/ethnicity and used a spectrophotometer to measure skin color at two anatomic sites. Skin color variables included L* (light/dark), a* (red/green), and b* (yellow/blue). As regards results, we found significant differences in L*, a*, and b* values by site and race/ethnicity in White, Asian, and Biracial participants. L*: F(3, 233) = 139.04, p < .01 and F(3, 233) = 118.47, p < .01. Black participants had significantly lower mean L* values and wider ranges of L*, a*, and b* as compared with other groups. In regard to application, these findings suggest that clinicians and researchers should plan and provide care based on skin color, rather than race/ethnicity.

Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings

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.

Stature estimation by Carrea's index and its reliability in different types of dental alignment

Stature is a measurable feature of the body, useful in human identification, which may include or exclude an individual from a missing persons list. The aim of this study is to analyze the Carrea´s index for stature estimation in dental arches with normal dentition, crowding and diastema. Plaster casts of 51 students of the Federal University of Paraíba were analyzed. Each hemiarch was divided according to the dental position, and the elements were measured with divider and digital calipers. Considering the normal and crowded dentition, the Carrea´s index presented a satisfactory success percentage, between 72.2% and 95.2%, with no statistically significant difference between sexes or between right and left sides. The presence of diastema reduced the number of matches to less than 62.5%. It was concluded that the Carrea´s index is a reliable method for height estimation in arches with normal and crowded dentitions, useful in males and females, and in the right and left sides. However, the method was not efficient in hemiarches with diastema.

Biorrevelações: testes de ancestralidade genética em perspectiva antropológica comparada

É cada vez maior o número de empresas que comercializam testes de ancestralidade genética a partir do DNA, sobretudo, na América do Norte. Tal fenômeno tem atraído a atenção das ciências sociais, em particular da antropologia. Neste artigo exploramos, enquanto um estudo de caso e a partir de uma perspectiva antropológica comparativa, os perfis de três empresas situadas em diferentes países: African Ancestry, nos EUA; Oxford Ancestors, na Inglaterra; Laboratório GENE, no Brasil. A partir da análise das suas respectivas páginas eletrônicas e de material divulgado na mídia, o intuito é tomar as duas primeiras como contraponto comparativo à última, de modo a avaliar o que as aproxima e distancia no tocante ao trato concedido ao potencial revelador de seus respectivos testes e, também, com que teor questões como pertença étnica/racial perpassam o merchandising de seus produtos e a sua postura pública. Em um plano mais amplo, argumenta-se que contextos sociopolíticos específicos influenciam as formas como os testes de ancestralidade genética são apresentados e justificados para seus respectivos públicos de consumidores. No caso específico da empresa brasileira, situá-la no panorama histórico-antropológico mais geral sobre "raça" e relações raciais, assim como nos debates correntes sobre o assunto, ajuda-nos a compreender como os testes de ancestralidade são justificados e apresentados à sociedade.