Genomic ancestry and ethnoracial self-classification based on 5,871 community-dwelling Brazilians (The Epigen Initiative)

Association of Early- to Midlife Weight Trajectories With Mid- to Late-Life Cognitive Decline in the ELSA-Brasil Study

BACKGROUND AND OBJECTIVES

While midlife obesity is consistently associated with cognitive decline in later life, there is limited understanding of how weight variations from early life to midlife affect cognitive decline. We investigated the association between early- to midlife weight trajectories and mid- to late-life cognitive decline.

METHODS

This is a longitudinal cohort study that used data from 3 waves (2008-2019) of the Brazilian Longitudinal Study of Adult Health, a multicenter cohort study that enrolled active and retired public servants aged 35+ years from public universities in Brazil. Participants with a history of stroke, missing cognitive data at baseline, and with incomplete body shape data were excluded from the analyses. Self-reported body shapes from ages 5 to 40 using the Stunkard Figure Rating Scale were categorized as underweight, normal, overweight, and obese. Sequence analysis and hierarchical clustering identified weight trajectories. Global cognition Z-scores were derived from memory (immediate recall, delayed recall, and recognition of a word list), phonemic and semantic verbal fluency, and Trail Making Test part B (TMT-B). Linear mixed models adjusted for sociodemographic, clinical, and lifestyle covariates investigated associations between clusters of weight trajectories and global cognition Z-scores. Inverse probability of attrition weighting was used to account for attrition bias.

RESULTS

Among 11,361 participants (mean age: 51.5 ± 8.6, 55% women, 42.4% Black/mixed race), "normal to overweight," "underweight to normal," and "stable overweight" trajectories exhibited faster global cognitive decline than "stable normal" trajectory (β = -0.024; 95% CI -0.043 to -0.005; p = 0.015; β = -0.026; 95% CI -0.040 to -0.012; p < 0.001; β = -0.034; 95% CI -0.066 to -0.001; p = 0.043, respectively), representing 4.6-6.5 excess years of cognitive aging over a median follow-up of 8 years. Cognitive decline associated with weight trajectories was driven mainly by declines in memory and TMT-B performance. Associations were observed only in Black/mixed races and women when stratified.

DISCUSSION

Weight gain and stable overweight trajectories from early life to midlife were associated with faster cognitive decline than stable normal weight trajectories. Weight management during early life may mitigate cognitive decline. Study limitations include reliance on self-reported body shape data, potential recall bias, and residual confounding from unmeasured early-life factors.

Influence of Cytokine-Related genetic variants in TNF, IL6, IL1β, and IFNγ genes in the thalidomide treatment for Erythema nodosum leprosum in a Brazilian population sample

Erythema nodosum leprosum (ENL), an inflammatory reaction in leprosy, causes painful nodules, fever, and malaise due to immune system activation. Thalidomide is an effective treatment, although associated with important adverse effects. We aimed to evaluate the association of genetic variants in genes encoding tumor necrosis factor alpha (TNF-α), interleukin-1 beta (IL-1β) and interleukin-6 (IL-6) with the response to treatment of ENL with thalidomide. 148 patients from the South and Northeast regions of Brazil were included. Genomic DNA was isolated from blood and/or saliva samples using commercial kits, and genetic variants in TNF, IL6, IL1β, and IFNγ genes were genotyped by TaqMan system. We identified an association between polymorphisms in TNF (rs1799964C, rs1800630A, rs1799724T and rs1800629A) IL1β (rs4848306G, rs1143623G, rs16944A, and rs1143627A), IL6 (rs2069840C and rs2069845G) and IFNγ (rs2430561T) with thalidomide dose variation in a time-dependent manner. Associations of IL6 and TNF haplotypes with thalidomide dosage variation over the time of treatment were also observed. Polymorphisms in TNF, IL6, IL1β, and IFNγ genes may modulate their expression levels, potentially impacting the required dosage of thalidomide in the treatment of ENL. Our findings should be confirmed in further studies to estimate the size effect of these polymorphisms on ENL treatment with thalidomide.

Subcontinental Genetic Diversity in the All of Us Research Program: Implications for Biomedical Research

The All of Us Research Program (All of Us) seeks to accelerate biomedical research and address the underrepresentation of minorities by recruiting over one million ethnically diverse participants across the United States. A key question is how self-identification with discrete, predefined race and ethnicity categories compares to genetic diversity at continental and subcontinental levels. To contextualize the genetic diversity in All of Us, we analyzed ~2 million common variants from 230,016 unrelated whole genomes using classical population genetics methods, alongside reference panels such as the 1000 Genomes Project, Human Genome Diversity Project, and Simons Genome Diversity Project. Our analysis reveals that participants within self-identified race and ethnicity groups exhibit a gradient of genetic diversity rather than discrete clusters. The distributions of continental and subcontinental ancestries show considerable variation within race and ethnicity, both nationally and across states, reflecting the historical impacts of U.S. colonization, the transatlantic slave trade, and recent migrations. All of Us samples filled most gaps along the top five principal components of genetic diversity in current global reference panels. Notably, "Hispanic or Latino" participants spanned much of the three-way (African, Native American, and European) admixture spectrum. Ancestry was significantly associated with body mass index (BMI) and height, even after adjusting for socio-environmental covariates. In particular, West-Central and East African ancestries showed opposite associations with BMI. This study emphasizes the importance of assessing subcontinental ancestries, as the continental approach is insufficient to control for confounding in genetic association studies.

Inpatient treatment for severe obesity: A retrospective cohort study in Brazil, comparing exposure variables in a secondary data analysis

INTRODUCTION

Very low-calorie diets with hospitalization have demonstrated promise as a viable therapeutic option for severe obesity and its associated comorbidities. However, large studies providing a comprehensive longitudinal observation of patients undergoing this therapy are lacking. We evaluated the effectiveness of treating severe obesity in hospitalized patients, using very low-calorie diets and clinical support to develop lifestyle changes.

METHODS

This study was a retrospective cohort comparing exposure variables in a secondary data analysis with a pre-post treatment design. Data were obtained from medical records of patients with severe obesity (grade II or III) treated in a Brazilian obesity specialist hospital from 2016 to 2022. The patients underwent a very low-calorie diet (500-800 kCal/day) and immersive changes in lifestyle habits, monitored by a multidisciplinary team. At 3 months, 777 patients presented complete data and 402 presented complete data at 6 months. The study compared changes in bioimpedance and laboratory tests, between men and women and age groups.

RESULTS

Three months of hospitalization yielded significant reductions in weight, body mass index (BMI), body fat, skeletal muscle mass, glucose, inflammatory, and lipid parameters. These reductions were more pronounced after 6 months, nearly doubling those observed at 3 months. In women, BMI and fat mass reduced by 10.4% and 15.2% at 3 months and 20.4% and 31.3% at 6 months, respectively. In men, BMI and fat mass decreased by 12.9% and 25.3 at 3 months and 23.6% and 45.3% at 6 months, respectively. Elderly individuals (aged ≥ 60 years) had smaller reductions in BMI and fat mass than non-elderly individuals (aged < 60 years) but still presented significant improvements.

CONCLUSION

This study suggests the viability of treating severe obesity by hospitalization with low-calorie diets and immersive lifestyle changes. This treatment modality significantly improves anthropometric measurements, glucose, lipids, and inflammatory markers, thereby reducing cardiovascular risk.

Steroid-Resistant Nephrotic Syndrome Is Associated With a Unique Genetic Profile in a Highly Admixed Pediatric Population

Introduction

The profile of genetic and nongenetic factors associated with progression to kidney failure (KF) in steroid-resistant nephrotic syndrome (SRNS) is largely unknown in admixed populations.

Methods

A total of 101 pediatric patients with primary SRNS were genetically assessed targeting Mendelian causes and APOL1 status with a 62-NS-gene panel or whole exome sequencing, as well as genetic ancestry. Variant pathogenicity was evaluated using the American College Medical of Genetics and Genomics (ACMG) criteria.

Results

Focal segmental glomerulosclerosis (FSGS) was diagnosed in 54% of patients whereas familial disease was reported by 13%. The global genetic ancestry was 65% European, 22% African, 10.5% Native American, and 2% East-Asian, while 96% of cases presented with the first 3 components. APOL1 high-risk genotypes were identified in 8% of families and causative Mendelian variants in 12%: NPHS1 = 3, NPHS2 = 3, PLCE1 = 2, WT1 = 2, COQ2 = 1, and CUBN = 1. Two novel causative variants arose in the Native American background. The percentage of African genetic ancestry did not associate with the number of APOL1 risk alleles. Forty-four percent of all patients progressed to KF. Mendelian forms and APOL1 high-risk genotypes were associated with faster progression to KF. Cox regression analyses revealed that higher non-European genetic ancestry, self-declared non-White ethnicity, age of onset <1 year or ≥9 years, and non-minimal change disease (MCD) histology associated with higher risk of KF, independently of genetic findings.

Conclusion

Mendelian variants and APOL1 high-risk genotype compose a unique causative genetic profile associated with pediatric SRNS in this highly admixed population, accounting for approximately 20% of families. This ancestry pattern is consistent with the identification of APOL1 high-risk genotypes in children with low proportion of African genetic ancestry. Self-declared ethnicity, age of manifestation and histology were independently associated with the risk of KF.

Genetic Ancestry and Self-Reported "Skin Color/Race" in the Urban Admixed Population of São Paulo City, Brazil

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual's genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations.

A nationwide study on immunosenescence biomarkers profile in older adults: ELSI-Brazil

Immunosenescence is a phenomenon caused by changes in the immune system, and part of these changes involves an increase in circulating immunological biomarkers, a process known as "Inflammaging." Inflammaging can be associated with many diseases related to older people. As the older population continues to grow, understanding changes in the immune system becomes essential. While prior studies assessing these alterations have been conducted in countries with Caucasian populations, this investigation marks a pioneering effort. The object of the study is to describe for the first time that the distribution of cytokines, chemokines, and growth factors serum levels, assessed by Luminex platform, has been examined in a Brazilian population-based study of older adult females and males by age. Blood samples from 2111 participants (≥50 years old) were analyzed at the baseline (2015/2016) of the ELSI-Brazil study. The exploratory variables considered in the study were age, sex, educational level, residence area, geographic region, alcohol and smoking consumption, physical activity, and self-reported medical diagnoses of hypertension, diabetes, asthma, arthritis, and cancer. The association between serum biomarker levels and age was assessed by a quantile regression model adjusted in the total population and stratified by sex. The significance level considered in the analysis was 0.05. The mean age of the participants was 62.9 years, with a slight majority of female (52.7 %). Differences were found between the sexes in the median circulating levels of the CCL11, CXCL10, and FGF biomarkers. Eight biomarkers showed significant associations with age, including the pro-inflammatory CXCL10, TNF-α, IL-6, IL-17, and IL-2; and type 2/regulatory CCL11 and IL-4, showing positive associations, and anti-inflammatory IL-1Ra showing a negative association. The results suggest similar associations between the sexes, revealing an inflammatory profile characterized by types 1 and 2. Remarkably, these findings reinforce the concept of the Inflammaging process in Brazilian population. These findings add novel insights to about the immunosenescence aspects in middle-income countries and help define biomarkers capable of monitoring inflammation in older adults.

Pharmacogenetic variability of tuberculosis biomarkers in native and mestizo Peruvian populations

In Peru, 29 292 people were diagnosed with tuberculosis in 2022. Although tuberculosis treatments are effective, 3.4%-13% are associated with significant adverse drug reactions, with drug-induced liver injury (DILI) considered the most predominant. Among the first-line antituberculosis drugs, isoniazid is the main drug responsible for the appearance of DILI. In liver, isoniazid (INH) is metabolized by N-acetyltransferase-2 (NAT2) and cytochrome P450 2E1 (CYP2E1). Limited information exists on genetic risk factors associated with the presence of DILI to antituberculosis drugs in Latin America, and even less is known about these factors in the native and mestizo Peruvian population. The aim of this study was to determine the prevalence of NAT2 and CYP2E1 genotypes in native and mestizo population. An analytical cross-sectional analysis was performed using genetic data from mestizo population in Lima and native participants from south of Peru. NAT2 metabolizer was determined as fast, intermediate and slow, and CYP2E1 genotypes were classified as c1/c1, c1/c2 and c2/c2, from molecular tests and bioinformatic analyses. Of the 472 participants, 36 and 6 NAT2 haplotypes were identified in the mestizo and native population, respectively. In mestizo population, the most frequent NAT2*5B and NAT2*7B haplotypes were associated with DILI risk; while in natives, NAT2*5G and NAT2*13A haplotypes were associated with decreased risk of DILI. For CYP2E1, c1/c1 and c1/c2 genotypes are the most frequent in natives and mestizos, respectively. The linkage disequilibrium of NAT2 single nucleotide polymorphisms (SNPs) was estimated, detecting a block between all SNPs natives. In addition, a block between rs1801280 and rs1799929 for NAT2 was detected in mestizos. Despite the limitations of a secondary study, it was possible to report associations between NAT2 and CYP2E alleles with Peruvian native and mestizo by prevalence ratios. The results of this study will help the development of new therapeutic strategies for a Tuberculosis efficient control between populations.

Lifestyle and incident dementia: A COSMIC individual participant data meta‐analysis

INTRODUCTION

The LIfestyle for BRAin Health (LIBRA) index yields a dementia risk score based on modifiable lifestyle factors and is validated in Western samples. We investigated whether the association between LIBRA scores and incident dementia is moderated by geographical location or sociodemographic characteristics.

METHODS

We combined data from 21 prospective cohorts across six continents (N = 31,680) and conducted cohort-specific Cox proportional hazard regression analyses in a two-step individual participant data meta-analysis.

RESULTS

A one-standard-deviation increase in LIBRA score was associated with a 21% higher risk for dementia. The association was stronger for Asian cohorts compared to European cohorts, and for individuals aged ≤75 years (vs older), though only within the first 5 years of follow-up. No interactions with sex, education, or socioeconomic position were observed.

DISCUSSION

Modifiable risk and protective factors appear relevant for dementia risk reduction across diverse geographical and sociodemographic groups.

HIGHLIGHTS

A two-step individual participant data meta-analysis was conducted. This was done at a global scale using data from 21 ethno-regionally diverse cohorts. The association between a modifiable dementia risk score and dementia was examined. The association was modified by geographical region and age at baseline. Yet, modifiable dementia risk and protective factors appear relevant in all investigated groups and regions.

Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts

Genome-wide association studies have been useful in identifying genetic risk factors for various phenotypes. These studies rely on imputation and many existing panels are largely composed of individuals of European ancestry, resulting in lower levels of imputation quality in underrepresented populations. We aim to analyze how the composition of imputation reference panels affects imputation quality in four target Latin American cohorts. We compared imputation quality for chromosomes 7 and X when altering the imputation reference panel by: 1) increasing the number of Latin American individuals; 2) excluding either Latin American, African, or European individuals, or 3) increasing the Indigenous American (IA) admixture proportions of included Latin Americans. We found that increasing the number of Latin Americans in the reference panel improved imputation quality in the four populations; however, there were differences between chromosomes 7 and X in some cohorts. Excluding Latin Americans from analysis resulted in worse imputation quality in every cohort, while differential effects were seen when excluding Europeans and Africans between and within cohorts and between chromosomes 7 and X. Finally, increasing IA-like admixture proportions in the reference panel increased imputation quality at different levels in different populations. The difference in results between populations and chromosomes suggests that existing and future reference panels containing Latin American individuals are likely to perform differently in different Latin American populations.

[Taking origins into account in medical reasoning in infectious and tropical diseases? A critical look]

Healthcare discriminations based on one's ethnic background is increasingly being studied in medicine. The scale of the Covid-19 pandemic has played an important role in bringing them to light. Data, although scarce, exist in France. These discriminations have an impact on the care pathway and contribute to the renunciation of care by the most affected populations. The issue of discrimination is particularly relevant in infectious diseases. Although the epidemiology of infectious diseases is unevenly distributed worldwide, erroneous social representations are prevalent and expose to a harmful prejudice against migrants with regard to infectious diseases. The transmissible nature of some infectious diseases reinforces their stigmatizing potential. In this context, it seems important to discuss the dimension to be given to social determinants, geographical origin, phenotype, and ethnicity in teaching and medical reasoning. The English-speaking world uses the concept of "race" in a structural way, whereas this "international standard" has not been applied in France until now. To improve the care of people from minority groups, it seems important to better document and teach a more nuanced clinical reasoning based on origin, without neglecting the importance of collecting and taking into account social determinants of health and environmental factors.

Distribution of pharmacogene allele and phenotype frequencies in Brazilian psychiatric patients

Purpose: This work was designed to identify the pharmacogenetic profile of Brazilian psychiatric patients receiving psychoactive drug treatment according to ethnicity. Methods: Based on the GnTech® database, this cross-sectional study analyzed data from self-reported sociodemographic and genetic results from the next-generation sequencing panel composed of 26 pharmacogenes from 359 psychotropic drug users. Results: Variant frequencies of multiple pharmacogenes presented differences between ethnicities (CYP3A5, CYP2D6, CYP1A2, CYP2B6, CYP3A4, UGT1A4, UGT2B15, ABCB1 rs1045642, ADRA2A rs1800544, COMT rs4680, GRIK4 rs1954787, GSK3B rs334558, GSK3B rs6438552, HTR1A rs6295, HTR2A rs7997012, HTR2C rs1414334, MTHFR rs1801131, OPRM1 rs1799971 and 5-HTTLPR), endorsing the necessity of individual-level analyses in drug treatment. Conclusion: A discussion of pharmacogenomic test implementation in psychiatric clinical practice is needed to improve treatment choices, especially in Brazil, a multiethnic country.

Traboulsi syndrome without features of Marfan syndrome caused by a novel homozygous ASPH variant associated with a heterozygous FBN1 variant

BACKGROUND

Traboulsi syndrome is a rare disease clinically characterized by facial dysmorphism, abnormal spontaneous filtering blebs, ectopia lentis (EL) and multiple anterior segment abnormalities.

MATERIAL AND METHODS

An 18-year-old female was referred to the Emergency Service of Hospital São Geraldo (HSG) claiming decreased right eye (RE) visual acuity associated with ocular pain that was noticed approximately 2 months earlier. She underwent a complete ophthalmic and physical examination including hands, ankle, wrist and chest X-ray, abdominal ultrasound, echocardiogram and genetic analysis (whole-exome sequencing).

RESULTS

The ophthalmic examination revealed a high myopia with spherical equivalent of - 9.50 D and best corrected visual acuity (BCVA) of 20/60 in RE and - 9.25 D with BCVA of 20/30 in the left eye (LE). Slit-lamp examination showed normal conjunctiva in both eyes (BE) and a superior-temporal cystic lesion in RE and nasal in LE; the flat anterior chamber in BE with the transparent crystalline lens touches the central corneal endothelium in the RE. Fundoscopy suggested glaucoma as the cup/disc ratio was 0.7, although the intraocular pressure (IOP) was 10 mmHg in BE without medication. Validation of data from whole exome demonstrated a novel splicing homozygous pathogenic variant (PV) (c.1765-1G>A) of the ASPH gene as well as a heterozygous variant of unknown significance (VUS) of the FBN1 gene (c.6832C>T).

CONCLUSION

We here report a novel splice-affecting homozygous pathogenic variant in the ASPH gene that was detected in a Brazilian patient with clinical features of Traboulsi syndrome.

Impact of tooth mineral tissues genes on dental caries: a birth-cohort study

OBJECTIVE

We aimed to investigate whether Single Nucleotide Polymorphisms present in the genes of tooth mineral tissues influence dental caries trajectory across the life course, and if there is an epistatic (gene-gene) interaction between these SNPs.

METHODS

A representative sample of all 5,914 births from the 1982 Pelotas birth cohort study was prospectively investigated. Dental caries trajectory across the life course was assessed at 15(n=888), 24(n=720), and 31 years old(n=539). Group-based trajectory modelling was used to identify distinct subgroups of individuals whose caries measurements followed a similar pattern over time. Genetic material was collected, and individuals were genotyped [rs4970957(TUFT1), rs1711437(MMP20), rs1784418(MMP20), rs2252070(MMP13), rs243847(MMP2), rs2303466(DLX3), rs11656951(DLX3), rs7501477(TIMP2), rs388286(BMP7), and rs5997096(TFIP11)]. Analyzes were performed for allele and genotype using logistic regression and generalized multifactor dimensionality reduction for epistatic interactions.

RESULTS

The analyses included 678 individuals, those with allele C (OR=0.74, CI95%[0.59-0.92]), genotype CC in the additive effect (OR=0.52, CI95%[0.31-0.89]), and the genotype TC/CC in dominant effect (OR=0.72, CI95%[0.53-0.98]) on the rs243847(MMP2) were associated with low caries trajectory. Individuals with the allele T (OR=0.79, CI95%[0.64-0.98]) and the genotype TC/CC in dominant effect (OR=0.66, CI95%[0.47-0.95]) on the rs5997096(TFIP11) were associated with low caries trajectory. Positive epistatic interactions were observed involving two (MMP2 and BMP7; p=0.006) and three (TUFT1, MMP2, and TFIP11; p<0.001) loci and high caries trajectory.

CONCLUSIONS

Some SNPs present in the genes of tooth mineral tissues were associated with caries trajectory and epistatic interactions increasing the network of SNPs involved in individual caries experience.

CLINICAL SIGNIFICANCE

Single nucleotide polymorphisms in the pathway of tooth mineral tissues genes may contribute significantly to the individual caries experience across the life course.

Genetic polymorphism (rs6587666) in FLG protects from eczema in admixed Brazilian children population with high African ancestry

Genetic variants in filaggrin (FLG) are key in eczema and are less common in Africans than in Europeans and Asians. Here we examined the association between FLG Single Nucleotide Polymorphisms (SNPs) and eczema in a population of admixed Brazilian children and whether African ancestry modifies this association. We included 1010 controls and 137 cases and ran logistic regressions between SNPs in FLG and eczema in the studied population and also stratified the analyses according to the degree of African ancestry. In addition, we tested the replication of the findings on an independent set of individuals, as well as, we verified the impact on FLG expression according to each SNP genotype. The T allele of SNP rs6587666 was negatively associated with eczema in additive model (OR: 0.66, 95% CI: 0.47-0.93, P: 0.017). Moreover, African ancestry modifies the association between rs6587666 and eczema. The effect of the T allele was higher among individuals with higher African ancestry and the association with eczema was lost in individuals with lower African ancestry. In our analyses the expression of FLG in skin was slightly downregulated by the presence of the T allele of rs6587666. In our population, the T allele of rs6587666 in FLG was associated with protection to eczema and the degree of African ancestry was able to modify the observed association.

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations

Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.

Impact of FOXP3 gene polymorphisms and gene-environment interactions in asthma and atopy in a Brazilian population

BACKGROUND

Polymorphisms in genes related to the activation and development of regulatory T cells (Tregs), such as FOXP3, may be associated with asthma and atopy development. Additionally, environmental factors such as exposure to infections can modify the effect of these associations. This study evaluated the impact of polymorphisms in the FOXP3 on the risk of asthma and atopy as also gene-environment interactions in these outcomes.

METHODS

This study included 1,246 children from the SCAALA program, between 4 and 11 years of age. DNA was extracted from peripheral blood and eight SNPs (rs2280883, rs11465476, rs11465472, rs2232368, rs3761549, rs3761548, rs2232365 and rs2294021) were genotyped using the 2.5 HumanOmni Beadchip from Illumina (San Diego, California, USA) or TaqMan qRT-PCR.

RESULTS

The rs2232368 (Allele T) was positively associated with asthma symptoms (OR=1.95, CI=1.04 to 3.66, p = 0.040) and skin prick test (SPT) reactivity to aeroallergens (OR=2.31, CI=1.16 to 4.59, p = 0.017). The rs3761549 (Allele T) was positively associated with SPT reactivity (OR=1.44, CI=1.03 to 2.02, p = 0.034). The rs2280883 (Allele C) was negatively associated with specific IgE to aeroallergens (OR=0.83, CI=0.70 to 0.99, p = 0.040). Furthermore, the rs2280883 played a protective role in the development of atopy only in individuals seropositive to Epstein-Barr virus (EBV) infection (OR=0.74, CI=0.60 to 0.92, p = 0.003 and OR=0.74; 95% CI=0.61-0.91, p = 0.007 for SPT and slgE respectively), but not in individuals without EBV infection.

CONCLUSION

Polymorphisms in the FOXP3 gene were associated with the risk of atopy and asthma development in our population. In addition, EBV infection had an effect modifier of the observed association for rs2280883 variant.

Variants in proinflammatory genes IL1RL1, IL1B and IRF4 are associated with overweight in a pediatric Brazilian population

BACKGROUND

Obesity is a chronic complex disease with great prevalence for children all over the world. Characterized for low-grade inflammation associated with several comorbidities such as resistance and type 2 diabetes mellitus (T2DM).

OBJECTIVES

To investigate whether genetic variants in IL10, IL1RL1, IL1B, IRF4, TNF, IL6, and IL33 genes are associated with being overweight in children.

METHODS

We performed the genotyping of 1004 children using Illumina 2.5 Human Omni bead chip, and association analysis on the genetic variants and the overweight through logistic regression adjusted for sex, age and components principal.

RESULTS

Of the seven genes analyzed, 16 SNVs significantly associated. Eleven variants in IL1RL1, two in IL1B and one in IRF4 genes increased overweight risk and two SNVs in IL1RL1 were associated with protection against overweight. The rs2287047-A was negatively associated (OR: 0.66, CI95%: 0.19-0.45) and had a reduced IL1RL1 expression in whole blood (p 0.033) in silico eQTL. The rs12203592-T, in IRF4, was positively associated with being overweight, and led to an increased gene expression in whole blood (p < 0.001) and adipose tissue (p < 0.001).

CONCLUSION

These results suggest that genetic variants in inflammatory genes may play an important role in the development of overweight in children.

Mutational spectrum of breast cancer susceptibility genes among women ascertained in a cancer risk clinic in Northeast Brazil

PURPOSE

There is a paucity of data on the spectrum and prevalence of pathogenic variants among women of African ancestry in the Northeast region of Brazil.

METHODS

We performed BROCA panel sequencing to identify inherited loss-of-function variants in breast cancer susceptibility genes among 292 Brazilian women referred to a single institution cancer risk assessment program.

RESULTS

The study included a convenient cohort of 173 women with invasive breast cancer (cases) and 119 women who were cancer-free at the time of ascertainment. The majority of the women self-reported as African-descended (67% for cases and 90.8% for unaffected volunteers). Thirty-seven pathogenic variants were found in 36 (20.8%) patients. While the spectrum of pathogenic variants was heterogeneous, the majority (70.3%) of the pathogenic variants were detected in high-risk genes BRCA1, BRCA2, PALB2, and TP53. Pathogenic variants were also found in the ATM, BARD1, BRIP1, FAM175A, FANCM, NBN, and SLX4 genes in 6.4% of the affected women. Four recurrent pathogenic variants were detected in 11 patients of African ancestry. Only one unaffected woman had a pathogenic variant in the RAD51C gene. Different risk assessment models examined performed well in predicting risk of carrying germline loss-of-function variants in BRCA1 and/or BRCA2 in breast cancer cases.

CONCLUSION

The high prevalence and heterogenous spectrum of pathogenic variants identified among self-reported African descendants in Northeast Brazil is consistent with studies in other African ancestry populations with a high burden of aggressive young onset breast cancer. It underscores the need to integrate comprehensive cancer risk assessment and genomic testing in the management of newly diagnosed Black women with breast cancer across the African Diaspora, enabling improved cancer control in admixed underserved and understudied populations.

Association between Polygenic Risk Scores for ADHD and Asthma: A Birth Cohort Investigation

OBJECTIVE

Shared genetic mechanisms have been hypothesized to explain the comorbidity between ADHD and asthma. To evaluate their genetic overlap, we relied on data from the 1982 Pelotas birth cohort to test the association between polygenic risk scores (PRSs) for ADHD (ADHD-PRSs) and asthma, and PRSs for asthma (asthma-PRSs) and ADHD.

METHOD

We analyzed data collected at birth, 2, 22, and 30 years from 3,574 individuals.

RESULTS

Subjects with ADHD had increased risk of having asthma (OR 1.92, 95% CI 1.01-3.66). The association was stronger for females. Our results showed no evidence of association between ADHD-PRSs and asthma or asthma-PRSs and ADHD. However, an exploratory analysis suggested that adult ADHD might be genetically associated with asthma.

CONCLUSION

Our results do not support a shared genetic background between both conditions. Findings should be viewed in light of important limitations, particularly the sample size and the self-reported asthma diagnosis. Studies in larger datasets are required to better explore the genetic overlap between adult ADHD and asthma.

Pharmacogenetics research in Brazil: a systematic review

Aim: Pharmacogenomics (PGx) is a rising scientific area in many countries, such as Brazil. Objectives: To identify biomarkers, therapeutic areas, probe drugs and regions/ethnicities most studied in the country in order to guide future studies. Materials & methods: Systematic review of 1060 studies (from 1968 to 2020) comprising 80 genes, six probe drugs and 3,819,233 individuals. Results: MTHFR and HLA-A/B were the most studied genes and metoprolol and dextromethorphan the most studied probe drugs. Oncology was the most studied therapeutic area considering PGx biomarkers. The country’s regions and ethnic groups were studied unevenly, with south/southeast and White people over-represented in respect to their demographic relevance, in detriment of the center-west/northeast/north and Black/mixed individuals. Conclusion: Many of the gaps and possible paths to be covered to reach even PGx data are pointed out by this review.

Epidemiology of interleukin-6: the 30-year follow-up of the 1982 Pelotas (Brazil) birth cohort study

BACKGROUND

Cardiovascular diseases are the main cause of death globally. Interleukin-6 (IL-6) is a biomarker of cardiovascular risk.

AIM

To investigate factors associated with IL-6 concentration in serum, from early life up to 30 years of age.

SUBJECTS AND METHODS

In the 2012-2013 follow-up, IL-6 was measured in 2809 participants of the 1982 Pelotas Birth Cohort (1369 males). Multivariable linear regressions, stratified by sex, were performed to evaluate the associations of African ancestry, family income and maternal education at birth, monthly income and education at 30 years, smoking status, harmful alcohol intake, physical activity, and body composition with IL-6, considering a conceptual hierarchical framework.

RESULTS

Males with low educational levels and current smokers had the highest mean IL-6. Among females, African ancestry and low monthly income were associated with the highest mean values for the outcome. Physical activity had an inverse association with IL-6 concentration among females. A direct relationship was observed between the measures of adiposity on IL-6, in both sexes.

CONCLUSION

Body composition was the main predictor for the outcome evaluated in males and females. Thus, the avoidance of overweight remains an important strategy for the prevention and control of cardiovascular risk and biomarkers associated with these diseases.

Evaluation of Polymorphisms in Toll-Like Receptor Genes as Biomarkers of the Response to Treatment of Erythema Nodosum Leprosum

Erythema nodosum leprosum (ENL) is an inflammatory complication caused by a dysregulated immune response to Mycobacterium leprae. Some Toll-like receptors (TLRs) have been identified as capable of recognizing antigens from M. leprae, triggering a wide antimicrobial and inflammatory response. Genetic polymorphisms in these receptors could influence in the appearance of ENL as well as in its treatment. Thus, the objective of this work was to evaluate the association of genetic variants of TLRs genes with the response to treatment of ENL with thalidomide and prednisone. A total of 162 ENL patients were recruited from different regions of Brazil and clinical information was collected from their medical records. Genomic DNA was isolated from blood and saliva samples and genetic variants in TLR1 (rs4833095), TLR2 (rs3804099), TLR4 (rs1927914), and TLR6 (rs5743810) genes were genotyped by TaqMan real-time PCR system. In order to evaluate the variants' association with the dose of the medications used during the treatment, we applied the Generalized Estimating Equations (GEE) analysis. In the present sample, 123 (75.9%) patients were men and 86 (53.1%) were in treatment for leprosy during the ENL episode. We found an association between polymorphisms in TLR1/rs4833095, TLR2/rs3804099, TLR4/rs1927914, and TLR6/rs5783810 with the dose variation of thalidomide in a time-dependent manner, i.e., the association with the genetic variant and the dose of the drug was different depending on the moment of the treatment evaluated. In addition, we identified that the association of polymorphisms in TLR1/rs4833095, TLR2/rs3804099, and TLR6/rs5783810 with the dose variation of prednisone also were time-dependent. Despite these associations, in all the interactions found, the influence of genetic variants on dose variation was not clinically relevant for therapeutic changes. The results obtained in this study show that TLRs polymorphism might play a role in the response to ENL treatment, however, in this context, they could not be considered as useful biomarkers in the clinical setting due small differences in medication doses. A larger sample size with patients with a more genetic profile is fundamental in order to estimate the association of genetic variants with the treatment of ENL and their clinical significance.

Impact of water fluoridation on dental caries decline across racial and income subgroups of Brazilian adolescents

OBJECTIVES

The aim of this study was to assess the impact of community water fluoridation (CWF) on differences in dental caries decline across racial and socioeconomic subgroups of Brazilian adolescents.

METHODS

Two nationwide Brazilian population-based oral health surveys were used (Brazilian Oral Health Survey 2003 and 2010). In total, 7,198 adolescents from 15 years to 19 years old living in 50 cities investigated in both surveys were included. The mean numbers of untreated decayed teeth (DT) according to racial (Whites vs. Browns/Blacks) and socioeconomic subgroups (at or above the minimum wage per capita vs. under) were analysed. Difference-in-differences negative binomial regressions were adjusted by schooling, age, and sex. Decayed, missing, and filled teeth and DT prevalence, calculated as a categorical variable, were used in sensitivity analyses.

RESULTS

The adjusted difference of reduction in DT was similar across socioeconomic subgroups (β=-0.05; 95% confidence interval [CI], -0.45 to 0.35) and favoured, but not to a significant degree, Whites (β=-0.34; 95% CI, -0.74 to 0.04) compared to Brown/Blacks in fluoridated areas. In non-fluoridated areas, significant differences were observed in the mean number of DT, favouring the higher socioeconomic subgroup (β=-0.26; 95% CI, -0.53 to -0.01) and Whites (β=-0.40; 95% CI, -0.69 to -0.11) in relation to their counterparts. The sensitivity analyses confirmed the findings.

CONCLUSIONS

The similar reduction in DT across income subgroups suggests that CWF has had a beneficial effect on tackling income inequalities in dental caries within a 7-year timeframe.

Epidemiology and costs of surgical treatment of developmental dysplasia of hip in the Brazilian Public Health System in a decade

Objective:

To describe and analyze the epidemiology and costs of surgical treatment of hip dysplasia in the Brazilian Public Health System.

Methods:

An ecological analytical study that evaluated a time series and the geographic distribution of surgical treatment of hip dysplasia in Brazil. Frequencies of cases, number of cases and associated factors were analyzed. Correlations, frequency maps and flow maps are presented and discussed.

Results:

During the study, 14,584 patients with dysplasia were admitted to hospitals according to Information Technology Department of the Public Health System. Patients underwent hospital treatment specific for dysplasia in 8,592 cases (at an average cost of R$ 2.225,50, total cost of R$ 19.124.086,25– updated values). In this group, mortality rate was 0.046% and mean hospitalization time was 4.41 days (standard deviation of 2,39 days). Age between 1 and 4 years (37.7%), female sex (64.5%) and white race (46%) were more frequent. Greater rates of specialists (R²=0.82; p<0.001), greater proportion of counties with high/very high human development index (R²=0.79; p<0.001), and higher per capita income (R²=0.68; p<0.001) correlated to greater rates of treatments undertaken per 1,000 live births (as per State of treatment). The factor most related to treatment rate per 1,000 live births (as per State of residence) was white race (R²=0.90; p<0.001). Southern states had higher treatment rates (as per State of residence, rate of 0.73/1,000), and Southeast states had greater absolute frequency of cases (46.7%) and greater flow of patients.

Conclusion:

The surgical treatment of hip dysplasia in Brazil occurs frequently, at relevant costs, and is distributed in a heterogenous and unequal fashion in the Public Health System. Southern states have a higher incidence of cases, and there is an association with racial and socioeconomic factors. There was no large variation in the incidence of cases over time.

Health ombudsman and racial inequities in Dental Specialities Centers performance in Brazil: A multilevel analysis

OBJECTIVE

This study aimed to verify racial differences in the performance of Dental Specialities Centers in Brazil, according to the presence of active health ombudsman on four primary outcomes: (1) access and dental appointment, (2) reception services, (3) bond and responsibility, and (4) social participation.

METHODS

Data came from the PMAQ-CEO national evaluation of public healthcare services, 2018-2019. The two main explanatory variables were the self-classified race at the individual level and the presence of the health ombudsman at the second level (level of services provision). Individual covariates included age, sex and schooling. Multilevel logistic regression was used to calculate the OR (Odds Ratios) in racial gaps according to the primary outcomes with individuals at the first level and public health services at the second level.

RESULTS

The analytical sample comprised of 8993 respondents. Brown people were less likely to report better Access (27%), good reception services (31%), bond and responsibility (30%) and social participation (22%) than Whites. Black people showed similar patterns. Dental Specialities Centers that use health ombudsman for planning have attenuated racial inequities in all analysed dimensions.

CONCLUSIONS

Dental Specialities Centers that use active health ombudsman for planning showed lower racial inequities in access, reception, bond and responsibility and social participation than those who did not use. Therefore, the health ombudsman should be implemented and used for planning better specialized dental services in Brazil.

Frailty Modifies the Association of Hypertension With Cognition in Older Adults: Evidence From the ELSI-Brazil

BACKGROUND

The relationship between hypertension and cognition in later life is controversial. We investigated whether the association of hypertension with cognition differs in older adults according to the frailty status using cross-sectional data from the Brazilian Longitudinal Study of Aging, a nationally representative sample of adults aged ≥50 years.

METHOD

Hypertension was defined by a medical diagnosis or measured blood pressure ≥140/90 mm Hg. Frailty status was assessed using the Cardiovascular Health Study criteria. We estimated the association of hypertension and systolic and diastolic blood pressure with global cognition, orientation, memory, and verbal fluency z-scores, using multiple linear regression models. We also investigated interactions between hypertension and frailty on cognitive performance and impairment.

RESULTS

We evaluated 8609 participants (mean age = 61.9 ± 9.6 years, 53% women). Participants with hypertension (59% of adults aged 50-64 and 77% of those aged ≥65 years) had poorer scores for global cognitive performance than those without hypertension, especially among adults aged 50-64 years (β = -0.09; 95% confidence interval = -0.15, -0.04; p = .001). However, frailty modified the associations of hypertension with cognitive performance and impairment in those aged ≥65 years (p-values for interaction = .01 and .02, respectively). Among nonfrail older adults, hypertension was associated with cognitive impairment. In contrast, among frail older adults, hypertension was related to better global and memory cognitive z-scores.

CONCLUSIONS

Hypertension was associated with worse cognitive performance. Among older adults, hypertension was related to cognitive impairment only in nonfrail participants. Frailty evaluation may help clinicians offer personalized hypertension management in older adults.

GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs

Several genome-wide association studies (GWAS) have been carried out with late-onset Alzheimer's disease (LOAD), mainly in European and Asian populations. Different polymorphisms were associated, but several of them without a functional explanation. GWAS are fundamental for identifying loci associated with diseases, although they often do not point to causal polymorphisms. In this sense, functional investigations are a fundamental tool for discovering causality, although the failure of this validation does not necessarily indicate a non-causality. Furthermore, the allele frequency of associated genetic variants may vary widely between populations, requiring replication of these associations in other ethnicities. In this sense, our study sought to replicate in 150 AD patients and 114 elderly controls from the South Brazilian population 18 single-nucleotide polymorphisms (SNPs) associated with AD in European GWAS, with further functional investigation using bioinformatic tools for the associated SNPs. Of the 18 SNPs investigated, only four were associated in our population: rs769449 (APOE), rs10838725 (CELF1), rs6733839, and rs744373 (BIN1-CYP27C1). We identified 54 variants in linkage disequilibrium (LD) with the associated SNPs, most of which act as expression or splicing quantitative trait loci (eQTLs/sQTLs) in genes previously associated with AD or with a possible functional role in the disease, such as CELF1, MADD, MYBPC3, NR1H3, NUP160, SPI1, and TOMM40. Interestingly, eight of these variants are located within long non-coding RNA (lncRNA) genes that have not been previously investigated regarding AD. Some of these polymorphisms can result in changes in these lncRNAs' secondary structures, leading to either loss or gain of microRNA (miRNA)-binding sites, deregulating downstream pathways. Our pioneering work not only replicated LOAD association with polymorphisms not yet associated in the Brazilian population but also identified six possible lncRNAs that may interfere in LOAD development. The results lead us to emphasize the importance of functional exploration of associations found in large-scale association studies in different populations to base personalized and inclusive medicine in the future.

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.

Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

BACKGROUND

Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%).

RESULTS

We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions.

CONCLUSIONS

Our data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.

Characteristics, outcomes and risk factors for mortality of 522 167 patients hospitalised with COVID-19 in Brazil: a retrospective cohort study

OBJECTIVE

To provide a comprehensive description of demographic, clinical and radiographic characteristics; treatment and case outcomes; and risk factors associated with in-hospital death of patients hospitalised with COVID-19 in Brazil.

DESIGN

Retrospective cohort study of hospitalised patients diagnosed with COVID-19.

SETTING

Data from all hospitals across Brazil.

PARTICIPANTS

522 167 hospitalised patients in Brazil by 14 December 2020 with severe acute respiratory illness, and a confirmed diagnosis for COVID-19.

PRIMARY AND SECONDARY OUTCOME MEASURES

Prevalence of symptoms and comorbidities was compared by clinical outcomes and intensive care unit (ICU) admission status. Survival was assessed using Kaplan Meier survival estimates. Risk factors associated with in-hospital death were evaluated with multivariable Cox proportional hazards regression.

RESULTS

Of the 522 167 patients included in this study, 56.7% were discharged, 0.002% died of other causes, 30.7% died of causes associated with COVID-19 and 10.2% remained hospitalised. The median age of patients was 61 years (IQR, 47-73), and of non-survivors 71 years (IQR, 60-80); 292 570 patients (56.0%) were men. At least one comorbidity was present in 64.5% of patients and in 76.8% of non-survivors. From illness onset, the median times to hospital and ICU admission were 6 days (IQR, 3-9) and 7 days (IQR, 3-10), respectively; 15 days (IQR, 9-24) to death and 15 days (IQR, 11-20) to hospital discharge. Risk factors for in-hospital death included old age, Black/Brown ethnoracial self-classification, ICU admission, being male, living in the North and Northeast regions and various comorbidities. Age had the highest HRs of 5.51 (95% CI: 4.91 to 6.18) for patients≥80, compared with those ≤20.

CONCLUSIONS

Characteristics of patients and risk factors for in-hospital mortality highlight inequities of COVID-19 outcomes in Brazil. As the pandemic continues to unfold, targeted policies that address those inequities are needed to mitigate the unequal burden of COVID-19.

Admixture/fine-mapping in Brazilians reveals a West African associated potential regulatory variant (rs114066381) with a strong female-specific effect on body mass and fat mass indexes

BACKGROUND/OBJECTIVES

Admixed populations are a resource to study the global genetic architecture of complex phenotypes, which is critical, considering that non-European populations are severely underrepresented in genomic studies. Here, we study the genetic architecture of BMI in children, young adults, and elderly individuals from the admixed population of Brazil.

SUBJECTS/METHODS

Leveraging admixture in Brazilians, whose chromosomes are mosaics of fragments of Native American, European, and African origins, we used genome-wide data to perform admixture mapping/fine-mapping of body mass index (BMI) in three Brazilian population-based cohorts from Northeast (Salvador), Southeast (Bambuí), and South (Pelotas).

RESULTS

We found significant associations with African-associated alleles in children from Salvador (PALD1 and ZMIZ1 genes), and in young adults from Pelotas (NOD2 and MTUS2 genes). More importantly, in Pelotas, rs114066381, mapped in a potential regulatory region, is significantly associated only in females (p = 2.76e-06). This variant is rare in Europeans but with frequencies of ~3% in West Africa and has a strong female-specific effect (95% CI: 2.32-5.65 kg/m² per each A allele). We confirmed this sex-specific association and replicated its strong effect for an adjusted fat mass index in the same Pelotas cohort, and for BMI in another Brazilian cohort from São Paulo (Southeast Brazil). A meta-analysis confirmed the significant association. Remarkably, we observed that while the frequency of rs114066381-A allele ranges from 0.8 to 2.1% in the studied populations, it attains ~9% among women with morbid obesity from Pelotas, São Paulo, and Bambuí. The effect size of rs114066381 is at least five times higher than the FTO SNPs rs9939609 and rs1558902, already emblematic for their high effects.

CONCLUSIONS

We identified six candidate SNPs associated with BMI. rs114066381 stands out for its high effect that was replicated and its high frequency in women with morbid obesity. We demonstrate how admixed populations are a source of new relevant phenotype-associated genetic variants.

Characterization of the Vaginal Microbiome in Women of Reproductive Age From 5 Regions in Brazil

BACKGROUND

Composition of the vaginal microbiome is strongly related to a woman's reproductive health and risk of sexually transmitted infections. Ethnoracial, behavioral, and environmental factors can influence microbiome. The Brazilian population is unique in terms of miscegenation of ethnic groups and behavioral characteristics across different regions. We aimed to characterize the vaginal microbiome of women from 5 geographical regions of Brazil.

METHODS

We sequenced V3-V4 regions of 16S rRNA gene in vaginal samples of 609 reproductive-aged women. We performed logistic regression analyses to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between sociodemographic and behavioral factors with Lactobacillus-depleted microbiome (community state type [CST] IV).

RESULTS

Vaginal samples were grouped into 5 CST: CST I (L. crispatus predominant, 30.5%), CST II (L. gasseri predominant, 4.4%), CST III (Lactobacillus iners predominant, 36.5%), CST IV (Lactobacillus-depleted, 27.4%), and CST V (L. jensenii predominant, 1.2%). Several factors were independently associated with CST IV, such as smoking (OR, 1.80; 95% CI, 1.02-3.18), number of partners (OR, 2.11; 95% CI, 1.20-3.70), and vaginal douching (OR, 2.24; 95% CI, 1.34-3.74). A protective effect was observed for milk/dairy intake (OR, 0.47; 95% CI, 0.27-0.82) and sitz bathing (OR, 0.43; 95% CI, 0.19-0.98).

CONCLUSIONS

Nearly two thirds of Brazilian women may be at an increased risk for adverse outcomes associated with a vaginal microbiota characterized by the depletion of Lactobacillus or dominance by L. iners, whose protective role has been widely questioned. Several factors related to sexual behavior and intimate hygiene were associated with CST IV.

Genetic variability in COVID-19-related genes in the Brazilian population

SARS-CoV-2 utilizes the angiotensin-converting enzyme 2 (ACE2) receptor and transmembrane serine protease (TMPRSS2) to infect human lung cells. Previous studies have suggested that different host ACE2 and TMPRSS2 genetic backgrounds might contribute to differences in the rate of SARS-CoV-2 infection or COVID-19 severity. Recent studies have also shown that variants in 15 genes related to type I interferon immunity to influenza virus might predispose patients toward life-threatening COVID-19 pneumonia. Other genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, IL6, CTSL, ABO, and FURIN) and HLA alleles have also been implicated in the response to infection with SARS-CoV-2. Currently, Brazil has recorded the third-highest number of COVID-19 cases worldwide. We aimed to investigate the genetic variation present in COVID-19-related genes in the Brazilian population. We analyzed 27 candidate genes and HLA alleles in 954 admixed Brazilian exomes. We used the information available in two public databases (http://www.bipmed.org and http://abraom.ib.usp.br/) and additional exomes from individuals born in southeast Brazil, the region of the country with the highest number of COVID-19 patients. Variant allele frequencies were compared with the 1000 Genomes Project phase 3 (1KGP) and gnomAD databases. We detected 395 nonsynonymous variants; of these, 325 were also found in the 1KGP and/or gnomAD. Six of these variants were previously reported to influence the rate of infection or clinical prognosis of COVID-19. The remaining 70 variants were identified exclusively in the Brazilian sample, with a mean allele frequency of 0.0025. In silico analysis revealed that seven of these variants are predicted to affect protein function. Furthermore, we identified HLA alleles previously associated with the COVID-19 response at loci DQB1 and DRB1. Our results showed genetic variability common to other populations and rare and ultrarare variants exclusively found in the Brazilian population. These findings might lead to differences in the rate of infection or response to infection by SARS-CoV-2 and should be further investigated in patients with this disease.

Genetic variants in the Brazilian population do not appear to explain the relatively high overall rates of COVID-19 cases compared to other countries, but could be relevant for risk assessment at the individual level. Iscia Lopes-Cendes of the University of Campinas and colleagues in Brazil examined gene sequences for variations in 27 genes reported to influence COVID-19 infection in Brazilians of mixed heritage and of people born in the southeast where case numbers are high. These studies included the ACE2 gene that codes for a receptor allowing SARS-CoV-2 to enter host cells. Genetic variants were also identified in two international genome databases. Seventy variants were unique to Brazilians, but computer modeling predicted only seven variants that could affect protein function. The team also looked for and found variants that could affect individual immunity to COVID-19. Similar genetic studies could help identify at-risk individuals and therapeutic targets.

Exploring a Region on Chromosome 8p23.1 Displaying Positive Selection Signals in Brazilian Admixed Populations: Additional Insights Into Predisposition to Obesity and Related Disorders

We recently reported a deviation of local ancestry on the chromosome (ch) 8p23.1, which led to positive selection signals in a Brazilian population sample. The deviation suggested that the genetic variability of candidate genes located on ch 8p23.1 may have been evolutionarily advantageous in the early stages of the admixture process. In the present work, we aim to extend the previous work by studying additional Brazilian admixed individuals and examining DNA sequencing data from the ch 8p23.1 candidate region. Thus, we inferred the local ancestry of 125 exomes from individuals born in five towns within the Southeast region of Brazil (São Paulo, Campinas, Barretos, and Ribeirão Preto located in the state of São Paulo and Belo Horizonte, the capital of the state of Minas Gerais), and compared to data from two public Brazilian reference genomic databases, BIPMed and ABraOM, and with information from the 1000 Genomes Project phase 3 and gnomAD databases. Our results revealed that ancestry is similar among individuals born in the five Brazilian towns assessed; however, an increased proportion of sub-Saharan African ancestry was observed in individuals from Belo Horizonte. In addition, individuals from the five towns considered, as well as those from the ABRAOM dataset, had the same overrepresentation of Native-American ancestry on the ch 8p23.1 locus that was previously reported for the BIPMed reference sample. Sequencing analysis of ch 8p23.1 revealed the presence of 442 non-synonymous variants, including frameshift, inframe deletion, start loss, stop gain, stop loss, and splicing site variants, which occurred in 24 genes. Among these genes, 13 were associated with obesity, type II diabetes, lipid levels, and waist circumference (PRAG1, MFHAS1, PPP1R3B, TNKS, MSRA, PRSS55, RP1L1, PINX1, MTMR9, FAM167A, BLK, GATA4, and CTSB). These results strengthen the hypothesis that a set of variants located on ch 8p23.1 that result from positive selection during early admixture events may influence obesity-related disease predisposition in admixed individuals of the Brazilian population. Furthermore, we present evidence that the exploration of local ancestry deviation in admixed individuals may provide information with the potential to be translated into health care improvement.

Genomic ancestry and metabolic syndrome in individuals with type 1 diabetes from an admixed population: a multicentre, cross-sectional study in Brazil

AIMS

To evaluate the relationship between self-reported colour-race, genomic ancestry, and metabolic syndrome in an admixed Brazilian population with type 1 diabetes.

METHODS

We included 1640 participants with type 1 diabetes. The proportions of European, African and Amerindian genomic ancestries were determined by 46 ancestry informative markers of insertion deletion. Two different sets of analyses were performed to determine whether self-reported colour-race and genomic ancestry were predictors of metabolic syndrome.

RESULTS

Metabolic syndrome was identified in 29.8% of participants. In the first model, the factors associated with metabolic syndrome were: female gender (odds ratio 1.95, P < 0.001); diabetes duration (odds ratio 1.04, P < 0.001); family history of type 2 diabetes (odds ratio 1.36, P = 0.019); and acanthosis nigricans (odds ratio 5.93, P < 0.001). Colour-race was not a predictive factor for metabolic syndrome. In the second model, colour-race was replaced by European genomic ancestry. The associated factors were: female gender (odds ratio 1.95, P < 0.001); diabetes duration (odds ratio 1.04, P < 0.001); family history of type 2 diabetes (odds ratio 1.39, P = 0.011); and acanthosis nigricans (odds ratio 6.12, P < 0.001). Physical exercise (≥3 times a week) was a protective factor (odds ratio 0.77, P = 0.041), and European genomic ancestry was not associated with metabolic syndrome but showed an odds ratio of 1.77 (P = 0.05).

CONCLUSIONS

Although a higher level of European genomic ancestry was observed among participants with metabolic syndrome in the univariate analysis, this association did not persist after multivariable adjustments. Further prospective studies in other highly admixed populations remain necessary to better evaluate whether the European ancestral component modulates the development of metabolic syndrome in type 1 diabetes.

CYP3A5 and PPARA genetic variants are associated with low trough concentration to dose ratio of tacrolimus in kidney transplant recipients

PURPOSE

Genetic polymorphisms have been associated with variation in the metabolism of tacrolimus (TAC) in kidney transplant patients. This study is aimed at assessing the impact of allelic variants of CYP3A5 and PPARA genes on the pharmacokinetics (PK) of TAC in Brazilian kidney transplant recipients in the first-year post-transplant.

METHODS

A total of 127 patients were included for genetic evaluation. Genomic DNA was isolated from peripheral blood and real-time PCR was used to analyze the main polymorphisms described for the genes CYP3A5 (rs776746; C > G) and PPARA (rs4823613; A > G and rs4253728; G > A).

RESULTS

CYP3A5 expressors showed a lower Co/dose ratio than non-expressors, with the median values of this parameter <1.01 ng/mL/mg in the first group at all evaluated times. Additionally, PPARA variant homozygotes had a lower Co/D ratio than wild allele carriers in the 12-month post-transplant period, with a median value of 0.65 ng/mL/mg. In the CYP3A5 expressers, the presence of the variant homozygous genotype PPARA was associated with a lower value of Co/D compared with the other genotypic groups at month 12.

CONCLUSION

In the population under study, polymorphisms on CYP3A5 and PPARA were identified as determining and independent factors associated with the reduction of Co/D of TAC. Thus, the genotyping of these genetic variants may be a useful tool for the individualized prescription of TAC in kidney transplant patients.

LRRK2 Gene Variants Associated With a Higher Risk for Alcohol Dependence in Multiethnic Populations

Background: Genetics influence the vulnerability to alcohol use disorders, and among the implicated genes, three previous studies have provided evidences for the involvement of LRRK2 in alcohol dependence (AD). LRRK2 expression is broadly dysregulated in postmortem brain from AD humans, as well as in the brain of mice with alcohol dependent-like behaviors and in a zebrafish model of alcohol preference. The aim of the present study was to evaluate the association of variants in the LRRK2 gene with AD in multiethnic populations from South and North America. Methods: Alcohol-screening questionnaires [such as CAGE and Alcohol Use Disorders Identification Test (AUDIT)] were used to determine individual risk of AD. Multivariate logistic regression analyses were done in three independent populations (898 individuals from Bambuí, Brazil; 3,015 individuals from Pelotas, Brazil; and 1,316 from the United States). Linkage disequilibrium and conditional analyses, as well as in silico functional analyses, were also conducted. Results: Four LRRK2 variants were significantly associated with AD in our discovery cohort (Bambuí): rs4768231, rs4767971, rs7307310, and rs1465527. Two of these variants (rs4768231 and rs4767971) were replicated in both Pelotas and US cohorts. The consistent association signal (at the LRRK2 locus) found in populations with different genetic backgrounds reinforces the relevance of our findings. Conclusion: Taken together, these results support the notion that genetic variants in the LRRK2 locus are risk factors for AD in humans.

Anthropological genetics perspectives on the transatlantic slave trade

During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.

A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373

Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (R_ST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.

How Ancestry Influences the Chances of Finding Unrelated Donors: An Investigation in Admixed Brazilians

A match of HLA loci between patients and donors is critical for successful hematopoietic stem cell transplantation. However, the extreme polymorphism of HLA loci - an outcome of millions of years of natural selection - reduces the chances that two individuals will carry identical combinations of multilocus HLA genotypes. Further, HLA variability is not homogeneously distributed throughout the world: African populations on average have greater variability than non-Africans, reducing the chances that two unrelated African individuals are HLA identical. Here, we explore how self-identification (often equated with "ethnicity" or "race") and genetic ancestry are related to the chances of finding HLA compatible donors in a large sample from Brazil, a highly admixed country. We query REDOME, Brazil's Bone Marrow Registry, and investigate how different criteria for identifying ancestry influence the chances of finding a match. We find that individuals who self-identify as "Black" and "Mixed" on average have lower chances of finding matches than those who self-identify as "White" (up to 57% reduction). We next show that an individual's African genetic ancestry, estimated using molecular markers and quantified as the proportion of an individual's genome that traces its ancestry to Africa, is strongly associated with reduced chances of finding a match (up to 60% reduction). Finally, we document that the strongest reduction in chances of finding a match is associated with having an MHC region of exclusively African ancestry (up to 75% reduction). We apply our findings to a specific condition, for which there is a clinical indication for transplantation: sickle-cell disease. We show that the increased African ancestry in patients with this disease leads to reduced chances of finding a match, when compared to the remainder of the sample, without the condition. Our results underscore the influence of ancestry on chances of finding compatible HLA matches, and indicate that efforts guided to increasing the African component of registries are necessary.

Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries

In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.

New variants in NLRP3 inflammasome genes increase risk for asthma and Blomia tropicalis-induced allergy in a Brazilian population

Atopic asthma is a chronic lung disease of lower airways caused mainly due to action of T-helper (Th) 2 type cytokines, eosinophilic inflammation, mucus hypersecretion and airway remodelling. Interleukin (IL)-33 increases type 2 immunity polarization in airway playing critical role in eosinophilic asthma. On the other hand, NLRP3 inflammasome activation results in the release of caspase-1 (Casp-1) which, in its turn, promotes IL-33 inactivation. Recent studies have shown associations between NLRP3 variants and inflammatory diseases. However, no study with genes in NLRP3 inflammassome route has been conducted so far with asthma and atopy in any population to date. Blood samples were collected from 1246 asthmatic and non-asthmatic children. Associations were tested for single nucleotide polymorphism (SNP)s in NLRP3 and CASP1 with asthma and markers of atopy and in cultures stimulated with Blomia tropicalis (Bt) mite crude extract. The T allele of rs4925648 (NLRP3) was associated with increased asthma risk (OR 1.50, P = 0.005). In addition, the T allele of rs12130711 polymorphism, whithin the same gene, acted as a protector factor for asthma (OR 0.78, P = 0.038). On the other hand, the C allele of rs4378247 NLRP3 variant was associated with lower levels of IL-13 production when peripheral blood cells were stimulated with Bt (OR 0.39, P = 4E-04). In addition, the greater the number of risk alleles in IL33/NLRP3/CASP1 route the greater was the risk for asthma. The T allele of rs7925706 CASP1 variant was also associated with increased risk for asthma (OR 1.47, P = 0.008). In addition, this same allele increased the eosinophil counts in blood (mm3) in asthmatic individuals compared with non-asthmatic (P = 0.0004). These results suggest that NLRP3 and CASP1 polymorphisms may be associated with susceptibility for asthma and markers of atopy in our population.

Nationwide vitamin D status in older Brazilian adults and its determinants: The Brazilian Longitudinal Study of Aging (ELSI)

Little is known about vitamin D status in older adults in South America, where exposures to ultra-violet radiation are high. We examined the distribution of serum 25-hydroxyvitamin D (25OHD) concentration and its determinants in a nationally representative sample of Brazilians aged 50 years and older. Explanatory variables included environment and individuals’ characteristics from the ELSI baseline survey (2015–16). Among the 2,264 participants (mean age = 62.6 years), the geometric mean of 25OHD concentration was 66.8 nmol/L. The prevalence of vitamin D deficiency (< 30 nmol/L) and insufficiency (< 50 nmol/L) were 1.7% (95% CI 1.0, 2.8) and 16% (95% CI 12, 20), respectively. Mean concentrations were lower in those geographical regions situated at lower latitudes. Those at the oldest age, women, self-classified as Black and Brown, living in urban areas and current smokers were more likely to have vitamin D insufficiency, independent of each other and other relevant factors. In contrast, individuals who eat fish regularly were considerably less likely to present lower concentration. Based on these findings it is possible to estimate that about 875,000 older Brazilians have vitamin D deficiency and 7.5 million its insufficiency.

No Race-Ethnicity Adjustment in CKD-EPI Equations Is Required for Estimating Glomerular Filtration Rate in the Brazilian Population

BACKGROUND

Glomerular filtration rate (GFR) is usually estimated from equations using serum creatinine (sCr), with adjustment for gender, age, and race (black or nonblack). The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) is the preferred equation for adults, but it was validated for the United States population. We intended to evaluate if the race-ethnicity adjustment proposed for the sCr-based CKD-EPI equations is appropriate for the Brazilian population.

METHODS

CKD outpatients had blood samples collected for determination of sCr and serum cystatin C (sCys) levels. GFR was measured (mGFR) by plasma clearance of 51Cr-EDTA and used as the reference. We compared values of mGFR and estimated GFR (eGFR) by CKD-EPI equations based on sCr (eGFRCr) and on the combination of sCr and sCys (eGFRCr-Cys). For African Brazilian patients, eGFR was calculated either without or with race adjustment. Accuracy was considered acceptable if the difference between the values of eGFR and mGFR was ≤30% (P30).

RESULTS

100 patients were enrolled (58 ± 14 years, 46% male, 39% white and 61% African Brazilian). Mean mGFR was 46.7 ± 29.2 ml/min/1.73 m2. Mean eGFRCr and eGFRCr-Cys without race adjustment were 47.8 ± 30.1 ml/min/1.73 m2 and 46.4 ± 30.3 ml/min/1.73 m2, respectively. The corresponding P30 accuracy values were 79.0% and 83.0%. In the African Brazilian subgroup, values for mean mGFR and eGFRCr either without or with race adjustment were 49.8 ± 32.2 ml/min/1.73 m2, 50.4 ± 32.7 ml/min/1.73 m2, and 58.4 ± 37.9 ml/min/1.73 m2 (P < 0.001 vs. mGFR), respectively. P30 accuracy values for eGFRCr either without or with race adjustment were 75.4% and 67.2%, respectively.

CONCLUSIONS

The use of CKD-EPI equations without race-ethnicity adjustment seems more appropriate for the Brazilian population.

The role of CACNA1C gene and childhood trauma interaction on bipolar disorder

Studies on gene x environment interaction (GxE) have provided vital information for uncovering the origins of complex diseases. When considering the etiology of bipolar disorder (BD), the role of such interactions is unknown. Here, we tested whether trauma during childhood could modify the effect of two polymorphisms in the CACNA1C gene (rs1006737 and rs4765913) in terms of susceptibility to BD. The study enrolled 878 Caucasian young adults in a cross-sectional population-based survey. BD diagnosis was performed using a clinical interview MINI 5.0, and trauma was assessed with the childhood trauma questionnaire (CTQ). Binary logistic regression models were employed to test the main effects of polymorphisms, haplotypes, and GxE interactions using sex as a confounder. We did not observe an association between the polymorphisms and diagnosis of BD. However, we noted that childhood trauma modified the effect of the rs4765913 polymorphism (p = .018) and the AA haplotype (rs1006737 - rs4765913) (p = .018) on BD susceptibility. A allele carriers of the rs4765913 polymorphism or the AA haplotype exposed to childhood trauma are more likely to develop BD compared to the individuals without a genetic risk. Thus, this study showed that the risk of developing BD in individuals exposed to childhood trauma was influenced by the individual's genetic background, varying according to the CACNA1C genotypes.

Brazilian cohort and genes encoding for drug-metabolizing enzymes and drug transporters

Background & aim: Genetic variability in drug absorption, distribution, metabolism and excretion (ADME) genes contributes to the high heterogeneity of drug responses. The present study investigated polymorphisms of ADME genes frequencies and compared the findings with populations from other continents, available in the 1000 Genome Project (1 KGP) and the Exome Aggregation Consortium (ExAC) databases. Methodology & results: We conducted a study of 100 patients in Brazil and a total of 2003 SNPs were evaluated by targeted next-generation sequencing in 148 genes, including Phase I enzymes (n = 50), Phase II enzymes (n = 38) and drug transporters (n = 60). Overall, the distribution of minor allele frequency (MAF) suggests that the distribution of 2003 SNPs is similar between Brazilian cohort, 1 KGP and ExAC; however, we found moderate SNP allele-frequency divergence between Brazilian cohort and both 1000 KGP and ExAC. These differences were observed in several relevant genes including CYP3A4, NAT2 and SLCO1B1. Conclusion: We concluded that the Brazilian population needs clinical assessment of drug treatment based on individual genotype rather than ethnicity.

Genetic variability of blood groups in southern Brazil

We evaluated genetic variability among the blood groups Kell (c.578C > T and c.1790T > C), Kidd (c.838A > G), Duffy (c.125A > G, c.265C > T and c.1-67T > C), Diego (c.2561C > T), MNS (c.143T > C) and Rh (c.676G > C) in Rio Grande do Sul in southern Brazil. Genetic profiling from 382 volunteer blood donors was performed through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a real-time PCR system. The sample was divided into two groups: Euro-Brazilian and Afro-Brazilian. A comparison with studies from other regions of Brazil and the 1000 Genomes Database showed significant differences for almost all polymorphisms evaluated in our population. Population differentiation between the Euro- and Afro-Brazilian groups was low (FST value 0.055). However, when each locus was evaluated individually, KEL*06 and FY*02N.01 allele frequencies were significantly higher in the Afro-Brazilian group than in the Euro-Brazilian group. Ethnic classification that uses phenotypic criteria to find blood units with rare antigens may be important when there is a need to detect blood units with an absence of Duffy antigens. There is also a greater probability of finding donors in the Afro-Brazilian group. Taken together, the data indicate strong European and African contributions to the gene pool, with intense admixture.

Role of Genetic Ancestry in 1,002 Brazilian Colorectal Cancer Patients From Barretos Cancer Hospital

Background: Colorectal cancer (CRC) is the third most frequent and the second deadliest cancer worldwide. The ethnic structure of the population has been gaining prominence as a cancer player. The purpose of this study was to determine the genetic ancestry of Brazilian CRC patients. Moreover, we intended to interrogate its impact on patients' clinicopathological features.

Methods: Retrospective observational cohort study with 1,002 patients with CRC admitted from 2000 to 2014 at Barretos Cancer Hospital. Following tumor DNA isolation, genetic ancestry was assessed using a specific panel of 46 ancestry informative markers. Survival rates were obtained by the Kaplan–Meier method, and the log-rank test was used to compare the survival curves. Multivariable Cox proportional regression models were used to estimate hazard ratios (HRs).

Results: We observed considerable admixture in the genetic composition, with the following average proportions: European 74.2%, African 12.7%, Asian 6.5%, and Amerindian 6.6%. The multivariate analysis for cancer-specific survival showed that clinical stage, lymphovascular invasion, and the presence of recurrence were associated with an increased relative risk of death from cancer (p < 0.05). High African proportion was associated with younger age at diagnosis, while high Amerindian proportion was associated with the mucinous histological subtype.

Conclusions: This represents the larger assessment of genetic ancestry in a population of Brazilian patients with CRC. Brazilian CRC patients exhibited similar clinicopathological features as described in Western countries.

Impact: Genetic ancestry components corroborated the significant admixture, and importantly, patients with high African proportion develop cancer at a younger age.