A systematic literature review on the European, African and Amerindian genetic ancestry components on Brazilian health outcomes

A Large Multicenter Brazilian Case-Control Study Exploring Genetic Variations in Interferon Regulatory Factor 6 and the Risk of Nonsyndromic Cleft Lip With or Without Cleft Palate

Nonsyndromic cleft lip with or without cleft palate (NSCL ± P) is strongly associated with both environmental and genetic risk factors, but its genetic underpinnings remain partially known. While variants in interferon regulatory factor 6 (IRF6) are linked to NSCL ± P risk in populations from Asia and Europe, studies on the highly admixed Brazilian population are scarce and have produced ambiguous results. This study aimed to investigate the contribution of IRF6 variants to the risk of NSCL ± P. Five tag-single nucleotide polymorphisms (rs599021, rs2073485, rs2235375, rs7552506, and rs642961) were analyzed in a large multicenter cohort composed of 1006 patients with NSCL ± P and 942 healthy controls. Statistical analyses involved multiple logistic regression tests consideration the tri-hybrid genetic origin of the Brazilian population, under a Bonferroni p value correcting for multiple comparisons. The A allele (OR: 1.43, 95% CI: 1.22-1.67, p < 0.0001) and AA genotype (OR: 2.04, 95% CI: 1.46-2.86, p < 0.0001) frequencies of rs642961 were significantly associated with NSCL ± P risk. Stratified analyses indicated that the variant is associated with susceptibility to both nonsyndromic cleft lip only (NSCLO) and nonsyndromic cleft lip and palate (NSCLP). However, the association with NSCLO was primarily observed in patients with high African ancestry, whereas the association with NSCLP was predominantly seen in patients with high European ancestry. No significant associations were found for the other investigated variants. Our results support the notion that the IRF6 rs642961 variant represents a marker of susceptibility to NSCL ± P in the Brazilian population, and that genetic ancestry composition plays a central role in the association with the cleft type.

Common, Intermediate and Well-Documented HLA Alleles in the Brazilian Population: An Analysis of the Brazilian Bone Marrow Donor Registry (REDOME)

This study investigates the HLA allele diversity in Brazil, a reflection of the country's unique history of population admixture. The international comparison of findings emphasises the importance of incorporating underrepresented populations into global HLA databases. We present a comprehensive analysis of HLA alleles within the Brazilian population, utilising high-resolution sequencing data from 298,000 unrelated haematopoietic stem cell volunteer donors registered with the Brazilian Bone Marrow Donor Registry (REDOME). Our research encompasses donors from all regions of Brazil, identifying HLA alleles that are catalogued as common, intermediate or well-documented (CIWD Version 3.0). We evaluated the alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1. At a two-field resolution, we identified 1969 alleles: 418 were classified as common, 358 as intermediate and 1193 as non-CIWD in Brazil. Notably, we report HLA alleles that, while not classified as common or intermediate in the CIWD 3.0 catalogue, are prevalent within the Brazilian population. A detailed list of alleles from the registry, presented at a two-field resolution and supplemented with grouped ARD levels, including three- or four-field resolution when available, serves as an essential reference for HLA typing frequencies specific to the Brazilian population.

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.

Evidence Mapping and Quality Analysis of Systematic Reviews on Various Aspects Related to Cleft Lip and Palate

BACKGROUND

Management of cleft lip and palate is interdisciplinary. An evidence-mapping approach was envisaged to highlight the existing gaps in this field, using only the highest level of evidence.

OBJECTIVES

To conduct evidence mapping and quality analysis of systematic reviews and meta-analyses related to any aspect of cleft lip and palate.

SEARCH METHODS

The cleft lip and palate field was divided into 9 domains and 50 subdomains and a method of categorization of systematic reviews was established. A comprehensive search strategy was carried out in seven databases along with the search of gray literature and references of included articles.

SELECTION CRITERIA

Systematic reviews related to any aspect of cleft lip and palate, conducted by a minimum of two reviewers, with a comprehensive search strategy and adequate quality analysis were included.

DATA COLLECTION AND ANALYSIS

A self-designed, pre-piloted data-extraction sheet was used to collect information that was analyzed through an expert group discussion. Quality analysis was performed using ROBIS-I, AMSTAR 2, and the PRISMA checklist.

RESULTS

A total of 144 systematic reviews published between 2008 and 2022 were included. The largest number of these could be categorized in the therapeutic domain (n = 58). A total of 27% of the studies were categorized as inconclusive, 40% as partially conclusive, and 33% as conclusive. As per ROBIS-I, 77% of reviews had high risk of bias while 58% were graded as critically low in quality as per AMSTAR 2. The majority of systematic reviews showed low reporting errors.

CONCLUSIONS

The majority of systematic reviews related to cleft lip and palate relate to therapeutic and prognostic domains and show high risk of bias and critically low quality regardless of the source journal. The results of this paper might serve as a starting point encouraging authors to carry out high-quality research where evidence is lacking.

REGISTRATION

A multidisciplinary expert-group formulated an a priori protocol, registered in Open Science Framework (DOI 10.17605/OSF.IO/NQDV2).

TP53 and p21 (CDKN1A) polymorphisms and the risk of systemic lupus erythematosus

BACKGROUND

The p53 and p21 proteins are important regulators of cell cycle and apoptosis and may contribute to autoimmune diseases, such as systemic lupus erythematosus (SLE). As genetic polymorphisms may cause changes in protein levels and functions, we investigated associations of TP53 and p21 (CDKN1A) polymorphisms (p53 72 G > C-rs1042522; p53 PIN3-rs17878362; p21 31 C > A-rs1801270; p21 70 C > T-rs1059234) with the development of systemic lupus erythematosus (SLE) in a Southeastern Brazilian population.

METHODS

Genotyping of 353 female volunteers (cases, n = 145; controls, n = 208) was performed by polymerase chain reaction, restriction fragment length polymorphism and/or DNA sequencing. Associations between TP53 and p21 polymorphisms and SLE susceptibility and clinical manifestations of SLE patients were assessed by logistic regression analysis.

RESULTS

Protective effect was observed for the genotype combinations p53 PIN3 A1/A1-p21 31 C/A, in the total study population (OR 0.45), and p53 PIN3 A1/A2-p21 31 C/C, in non-white women (OR 0.28). In Whites, p53 72 C-containing (OR 3.06) and p53 PIN3 A2-containing (OR 6.93) genotypes were associated with SLE risk, and higher OR value was observed for the combined genotype p53 72 G/C-p53 PIN3 A1/A2 (OR 9.00). Further, p53 PIN3 A1/A2 genotype was associated with serositis (OR 2.82), while p53 PIN3 A2/A2 and p53 72 C/C genotypes were associated with neurological disorders (OR 4.69 and OR 3.34, respectively).

CONCLUSIONS

Our findings showed that the TP53 and p21 polymorphisms included in this study may have potential to emerge as SLE susceptibility markers for specific groups of patients. Significant interactions of the TP53 polymorphisms with serositis and neurological disorders were also observed in SLE patients.

The performance of the MODY calculator in a non-Caucasian, mixed-race population diagnosed with diabetes mellitus before 35 years of age

BACKGROUND

A maturity-onset diabetes of the young (MODY) calculator has been described and validated for use in European Caucasians. This study evaluated its performance in Brazilians diagnosed with diabetes mellitus (DM) before 35 years of age.

METHODS

The electronic records of 391 individuals were reviewed in 2020 at the diabetes clinic of a quaternary hospital in São Paulo were analyzed: 231 with type 1 DM (T1DM), 46 with type 2 (T2DM) and 114 with MODY. The MODY calculator was applied to the three groups. A receiver operating characteristic curve was calculated to obtain cut-off points for this population.

RESULTS

The principal differences between the MODY and the T1DM and T2DM groups were body mass index, a positive family history of diabetes and mean HbA1c level. Age at diagnosis in the MODY group was only significantly different compared to the T2DM group. Specificity and sensitivity were good for the cut-off points of 40%, 50% and 60%, with the accuracy of the model for any of these cut-off points being > 95%.

CONCLUSION

The capacity of the calculator to identify Brazilian patients with MODY was good. Values ≥ 60% proved useful for selecting candidates for MODY genetic testing, with good sensitivity and specificity.

Basic biochemical and hematological parameters of structural hemoglobin variants in the postpartum women and their respective newborn from Manaus, Amazonas, Brazil

The present study aimed at estimating the prevalence of structural hemoglobinopathies in newborn and describing the hematological and biochemical characteristics between postpartum women (PW) and their respective newborns (NB) at a public maternity hospital in Manaus, Amazonas state, Brazil. In total, 825 NB and 820 PW were included in the study. Hematological and biochemical analysis and screening of structural hemoglobinopathies were performed and compared in groups of individuals (NICU or not; hemoglobin genotypes; gestational age and prenatal). The age of PW ranged from 13 to 44 years old (mean of 23.7 ± 6.6 years), with 45.9% pregnant for the first time and 54.1% multiparous. Reported receiving prenatal care 88% and regarding the type of delivery, 47.7% had delivered by cesarean section. Among the births, 19.4% were born premature and 8.3% were admission to the neonatal intensive care unit (NICU). The male NB represented 53.4% of the total. Sickle cell trait (FAS) was found in 16 (1.94%) and heterozygous for D hemoglobin (FAD) in 6 (0.73%) newborns. A statistically significant values was found between the previous history of miscarriage and increase of Mean corpuscular volume (MCV) (p < .001), Red blood cell distribution width (RDW) (p = .003), total and indirect bilirubin concentration (p < .001) and LDL cholesterol (p = .004). Hemoglobin levels below 13.5 g/dL was found in 66% black newborns, compared with 15% of Afro-Brazilian and 5% of whites. The frequency of structural hemoglobinopathies was higher in African-Brazilian newborn babies (78%) and those who with low birth weight had a higher frequency of NICU (35.7%). Interestingly, underage mothers had a higher frequency of NB with low birth weight and premature birth. Postpartum women who had children carriers of FAS and FAD had a higher frequency of urinary tract infection (65.2%) and moderate anemia (23.8%). This study estimated for the first time the prevalence of structural hemoglobinopathies in NB in Manaus, Amazonas, Brazil. Despite the small prevalence of, we highlight the importance of early diagnosis of hemoglobin variants, contributing to the improvement of the quality of life of PW and your NB, reinforce the need to implement educational and prevention programs to raise awareness among the population and in order to counsel parents regarding the probability of having a child with abnormal hemoglobins homozygous as HbSS or HbCC.

Clinical and genetic characterization and long-term evaluation of individuals with maturity-onset diabetes of the young (MODY): The journey towards appropriate treatment

AIMS

To describe the clinical and genetic characteristics and long-term follow-up of a cohort with maturity-onset diabetes of the young (MODY), and to evaluate how molecular diagnosis impacted on treatment.

METHODS

A large observational, retrospective, cohort study included individuals referred to the University of São Paulo's Monogenic Diabetes Unit between 2011 and 2020. Comprehensive clinical and genetic evaluations were performed.

RESULTS

Overall, 228 individuals (190 GCK-MODY and 38 HNF1A-MODY) were enrolled. Sixty-two different GCK gene mutations (5 novel) and 17 HNF1A gene mutations (2 novel) were found. Data were available on treatment status for 76 index individuals with GCK-MODY. Before molecular diagnosis, nutritional intervention alone was used in 41 cases (53.9%). After molecular diagnosis, this number increased to 72 (94.8%). Glycated haemoglobin (HbA_1c) remained stable over the 6-year follow-up period: 6.5% (47 mmol/mol) at the first and 6.3% (45 mmol/mol) at the final visit (p = 0.056). Prior to molecular diagnosis, 7/21 (33.3%) HNF1A-MODY individuals were using sulfonylurea compared to 17/21 (81%) after testing. After a median of 5 years on sulfonylureas, HbA_1c values improved from 7.5% (58 mmol/mol) to 6.5% (48 mmol/mol) (p = 0.006).

CONCLUSIONS

Molecular diagnosis resulted in appropriate adjustment of treatment in approximately 80% of participants with GCK-MODY or HNF1A-MODY.

Skin Color and Attractiveness Modulate Empathy for Pain: An Event-Related Potential Study

Although racial in-group bias in empathy for pain has been reported, empathic responses to others’ pain may be influenced by other characteristics besides race. To explore whether skin color and attractiveness modulate empathy for pain, we recorded 24 participants’ reactions to painful faces from racial in-group members with different skin color (fair, wheatish, or dark) and attractiveness (more or less attractive) using event-related potentials (ERPs). Results showed that, for more attractive painful faces, dark skin faces were judged as less painful and elicited smaller N2 amplitudes than fair- and wheatish-skinned faces. However, for less attractive faces, there were no significant differences among the three skin colors. Our findings suggest that empathy for pain toward racial in-group members may be influenced by skin color and attractiveness.

Why do we pick similar mates, or do we?

Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the 'how') of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. 'the why') for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.

Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations

Long chain polyunsaturated fatty acids (LC-PUFAs) have critical signaling roles that regulate dyslipidemia and inflammation. Genetic variation in the FADS gene cluster accounts for a large portion of interindividual differences in circulating and tissue levels of LC-PUFAs, with the genotypes most strongly predictive of low LC-PUFA levels at strikingly higher frequencies in Amerind ancestry populations. In this study, we examined relationships between genetic ancestry and FADS variation in 1102 Hispanic American participants from the Multi-Ethnic Study of Atherosclerosis. We demonstrate strong negative associations between Amerind genetic ancestry and LC-PUFA levels. The FADS rs174537 single nucleotide polymorphism (SNP) accounted for much of the AI ancestry effect on LC-PUFAs, especially for low levels of n-3 LC-PUFAs. Rs174537 was also strongly associated with several metabolic, inflammatory and anthropomorphic traits including circulating triglycerides (TGs) and E-selectin in MESA Hispanics. Our study demonstrates that Amerind ancestry provides a useful and readily available tool to identify individuals most likely to have FADS-related n-3 LC-PUFA deficiencies and associated cardiovascular risk.

An Analysis of Racial and Ethnic Backgrounds Within the CASiRe International Cohort of Sickle Cell Disease Patients: Implications for Disease Phenotype and Clinical Research

Millions are affected by sickle cell disease (SCD) worldwide with the greatest burden in sub-Saharan Africa. While its origin lies historically within the malaria belt, ongoing changes in migration patterns have shifted the burden of disease resulting in a global public health concern. We created the Consortium for the Advancement of Sickle Cell Research (CASiRe) to understand the different phenotypes of SCD across 4 countries (USA, UK, Italy, and Ghana). Here, we report the multi-generational ethnic and racial background of 877 SCD patients recruited in Ghana (n = 365, 41.6%), the USA (n = 254, 29%), Italy (n = 81, 9.2%), and the UK (n = 177, 20.2%). West Africa (including Benin Gulf) (N = 556, 63.4%) was the most common geographic region of origin, followed by North America (N = 184, 21%), Caribbean (N = 51, 5.8%), Europe (N = 27, 3.1%), Central Africa (N = 24, 2.7%), and West Africa (excluding Benin Gulf) (N = 21, 2.4%). SCD patients in Europe were primarily West African (73%), European (10%), Caribbean (8%), and Central African (8%). In the USA, patients were largely African American (71%), Caribbean (13%), or West African (10%). Most subjects identified themselves as Black or African American; the European cohort had the largest group of Caucasian SCD patients (8%), including 21% of the Italian patients. This is the first report of a comprehensive analysis of ethnicity within an international, transcontinental group of SCD patients. The diverse ethnic backgrounds observed in our cohort raises the possibility that genetic and environmental heterogeneity within each SCD population subgroup can affect the clinical phenotype and research outcomes.

CYP3A5*3 and CYP2C8*3 variants influence exposure and clinical outcomes of tacrolimus-based therapy

Aim: The influence of variants in pharmacokinetics-related genes on long-term exposure to tacrolimus (TAC)-based therapy and clinical outcomes was investigated. Patients & methods: Brazilian kidney recipients were treated with TAC combined with everolimus (n = 178) or mycophenolate sodium (n = 97). The variants in CYP2C8, CYP2J2, CYP3A4, CYP3A5, POR, ABCB1, ABCC2, ABCG2, SLCO1B1 and SLCO2B1 were analyzed. Main results: CYP3A5*3/*3 genotype influenced increase in TAC concentration from week 1 to month 6 post-transplantation (p < 0.05). The living donor and CYP2C8*3 variant were associated with reduced risk for delayed graft function (OR = 0.07; 95% CI = 0.03-0.18 and OR = 0.45; 95% CI = 0.20-0.99, respectively, p < 0.05). Conclusion: The CYP3A5*3 variant is associated with increased early exposure to TAC. Living donor and CYP2C8*3 variant seem to be protective factors for delayed graft function in kidney recipients.

Amerindian genetic ancestry as a risk factor for tuberculosis in an amazonian population

In recent years, the incidence of tuberculosis (TB) has declined worldwide, although this disease still occurs at relatively high rates in Amerindian populations. This suggests that the genetic ancestry of Amerindians may be an important factor in the development of infections, and may account for at least some of the variation in infection rates in the different populations. The present study investigated the potential influence of Amerindian genetic ancestry on susceptibility to tuberculosis in an Amazon population. The study included 280 patients diagnosed with tuberculosis and 138 asymptomatic hospital employees with no history of TB, but who were in contact with bacterially active TB patients. Ancestry analysis was run on a set of 61 Ancestry-Informative Markers to estimate European, African, and Amerindian genetic ancestry using STRUCTURE v2.2. The TB group had significantly higher Amerindian ancestry in comparison with the control group, and significantly lower European ancestry. Amerindian ancestry in the 20–60% range was found to be the principal risk factor for increased susceptibility to TB. The results of the study indicate that Amerindian ancestry is an important risk factor for susceptibility to TB in the admixed population of the Brazilian Amazon region.