Linkage disequilibrium patterns and genetic structure of Amerindian and non-Amerindian Brazilian populations revealed by long-range X-STR markers

Blood groups in Native Americans: a look beyond ABO and Rh

The study presents comparisons between blood group frequencies beyond ABO and Rh blood systems in Native American populations and previously published data from Brazilian blood donors. The frequencies of Diego (c.2561C>T, rs2285644), Kell (c.578C>T, rs8176058), Duffy (c.125A>G, rs12075, c.1-67T>C, rs2814778) and Kidd (c.838A>G, rs1058396) variants in Kaingang (n=72) and Guarani (n=234) populations from Brazil (1990-2000) were obtained and compared with data from these populations sampled during the 1960s and with individuals of different Brazilian regions. Data showed high frequencies of DI*01 and FY*01 alleles: 11.8% and 57.6% in Kaingang and 6.8% and 75.7% in Guarani groups, respectively. The main results indicated: (1) reduction in genetic distance over time of Kaingang and Guarani in relation to other Brazilian populations is suggestive of ongoing admixture; (2) significant differences in some frequencies of blood group markers (especially Diego, Kidd and Duffy) in relation to Native Americans and individuals from different geographical regions of Brazil. Our study shows that the frequency of red blood cell polymorphisms in two Native American groups is very different from that of blood donors, when we evaluated blood groups different from ABO and Rh systems, suggesting that a better ethnic characterization of blood unit receptors is necessary.

Deletional Alpha-Thalassemia Alleles in Amazon Blood Donors

Alpha-thalassemia is highly prevalent in the plural society of Brazil and is a public health problem. There is limited knowledge on its accurate frequency and distribution in the Amazon region. Knowing the frequency of thalassemia and the prevalence of responsible mutations is, therefore, an important step in the understanding and control program. Hematological and molecular data, in addition to serum iron and serum ferritin, from 989 unrelated first-time blood donors from Amazonas Hemotherapy and Hematology Foundation (FHEMOAM) were collected. In this study, the subjects were screened for -α ^3.7/4.2/^20.5, -^SEA, -^FIL, and -^MED deletions. Alpha-thalassemia screening was carried out between 2016 and 2017 among 714 (72.1%) male and 275 (27.9%) female donors. The aims of this analysis were to describe the distribution of various alpha-thalassemia alleles by gender, along with their genotypic interactions, and to illustrate the hematological changes associated with each phenotype. Amongst the patients, 5.35% (n = 53) were diagnosed with deletion -α ^-3.7 and only one donor with α ^-4.2 deletion. From the individuals with -α ^-3.7, 85.8% (n = 46) were heterozygous and 14.20% (n = 7) were homozygous. The frequency of the -α ^-3.7 deletion was higher in male (5.89%) than in female (4.0%). There is no significant difference in the distribution of -α ^-3.7 by gender (p = 0.217). The -α ^20.5, -^SEA, and -^MED deletions were not found. All subjects were analyzed for serum iron and serum ferritin, with 1.04% being iron deficient (n = 5) and none with very high levels of stored iron (>220 µg/dL). Alpha-thalassemia-2^3.7kb deletion was the most common allele detected in Manaus blood donors, which is a consistent result, once it is the most common type of α-thalassemia found throughout the world. As expected, the mean of hematological data was significantly lower in alpha-thalassemia carriers (p < 0.001), mainly homozygous genotype. Leukocytes and platelet count did not differ significantly. Due to the small number of individuals with iron deficiency found among blood donors, the differential diagnosis between the two types of anemia was not possible, even because minor changes were found among hematological parameters with iron deficiency and α-thalassemia. Despite this, the study showed the values of hematological parameters, especially MCV and MCH, are lower in donors with iron deficiency, especially when associated with α-thalassemia, and therefore, it may be useful to discriminate different types of microcytic anaemia. In conclusion, we believed screening for thalassemia trait should be included as part of a standard blood testing before blood donation. It should be noted that this was the first study to perform the screening for alpha deletions in blood donors from the Manaus region, and further studies are required to look at the effects of donated thalassemic blood.

Distribution of CYP2D6 alleles and phenotypes in the Brazilian population

The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions.

Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample

We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni's correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PD(F)) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F (ST) between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.

Extensive survey of 12 X-STRs reveals genetic heterogeneity among Brazilian populations

The admixed Brazilian population shows high levels of genetic variability, which resulted from the contribution of three main ethnicities, Amerindian, European, and African. However, due to its huge territory, admixing has been asymmetrical, i.e., the relative contribution from each ethnicity has been unequal in the five geopolitical regions of the country. The aim of this study was to describe genetic variability using a panel of short-tandem repeats on the X chromosome (X-STR) in order to perform a comprehensive evaluation of the usefulness of such markers for forensic purposes in Brazil. Twelve X-STR (DXS9895, DXS7132, DXS6800, DXS9898, DXS6789, DXS7133, GATA172D05, DXS7130, HPRTB, GATA31E08, DXS7423, and DXS10011) were chosen and tested in a sample of 2,234 individuals belonging to 16 out of the 27 Brazilian States, representing all of its five geopolitical regions. No markers showed significant deviation from the Hardy-Weinberg equilibrium, even when analyses were partitioned to represent geopolitical regions. Genetic diversity per locus ranged from 67% (DSX7133) to 95% (DXS10011), and the State of Ceará showed the highest average genetic diversity (79% for all 12 X-STR markers). Considering the Brazilian population as a whole, the power of discrimination of the 12 X-STR panel in females (PDF) was 0.999999999999994, while the power of discrimination in males (PDM) was 0.9999999969. Such high values suggest the potential of that panel to be used in forensic applications and relatedness tests among individuals. Comparisons among the Brazilian populations investigated revealed significant differences when they were compared among each other, a pattern that was maintained when additional populations from Europe and Latin America were compared to Brazilians. Our results highlight the need and usefulness of specific genetic database for forensic purposes in Brazilian populations.

Prevalence of common α-thalassemia determinants in south Brazil: Importance for the diagnosis of microcytic anemia

Alpha thalassemia has not been systematically investigated in Brazil. In this study, 493 unrelated individuals from the southernmost Brazilian state of Rio Grande do Sul were screened for deletional forms of α-thalassemia. One hundred and one individuals had microcytic anemia (MCV < 80 fL) and a normal hemoglobin pattern (Hb A ₂ < 3.5% and Hb F < 1%). The subjects were screened for - α^3.7 , - α^4.2 , - α^20.5 , — ^SEA and — ^MED deletions but only the - α^3.7 allele was detected. The - α^3.7 allele frequency in Brazilians of European and African ancestry was 0.02 and 0.12, respectively, whereas in individuals with microcytosis the frequency was 0.20. The prevalence of α-thalassemia was significantly higher in individuals with microcytosis than in healthy individuals (p = 0.001), regardless of their ethnic origin. There were also significant differences in the hematological parameters of individuals with - α^3.7 / αα, - α^3.7 /- α^3.7 and β-thalassemia trait compared to healthy subjects. These data suggest that α-thalassemia is an important cause of microcytosis and mild anemia in Brazilians.

Brief communication: patterns of linkage disequilibrium and haplotype diversity at Xq13 in six Native American populations

Comparative studies of linkage disequilibrium (LD) can provide insights into human demographic history. Here, we characterize LD in six Native American populations using seven microsatellite markers in Xq13, a region of the genome extensively studied in populations around the world. Native Americans show relatively low diversity and high LD, in agreement with recent genome-wide survey and a scenario of sequential founder effects accompanying human population dispersal around the globe. LD in Native Americans is similar to that observed in some recently described small population isolates and higher than in large European isolates (e.g., Finns), which have been extensively analyzed in medical genetics studies. Haplotype analyses are consistent with a colonization of the New World by a differentiated East Asian population, followed by extensive genetic drift in the Americas.

Genetic profile characterization of 10 X-STRs in four populations of the southeastern region of Brazil

Ten X-chromosomal short tandem repeats (DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423) were analyzed in four populations of the southeastern region of Brazil (São Paulo, Rio de Janeiro, Vitória and Belo Horizonte). No deviations from the Hardy-Weinberg equilibrium were observed for any of the analyzed loci in the four populations. The average diversity per locus varied between 68% for DXS8378, DXS7133, and DXS7423 and 83%, for DXS6809, with Rio de Janeiro being the most diverse population. Overall power of discrimination values in females varied between 0.99999999990 and 0.99999999997 and between 0.9999991 and 0.9999995 in males. These high values show the potential of this system for forensic application and relationships' testing in the studied groups. Genetic comparisons (exact tests of population differentiation and pairwise genetic distances) revealed significant differences between Brazilian and other populations from Europe, Latin America and Africa, as well as among different Brazilian populations.