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- Y-chromosome lineages from Portugal, Madeira and Açores record elements of sephardim and berber ancestryPublication . Gonçalves, Rita; Freitas, Ana; Branco, Marta; Rosa, Alexandra; Fernandes, Ana T.; Zhivotovsky, Lev A.; Underhill, Peter A.; Kivisild, Toomas; Brehm, AntónioA total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Ac¸ores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese subpopulations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.
- Mitochondrial portraits of the Madeira and Açores archipelagos witness different genetic pools of its settlersPublication . Brehm, António; Pereira, Luísa; Kivisild, Toomas; Amorim, AntónioWe have studied the matrilineal genetic composition of the Madeira and Açores north Atlantic archipelagos, which were settled by the Portuguese in the 15th century. Both archipelagos, and particularly Madeira, were involved in a complex commercial network established by the Portuguese, which included the trading of slaves across the Atlantic. One hundred and fifty-five mtDNAs sampled from the Madeira and 179 from the Açores archipelagos were analysed for the hypervariable segment I (HVS-I), and for haplogroup-diagnostic coding-region RFLPs. The different settlement histories of both groups of islands are well reflected in their present day mtDNA pool. Although both archipelagos show identical diversity values, they are clearly different in their haplogroup content. Madeira displays a stronger sub-Saharan imprint, with haplogroups L1-L3 constituting about 13% of the lineages. Also, the relative frequencies of L sub-clusters in Madeira and mainland Portugal suggests that, at least in part, African presence in Madeira can be attributed to a direct gene flow from West Africa and not via Portugal. A comparison of the genetic composition of these two archipelagos with the Canary Islands, specially taking into account that their European source population was essentially from the Iberian Peninsula, testifies the stronger impact of the North African U6 cluster in the Canaries. This group is present in Madeira at a moderate frequency, but very reduced in the Açores. Nevertheless the recorded introduction of Canary native Guanches, who are characterized by the presence of particular sub-clade U6b1, has left no detectable imprints in the present day population of Madeira.
- Distribution of HLA alleles in Portugal and Cabo Verde. Relationships with the slave trade routePublication . Spínola, Hélder; Brehm, A.; Williams, F.; Jesus, J.; Middleton, D.HLA-A,-B, and -DR frequencies were analysed in populations from Portugal and the Madeira and Cabo Verde Archipelagos, aiming to characterize their genetic composition. Portuguese settlers colonized both Archipelagos in the 15th and 16th centuries. Madeira received many sub-Saharan slaves to work in the sugar plantations, and Cabo Verde served as a pivotal market in the Atlantic slave trade and was populated by individuals coming from the Senegambia region of the West African coast. The population of Madeira shows the highest genetic diversity and the presence of alleles and haplotypes usually linked to sub-Saharan populations, the haplotypes accounting for 3±5% of the total. Cabo Verde presents typical markers acknowledged to be of European or IberoMediterranean origin, thus revealing the admixture of European settlers with Sub-Saharan slaves. Altogether the number of European haplotypes reaches 15% of the total. The Portuguese population shows a perceivable and significant heterogeneity both in allele and haplotype frequencies, unveiling a differential input of peoples from different origins. A PCA of the populations studied, plus other relevant ones, clearly shows gene heterogeneity in mainland Portugal as well as the differences and relationships between these populations and Madeira and Cabo Verde.
- HLA genes in Portugal inferred from sequence-based typing: in the crossroad between Europe and AfricaPublication . Spínola, H.; Middleton, D.; Brehm, A.The human leukocyte antigen-A (HLA-A), -B and -DRB1 polymorphism was examined in the Portuguese population, discriminating between North, Centre and South inhabitants. All data were obtained at high-resolution level, using sequence-based typing. The most frequent allele at each locus was A* 020101 (26%), B* 440301 and B* 510101 (12% each) and DRB1* 070101 (15%). The predominant three-locus haplotype was A*020101B*440301-DRB1*070101 (3.1%), highly frequent in North Portugal (5.4%), lower in Centre (2%) and absent in the South. The present study demonstrates that the Portuguese population has been genetically influenced by Europeans and North Africans, via several historic immigrations. North Portugal seems to concentrate, probably due to the pressure of Arab expansion, an ancient genetic pool originated from several North Africans and Europeans, influences throughout millenniums. South Portugal shows a North African genetic influence, probably of recent origin by means of Berbers accompanying Arab expansion. We found that Centre Portugal is the distribution limit of some alleles and haplotypes that characterize the North or the South of the country. Despite North, Centre and South Portugal not being significantly different in allele frequencies, this study shows that HLA allele and haplotype frequencies are not homogeneous in the country. North and South Portugal show more similarity to North Africans in opposition to Centre which appears closer to Europeans.
- Genetic risk analysis of coronary artery disease in a population based study in Portugal, using a genetic risk score of 31 variantsPublication . Pereira, Andreia; Mendonça, Maria Isabel; Borges, Sofia; Freitas, Sónia; Henriques, Eva; Rodrigues, Mariana; Freitas, Ana Isabel; Sousa, Ana Célia; Brehm, António; Reis, Roberto Palma dosBackground: Genetic risk score can quantify individual’s predisposition to coronary artery disease; however, its usefulness as an independent risk predictor remains inconclusive. Objective: To evaluate the incremental predictive value of a genetic risk score to traditional risk factors associated with coronary disease. Methods: Thirty-three genetic variants previously associated with coronary disease were analyzed in a case-control population with 2,888 individuals. A multiplicative genetic risk score was calculated and then divided into quartiles, with the 1st quartile as the reference class. Coronary risk was determined by logistic regression analysis. Then, a second logistic regression was performed with traditional risk factors and the last quartile of the genetic risk score. Based on this model, two ROC curves were constructed with and without the genetic score and compared by the Delong test. Statistical significance was considered when p values were less than 0.05. Results: The last quartile of the multiplicative genetic risk score revealed a significant increase in coronary artery disease risk (OR = 2.588; 95% CI: 2.090-3.204; p < 0.0001). The ROC curve based on traditional risk factors estimated an AUC of 0.72, which increased to 0.74 when the genetic risk score was added, revealing a better fit of the model (p < 0.0001). Conclusions: In conclusion, a multilocus genetic risk score was associated with an increased risk for coronary disease in our population. The usual model of traditional risk factors can be improved by incorporating genetic data.
- The genetic variant C825T of the beta 3 subunit of G protein is associated with hypertension in a Portuguese populationPublication . Sousa, Ana Célia; Reis, Roberto Palma dos; Pereira, Andreia; Borges, Sofia; Gouveia, Sara; Spínola, Adelaide; Freitas, Ana Isabel; Guerra, Graça; Góis, Teresa; Rodrigues, Mariana; Henriques, Eva; Ornelas, Ilídio; Freitas, Carolina; Pereira, Décio; Brehm, António; Mendonça, Maria IsabelHypertension is an important public health problem, affecting about 25% of the adult population worldwide.1 Genetic and environmental factors contribute to its pathogenesis. The T allele of the C825T polymorphism of the beta 3 subunit of G protein (rs5443) leads to the production of a truncated variant that enhances intracellular signaling and may interfere with the regulation of blood pressure. This genetic variant has been described as a risk factor for hypertension, although study results are controversial.
- Population data of five STRs in three regions from PortugalPublication . Fernandes, Ana Teresa; Brehm, AntonioAllele and haplotype frequencies of five chromosome STR loci (CD4, TPO, FES, TH01 and VWA) were determined for unrelated males throughout Portugal. This report presents STR data for three separate regions of Portugal, being the first time that data on the south of the country is presented. This study reveals that the three regions from Portugal are not genetically homogeneous. The north of Portugal presents significant differences in the CD4 locus, when compared with the other two populations. When compared with Madeira and Ac¸ores, the three regions show a different behavior at TPO and VWA loci.
- Mitochondrial portrait of the Cabo Verde archipelago: the Senegambian outpost of Atlantic slave tradePublication . Brehm, A.; Pereira, L.; Bandelt, H.-J.; Prata, M. J.; Amorim, A.In order to study the matrilineal genetic composition in Cabo Verde (Republic of Cape Verde), an archipelago that used to serve as a Portuguese entrepôt of the Atlantic slave trade, we have analysed a total of 292 mtDNAs sampled from the seven inhabited islands for the hypervariable segment I (HVS-I) and some characteristic RFLPs of the coding regions. The different settlement history of the northwestern group of the islands is well reflected in the mtDNA pool. The total Cabo Verde sample clearly displays the characteristic mitochondrial features of the Atlantic fringe of western Africa and testifies to almost no mitochondrial input from the Portuguese colonizers.
- The genetic background of metabolic trait clusters in children and adolescentsPublication . Silventoinen, Karri; Gouveia, Élvio; Jelenkovic, Aline; Maia, José; Antunes, António M.; Carvalho, Miguel Â. A. Pinheiro de; Brehm, António M.; Thomis, Martine; Lefevre, Johan; Kaprio, Jaakko; Freitas, DuarteBackground: It is well known that the metabolic risk factors of cardiovascular diseases are correlated, but the background of this clustering in children is more poorly known than in adults. Thus, we studied the contribution of genetic and environmental factors to the clustering of metabolic traits in childhood and adolescence. Methods: Nine metabolic traits were measured in 214 complete twin pairs aged 3 to 18 years in the Autonomous Region of Madeira, Portugal, in 2007 and 2008. The variation of and covariations between the traits were decomposed into genetic and environmental components by using classical genetic twin modeling. Results: A model including additive genetic and environmental factors unique for each twin individual explained the variation of the metabolic factors well. Under this model, the heritability estimates varied from 0.47 (systolic blood pressure in children under 12 years of age) to 0.91 (HDL cholesterol in adolescents 12 years of age or older). The most systematic correlations were found between adiposity (body mass index and waist circumference) and blood lipids (HDL cholesterol, LDL cholesterol and triglycerides), as well as blood pressure. These correlations were mainly explained by common genetic factors. Conclusions: Our results suggest that obesity, in particular, is behind the clustering of metabolic factors in children and adolescents. Both general and abdominal obesity partly share the same genetic background as blood lipids and blood pressure. Obesity prevention already in childhood is important in reducing the risk of metabolic diseases in adulthood.
- Discrepancies in HLA Typing by PCR-SSOP and SBT Techniques: a case studyPublication . Spínola, Hélder; Bruges-Armas, Jácome; Brehm, AntónioSix hundred twenty-one samples from Portugal, the Cabo Verde archipelago, and Guinea-Bissau were typed for HLA-A, HLA-B, and HLADRB1usingthepolymerasechainreaction–sequence-specificoligonucleotide probe (PCR-SSOP) method and the sequence-based typing (SBT) method to characterizeandcomparediscrepanciesbetweenthetwomethods.Fifty-three alleles (4.27% of 1,242 chromosomes typed) identified by the PCR-SSOP method were not concordant with the results obtained using the SBT method. Thirty-four (2.74% of total chromosomes typed) PCR-SSOP mistyping results were discrepancies inside the same allele group and 19 others (1.53% of total chromosomes typed) were relative to nonconcordant results between different groups. PCR-SSOP allele mistyping is the result of interpretation difficulties resulting from less intense, absent, or dubious hybridization patterns. Noncommercial PCR-SSOP procedures are highly exigent on the technicians’ experience and the availability of properly calibrated high-precision equipment.