The Iberian legacy into a young genetic xeroderma pigmentosum cluster in central Brazil.

In central Brazil, in the municipality of Faina (state of Goiás), the small and isolated village of Araras comprises a genetic cluster of xeroderma pigmentosum (XP) patients. The high level of consanguinity and the geographical isolation gave rise to a high frequency of XP patients. Recently, two founder events were identified affecting that community, with two independent mutations at the POLH gene, c.764 + 1 G > A (intron 6) and c.907 C > T; p.Arg303* (exon 8). These deleterious mutations lead to the xeroderma pigmentosum variant syndrome (XP-V). Previous reports identified both mutations in other countries: the intron 6 mutation in six patients (four families) from Northern Spain (Basque Country and Cantabria) and the exon 8 mutation in two patients from different families in Europe, one of them from Kosovo. In order to investigate the ancestry of the XP patients and the age for these mutations at Araras, we generated genotyping information for 22 XP-V patients from Brazil (16), Spain (6) and Kosovo (1). The local genomic ancestry and the shared haplotype segments among the patients showed that the intron 6 mutation at Araras is associated with an Iberian genetic legacy. All patients from Goiás, homozygotes for intron 6 mutation, share with the Spanish patients identical-by-descent (IBD) genomic segments comprising the mutation. The entrance date for the Iberian haplotype at the village was calculated to be approximately 200 years old. This result is in agreement with the historical arrival of Iberian individuals at the Goiás state (BR). Patients from Goiás and the three families from Spain share 1.8 cM (family 14), 1.7 cM (family 15), and a more significant segment of 4.7 cM within family 13. On the other hand, the patients carrying the exon 8 mutation do not share any specific genetic segment, indicating an old genetic distance between them or even no common ancestry.

Long noncoding RNA polymorphisms influence susceptibility to endemic pemphigus foliaceus.

BACKGROUND: Pemphigus foliaceus (PF) is an epidermal autoimmune disease, characterized by the presence of autoantibodies against the desmosomal protein desmoglein 1. Genetic and environmental factors contribute to PF, a complex disease that is endemic in Brazil and Colombia and neighbouring countries, and in Tunisia. Long noncoding RNAs (lncRNAs) may participate in gene regulation by interacting with DNA, proteins and other RNAs. Dysregulation of lncRNAs has recently been recognized as an important coplayer in the onset or progression of complex diseases. In addition, single-nucleotide polymorphisms (SNPs) located in lncRNA genes have been associated with differential risk to cancer, autoimmunity and infection. OBJECTIVES: Here, we aimed to investigate whether SNPs in lncRNA genes are associated with differential susceptibility to endemic PF. MATERIALS AND METHODS: We integrated data from the lncRNA SNP database with genome-wide genotype data obtained for 229 patients and 6681 controls. We tested the association between endemic PF and 2080 SNPs located in lncRNAs applying logistic regression. RESULTS: The most significantly associated SNP was rs7144332 (OR = 1·63, P = 2·8 × 10-6 ), located in the lncRNA gene AL110292·1. Results for five other SNPs were suggestive of association (P < 0·001). In silico analysis indicated that five of the six SNPs impact transcription, three may influence lncRNA's secondary structure, and three may alter microRNA-lncRNA interactions. CONCLUSIONS: We showed, for the first time, that variation in lncRNA genes may influence pemphigus pathogenesis. Our findings highlight the importance of lncRNA variation in autoimmune and possibly other complex diseases and suggest polymorphisms for functional validation.

Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease.

Hematopoietic stem-cell transplantation (HSCT) is currently the only established curative treatment for sickle cell disease (SCD), but is limited by donor availability. Ethnicity is thought to have an impact on the complications experienced by patients that undergo HSCT and on the likelihood of identifying an human leukocyte antigen (HLA) matched donor. In the present study, we investigated the genomic ancestry and the distribution of HLA allele groups in Brazilian patients with SCD, compared these HLA profiles to worldwide populations and evaluate the availability of HLA-matched donors. A broad intercontinental admixture of patients with SCD was observed, with African ancestry ranging from 6.7% to 93.4%. In a dendrogram based on HLA frequencies, Brazilian patients with SCD were included in a branch containing only populations with a significant African component. Among the 126 patients evaluated, 10 (8%) found a HLA-matched unrelated donor in a database of 18 134 donors. Self-reported white, brown and black matched donors were identified, and no significant difference in the percentage of compatible donors was observed between these ethnic groups. Our results show that Brazilian patients with SCD are very admixed, indicating that this group is a promising target for admixture mapping of genes involved in complications after HSCT. Additional studies may help to clarify the impact of the genetic diversity and admixture of these patients on the donor availability.

Noninvasive fetal RHD genotyping from maternal plasma in an admixed Brazilian population.

We evaluated the efficacy of noninvasive fetal Rhesus D (RHD) genotyping from maternal plasma in a highly admixed population. Fifty-five blood samples from RhD-negative pregnant women from Brazil were processed for extraction of cell-free plasma DNA. Real-time PCR was performed to amplify segments of exons 5 and 7 from the RHD gene, as well as for detection of the SRY gene to confirm the presence of fetal DNA. Fetal genotyping results were compared with the RhD phenotype determined from newborn cord blood samples obtained at birth. Thirty-two samples were RHD-positive, 18 were RHD-negative and 5 were inconclusive due to amplification of only one RHD exon. In 43 samples, the fetal RHD genotype was compared to the neonatal RhD phenotype, and only one result was discordant, due to false-negative serology. There was one false SRY genotyping negative result. We conclude that noninvasive fetal RHD genotyping from maternal blood provides accurate results and suggests its viability as a clinical tool for the management of RhD-negative pregnant women in an admixed population.

Development of two multiplex mini-sequencing panels of ancestry informative SNPs for studies in Latin Americans: an application to populations of the State of Minas Gerais (Brazil).

Admixture occurs when individuals from parental populations that have been isolated for hundreds of generations form a new hybrid population. Currently, interest in measuring biogeographic ancestry has spread from anthropology to forensic sciences, direct-to-consumers personal genomics, and civil rights issues of minorities, and it is critical for genetic epidemiology studies of admixed populations. Markers with highly differentiated frequencies among human populations are informative of ancestry and are called ancestry informative markers (AIMs). For tri-hybrid Latin American populations, ancestry information is required for Africans, Europeans and Native Americans. We developed two multiplex panels of AIMs (for 14 SNPs) to be genotyped by two mini-sequencing reactions, suitable for investigators of medium-small laboratories to estimate admixture of Latin American populations. We tested the performance of these AIMs by comparing results obtained with our 14 AIMs with those obtained using 108 AIMs genotyped in the same individuals, for which DNA samples is available for other investigators. We emphasize that this type of comparison should be made when new admixture/population structure panels are developed. At the population level, our 14 AIMs were useful to estimate European admixture, though they overestimated African admixture and underestimated Native American admixture. Combined with more AIMs, our panel could be used to infer individual admixture. We used our panel to infer the pattern of admixture in two urban populations (Montes Claros and Manhuaçu) of the State of Minas Gerais (southeastern Brazil), obtaining a snapshot of their genetic structure in the context of their demographic history.

Microsatellite loci: determining the genetic variability of Plasmodium vivax.

OBJECTIVE: To describe the genetic diversity of Plasmodium vivax isolates from different areas in the Brazilian Amazon using 11 polymorphic microsatellites and to evaluate the correlation between microsatellite variation and repeat array length. METHODS: Microsatellites with variable repeat units and array lengths were selected using in silico search of the P. vivax genome. We designed primers and amplified the selected loci in DNA obtained from patients with P. vivax acute infections. RESULTS: Positive correlation between repeat array length and microsatellite variation was detected independently of the size of repeat unit (di, tri, or tetranucleotide). We used these markers to describe the genetic variability of P. vivax isolates from four geographic regions of the Brazilian Amazon. Substantial variability was observed among P. vivax isolates within populations, concurrent with high levels of multiple-clone infections and high linkage disequilibrium. Overall, structured populations were observed with moderate to high genetic differentiation. CONCLUSION: The markers studied are useful tools for assessing population structure of P. vivax, as demonstrated for Brazilian populations and for searching for evidence of recent selection events associated with different phenotypes, such as drug resistance.

Characterization of a candidate locus for malaria susceptibility in human populations: a (TA)n microsatellite in the promoter region of the CYBB gene, the gp91 phox subunit of the NADPH oxidase.

We have analysed the linkage disequilibrium pattern between the promoter TA microsatellite and Single Nucleotide Polymorphism (SNP) haplotypes for the CYBB gene. None of the CYBB SNPs serve as good surrogates for the microsatellite alleles, previously associated with mild malaria. Thus, the candidate (TA)(n) microsatellite should be directly tested in genetic epidemiology studies.

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

N-acetyltransferase 2 (NAT2), an important enzyme in clinical pharmacology, metabolizes antibiotics such as isoniazid and sulfamethoxazole, and catalyzes the transformation of aromatic and heterocyclic amines from the environment and diet into carcinogenic intermediates. Polymorphisms in NAT2 account for variability in the acetylator phenotype and the pharmacokinetics of metabolized drugs. Native Americans, settled in rural areas and large cities of Latin America, are under-represented in pharmacogenetics studies; therefore, we sequenced the coding region of NAT2 in 456 chromosomes from 13 populations from the Americas, and two from Siberia, detecting nine substitutions and 11 haplotypes. Variants *4 (37%), *5B (23%) and *7B (24%) showed high frequencies. Average frequencies of fast, intermediate and slow acetylators across Native Americans were 18, 56 and 25%, respectively. NAT2 intra-population genetic diversity for Native Americans is higher than East Asians and similar to the rest of the world, and NAT2 variants are homogeneously distributed across native populations of the continent.

Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus.

Interleukin-13 (IL-13) is a cytokine involved in Th2 immune response, which plays a role in susceptibility to infection by extracellular parasites as well as complex diseases of the immune system such as asthma and allergies. To determine the pattern of genetic diversity at the IL13 gene, we sequenced 3950 bp encompassing the IL13 gene and its promoter in 264 chromosomes from individuals originating from East and West Africa, Europe, China and South America. Thirty-one single-nucleotide polymorphisms (SNPs) arranged in 88 haplotypes were indentified, including the nonsynonymous substitution Arg130Gln in exon 4, which differs in frequency across ethnic groups. We show that genetic diversity and linkage disequilibrium (LD) are not evenly distributed across the gene and that sites in the 5' and 3' regions of the gene show strong differentiation among continental groups. We observe a divergent pattern of haplotype variation and LD across geographic regions and we identify a set of htSNPs that will be useful for functional genetic association studies of complex disease. We use several statistical tests to distinguish the effects of natural selection and demographic history on patterns of genetic diversity at the IL13 locus.

Body size, composition, and blood pressure of high-altitude Quechua from the Peruvian Central Andes (Huancavelica, 3,680 m).

Although much information is available about the effects of high altitude on physiological characteristics, less is know about its effect on body composition. In the present study, anthropometric and body composition variables were investigated in a sample of 77 adult Quechua males from the Peruvian Central Andes (Huancavelica, 3,680 m). The subjects are shorter in relation to body weight than other ethnic groups, whereas body proportions are macrocormic (indicating a long trunk relative to the lower extremities), with intermediate values of the acromial-iliac index. All skinfold thicknesses are low (approximately 15th percentiles of NHANES reference values for the triceps and subscapular skinfolds), but tend to be higher than in the other Quechua populations. Similar results are obtained when percentage fat is estimated. Somatotypes are dominant in mesomorphy with very low ectomorphy. Comparison with a sample of high-altitude Kirghiz (3,200 m), previously studied with the same methods, shows higher values in the Peruvian sample for all variables related to adiposity. The presence of low adiposity in the Quechua population could be associated with stresses of the high-altitude environment. Mean values of blood pressure are very low and there is no correlation with age.

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome.

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.

Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations.

A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories.

Lung volume, chest size, and hematological variation in low-, medium-, and high-altitude central Asian populations.

To evaluate adaptive responses to high-altitude environment, we examined three groups of healthy adult males from Central Asia: 94 high-altitude (HA) Kirghiz subjects (3,200 m above sea level); 114 middle-altitude (MA) Kazakh subjects (2,100 m), and 90 low-altitude (LA) Kirghiz subjects (900 m). Data on chest size (chest perimeter and chest diameter), lung volume (forced expiratory volume (FEV) and forced expiratory volume in 1 sec (FEV1)), and hematological parameters (hemoglobin, erythrocytes, hematocrit, and SaO(2)) are discussed. The results show that 1) chest shape is less flat in the samples living at higher altitude. In the HA sample, chest perimeter is lower but chest excursion is high. 2) In the highlanders, forced vital capacity (FVC) and FEV1 are no higher than in the other samples, even when corrected for stature and body weight. The negative correlation between FVC-FEV1 and age decreases with increasing altitude. 3) The HA and MA samples have higher values of hemoglobin, erythrocytes, and hematocrit. The HA sample has lower SaO(2) and higher arterial oxygen content than the LA sample. No association between hematocrit and age was detected in the four samples. The results indicate that the high-altitude Kirghiz present features of developmental acclimatization to hypobaric hypoxia which are also strongly influenced by other major high-altitude environmental stresses.

Hematological and pulmonary responses to high altitude in Quechuas: a multivariate approach.

This study investigates the relationships among hematological variables, pulmonary function, and age in a sample of high-altitude natives. The following anthropometric and physiological variables were examined in 77 adult Quechua males from the Peruvian Central Andes (Huancavelica, 3,680 m): height, weight, sitting height, chest diameters, chest and abdominal circumferences, forced vital capacity (FVC), forced expiratory volume at 1 sec (FEV1), peak expiratory flow (PEF), hemoglobin concentration (Hb), red blood cells (RBC), hematocrit (Htc), diastolic and systolic blood pressure, body temperature, pulmonary rate, and pulse rate. The means of these variables for the Huancavelica sample fall within the range of variability previously observed in Andean populations. Principal components analysis and canonical correlation analysis suggest that in this native Andean population: 1) aging decreases lung function but does not affect hematological features, and 2) there is a negative age-independent correlation between lung function (FVC, FEV1, PEF) and hematological traits (Hb, RBC, Htc).

Surnames and genetic structure of a high-altitude Quechua community from the Ichu River Valley, Peruvian Central Andes, 1825-1914.

Changes in isolation, inbreeding, population subdivision, and isonymous relationships are examined in six Quechua communities from the upper valley of the Ichu River in the Peruvian Central Andes (3700 m). All marriages registered between 1825 and 1914 in the Parish of Santa Ana were analyzed. The data (1680 marriages) were divided into 2 periods (1825-1870 and 1871-1914) and into the 6 villages that constitute the parish. Endogamy rates are between 81% and 100%, indicating high levels of reproductive isolation. The inbreeding indicated by isonymy (Ft, Fr, and Fn) is lower than in other mountain populations studied. Isonymy values, calculated from the different surname combinations made possible by the Ibero-American Surnames System, indicate a strong rejection of consanguineous marriages, particularly between patrilineal relatives, in agreement with the parental structure typical of Andean populations. The comparison between observed and expected repeated-pair values reveals a moderate level of subdivision within populations, which could be related to cultural and socioeconomic factors. Nonmetric multidimensional scaling was used to investigate temporal changes in the isonymous relationships among the communities. The results reveal a decrease in the interpopulational variability measured by surnames, in agreement with an increase in exogamy. Surnames and data contained in historical and demographic records yield reliable information, and they can be used to reconstruct the biological history of Amerindian populations over the last few centuries.