Biomedical subjects

Leonor Gusmão

Publications and source records attributed to Leonor Gusmão.

At least 19 recordsLinked to original sources

PubMed2007

Genetic diversity of 10 X chromosome STRs in northern Portugal.

Genetic data of 10 X chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) were obtained in a sample of unrelated males born in the five northern Portuguese districts. In a global sample of 347 individuals, no shared haplotypes were found for this set of markers and single locus gene diversities were high, varying between 0.678 for DXS7423 and 0.921 for DXS8377. Linkage disequilibrium analysis did not reveal consistent evidence of association between the X-STRs used. Population comparisons of northern Portuguese districts (exact test of population differentiation; pairwise genetic distances) and analysis of molecular variance supported genetic homogeneity of this region and therefore a common genetic database was considered. In comparisons with other European data, the only population samples showing statistically significant differences to northern Portugal were Germany and Latvia. The present work demonstrates that these genetic markers are highly discriminating and therefore useful for human identification purposes and anthropological research.

Chromosomes, Human, X↗

PubMed2006

Testing for genetic structure in different urban Argentinian populations.

Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.

Argentina↗

PubMed2006

Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia).

Haplotype data were obtained from a sample of 173 unrelated male individuals from Cartagena (Colombia), for 16 Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10). No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Cartagena. Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of Iberian origin.

Chromosomes, Human, Y↗

PubMed2006

Micro-phylogeographic and demographic history of Portuguese male lineages.

The clinal pattern observed for the distribution of Y-chromosome lineages in Europe is not always reflected at a geographically smaller scale. Six hundred and sixty-three male samples from the 18 administrative districts of Portugal were typed for 25 Y-chromosome biallelic and 15 microsatellite markers, in order to assess the degree of substructuring of male lineage distribution. Haplogroup frequency distributions, Analysis of Molecular Variance (AMOVA) and genetic distance analyses at both Y-SNP and Y-STR levels revealed a general genetic homogeneity of Portuguese sub-populations. The traditional division of the country in north, central and south, which is usually considered in studies addressing questions of the genetic variation distribution in Portugal, was not reflected in the Y-haplotype distribution. Instead, just one sub-region (Alentejo) stood out due to the presence of high diversity levels and a higher number of different lineages, at higher frequencies than in other regions. These results are reconciled with the historical evidence available, assuming that from prehistorical times down to the end of the medieval period this region harboured the most diverse groups of people and, because of economic depression, remained relatively isolated from recent homogenisation movements. The finding of a broadly homogeneous background for the Portuguese population has vast repercussions in forensic, epidemiological and association studies.

Chromosomes, Human, Y↗

PubMed2005

Y-chromosome STRs in an Antioquian (Colombia) population sample.

Haplotype data were obtained from a sample of 777 unrelated male individuals from Antioquia Department (Colombia), for eight Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392 and DYS393). A total of 442 different haplotypes were identified of which 334 were represented only once in the database and the most frequent haplotype was found in 32 individuals. A high haplotype diversity was found (99.45%). Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of lberian origin.

Chromosomes, Human, Y↗

PubMed2005

Autosomic STR population data in two Caribbean samples from Colombia.

In this work, a sample of 124 unrelated individuals from San Andres Island and Santa Marta City (Colombia) was studied for the nine STRs included in the AmpFlSTR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA). Although these two populations are geographically apart, San Andres is an Island in the middle of Caribbean Sea (about 480 miles northwest the Colombian mainland) and Santa Marta City located in the coast, exact test showed no differentiation between both population samples (P=0.39445+/-0.0805). Therefore, allele frequencies and parameters of forensic interest were estimated for the global sample.

Colombia↗

PubMed2005

Y-chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia.

The 11 Y-chromosomal short tandem repeats (STRs) included in the Promega Corporation PowerPlex Y System (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) were typed in three ethnic groups ("Andalusians", Berber and Arab) and one cosmopolitan population (Tunis) from Tunisia, summing up 247 individuals, and 139 different haplotypes. Focusing the analysis on the seven Y-STRs of the YHRD Minimal Haplotype Core (DYS385 excepted), "Andalusians" showed no differences from the Cosmopolitan and the Arab samples previously published (our Arab sample presented an extremely low haplotype diversity), but were different from the Berbers. The Berbers from Tunisia were not different from those from Morocco.

Chromosomes, Human, Y↗

PubMed2005

Analysis of STR loci in Cartagena, a Caribbean city of Colombia.

Allele frequencies, together with some parameters of forensic interest were estimated for nine STRs included in the AmpF/STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) in a sample of 215 unrelated individuals from Cartagena (Colombia). For all loci, no significant deviations from Hardy-Weinberg equilibrium were observed. Comparative analysis results between our data and those from other Colombian and African population samples revealed significant differences, except with two Colombian Caribbean Coast sub-regions.

Colombia↗

PubMed2005

Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR Yfiler) in two Tunisian Berber communities.

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFLSTR Yfiler PCR Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were typed in two Berber communities, a small village (Takrouna) and a town (Sejenane), from North Tunisia. As expected, diversity was higher in the town, even when compared with a pool of three small Berber communities, probably due to the combination of different founder effects and genetic drifts operating in the small villages.

Chromosomes, Human, Y↗

PubMed2005

The genetic legacy of western Bantu migrations.

There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing-if any-the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.

Africa↗

PubMed2005

Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa).

Nine Y-STR loci from the "minimal haplotype" included in Y-STR Haplotype Reference Databases (YHRD) together with eight additional Y-STRs (DYS437, DYS438, DYS439, DYS460, DYS461, GATA C4, GATA H4 and GATA A10) were analyzed in a sample of 101 males from Equatorial Guinea living in Madrid. Haplotype and allelic frequencies were calculated and genetic diversities were estimated for each genetic system as well as for the whole haplotype. An unexpected high frequency (6%) of intermediate alleles (13.2 and 14.2) was found in DYS385. For DYS19, two alleles were found in one sample. Another sample failed to amplify with DYS393 primers using either PowerPlex Y System (Promega Corporation) or the Y-PLEXtrade mark 12 (Reliagene, New Orleans, LA) commercial kits. Comparison between Equatorial Guinea and another African population (Mozambique; South East Coast) revealed a significant pairwise Phi(st) value between them (Phi(st)=0.03309; P=0.00000).

Chromosomes, Human, Y↗

PubMed2005

STR allelic frequencies for an African population sample (Equatorial Guinea) using AmpFlSTR Identifiler and Powerplex 16 kits.

We present allele frequencies and forensic parameters for 17 STRs included in the AmpFlSTR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) in a sample of 134 unrelated individuals from Equatorial Guinea located in Western Africa, between Cameroon and Gabon. Hardy-Weinberg equilibrium was tested for each locus and the sample was compared with five African databases: Promega's and AB Applied Biosystems African-Americans and samples from Mozambique, from Cabinda (Angola) and Guinea-Bissau.

DNA Fingerprinting↗

PubMed2005

New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes.

Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions.

Candida albicans↗

PubMed2005

Y chromosome STR typing.

Because of their unique transmission properties and male specificity, markers located on the nonrecombining region of the Y chromosome (NRY) have become an important tool in forensic investigation. In the past few years, more than 50 polymorphic Y chromosome-specific short tandem repeats (STRs) have been described and a set of 9 loci were selected, considered as the minimal haplotype included in the forensic databases, Y-STR Haplotype Reference Databases, the largest now available online (http://www.yhrd.org). Here, we describe a multiplex amplification strategy developed for ABI platforms to amplify the nine loci included in the minimal haplotype (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) as well as a second set of markers (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4, and GATA H4) used to improve the minimal haplotype diversity and, hence, the discrimination power. Together, these 17 Y-STRs can be used to define highly discriminative haplotypes, providing a powerful tool in male lineage identification.

Base Sequence↗

PubMed2004

Population and mutation analysis of 17 Y-STR loci from Rio de Janeiro (Brazil).

The 17 Y chromosome STR loci DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, GATA C4, GATA H4 and GATA A10 were analyzed in a male sample of 126 unrelated individuals from Rio de Janeiro. No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Rio de Janeiro. Pairwise haplotype analysis showed no significant differences in the comparison of Rio de Janeiro with Iberian samples from different regions of Portugal and Spain, as well as with other Caucasian samples from South America, namely Costa Rica, Buenos Aires (Argentina) and Sao Paulo (Brazil). The same set of Y-STRs was also typed in 119 father/son pairs and among 2,023 allele transfers, 8 mutations were observed with an overall mutation rate of 0.003955+/-0.001396 per locus/meiosis across the 17 loci. Except in one case, all mutations were single step. For DYS438 a four-step mutation was found which has never been reported before, where allele 10 mutated to allele 6.

Brazil↗

PubMed2004

A Basque Country autochthonous population study of 11 Y-chromosome STR loci.

Haplotype, allele frequencies and population data of 11 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438 and DYS439 were determined from a sample of 168 unrelated autochthonous male individuals from the Basque Country. The eight surnames and birth places of the grandparents of all analyzed individuals were of Basque origin. A total of 89 haplotypes were identified by the 11 Y-STR loci. The haplotype diversity (97.49%) and discrimination capacity (52.98%) were calculated. Comparisons were made with previously published haplotype data on other Iberian population samples and significant differences were found.

Chromosomes, Human, Y↗

PubMed2004

Population data for 16 Y-chromosome STRs in four populations from Pyrenees (Spain).

Population frequencies for the eight Y-STR loci included in the "minimal haplotype" from Y-STR Haplotype Reference Database (YHRD) plus other eight Y-STRs (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA H4 and GATA A10) were obtained for a sample of 133 males from four main geographical areas in the Pyrenees (Spain): Vall D'Aran (Lérida), Cerdanya (Gerona), Alt Urgell (Lérida) and Jacetania (Huesca). Haplotype diversities were estimated in the four populations.

Chromosomes, Human, Y↗

PubMed2004

STR analysis of artificially degraded DNA-results of a collaborative European exercise.

Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR) fragments after increased PCR cycle numbers, artefact signals and allelic drop-out. Based on the observations, strategies are discussed to overcome these problems. The strategies include careful balancing of the amount of template DNA and the PCR cycle numbers, the reaction volume and the amount of Taq polymerase. Furthermore, a careful evaluation of the results of the fragment analysis and of automated allele calling is necessary to identify the correct alleles and avoid artefacts.

Alleles↗