Leonor Gusmão

University of Porto, Oporto, Porto, Portugal

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Publications (329)697.67 Total impact

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    Nádia Pinto · Leonor Gusmão · António Amorim

    Full-text · Dataset · Feb 2016
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    Full-text · Dataset · Jan 2016
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    Full-text · Dataset · Jan 2016
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    ABSTRACT: The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order i) the sequence, ii) the alignment, and iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data.
    Full-text · Article · Jan 2016 · Forensic Science International: Genetics
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    ABSTRACT: There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
    Full-text · Article · Jan 2016 · Human Genetics

  • No preview · Article · Nov 2015 · Forensic Science International: Genetics
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    ABSTRACT: Different host genetic variants may be related to the virulence and transmissibility of pandemic Influenza A(H1N1)pdm09, influencing events such as binding of the virus to the entry receptor on the cell of infected individuals and the host immune response. In the present study, two genetic variants of the ST3GAL1 gene, which encodes the Siaα2-3Galβ1- receptor to which influenza A(H1N1)pdm09 virus binds for entry into the host cell, were investigated in an admixed Brazilian population. First, the six exons encoding the ST3GAL1 gene were sequenced in 68 patients infected with strain A(H1N1)pdm09. In a second phase of the study, the rs113350588 and rs1048479 polymorphisms identified in this sample were genotyped in a sample of 356 subjects from the northern and northeastern regions of Brazil with a diagnosis of pandemic influenza. Functional analysis of the polymorphisms was performed in silico and the influence of these variants on the severity of infection was evaluated. The results suggest that rs113350588 and rs1048479 may alter the function of ST3GAL1 either directly through splicing regulation alteration and/or indirectly through LD with SNP with regulatory function. In the study the rs113350588 and rs1048479 polymorphisms were in linkage disequilibrium in the population studied (D' = 0.65). The GC haplotype was associated with an increased risk of death in subjects with influenza (OR = 4.632, 95% CI = 2.10;1.21). The AT haplotype was associated with an increased risk of severe disease and death (OR = 1.993, 95% CI = 1.09;3.61 and OR 4.476, 95% CI = 2.37;8.44, respectively). This study demonstrated for the first time the association of ST3GAL1 gene haplotypes on the risk of more severe disease and death in patients infected with Influenza A(H1N1)pdm09 virus.
    Full-text · Article · Oct 2015 · PLoS ONE
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    ABSTRACT: In sexual-assault cases, the use of DNA databases may be decisive in identifying perpetrators. Particularly, the analysis of Y chromosome STRs may play a crucial role in the study of the male portion in (i) male/female cell mixtures, (ii) mixed DNA profiles from more than one perpetrator, or from perpetrators and the sexual partners (iii) and azoospermic or oligospermic perpetrators. The analysis of Y chromosome specific markers can be also important in the study of the geographic ancestry of male lineages. The aim of this study was to genotype samples collected from sexual-assault cases in Brasília, Brazil, using the PowerPlex Y-23 System and to construct a Y-STR database of these profiles in the Instituto de Pesquisa de DNA Forense da Polícia Civil do Distrito Federal (Forensic DNA Research Institute of the Federal District Civil Police) in Brasília, in order to aid forensic casework. A total of 650 evidentiary samples were previously typed for autosomal STRs and, using a DNA database of STRs profiles of biological evidence from sexual assaults, we found 78 serial rapists who attacked 223 women in Brasília. In this work, we analyse 420 complete 23 Y-STR profiles (haplotypes) and we present the results of YSTR analysis in sexual-assault cases. To assess the substructure of Brazilian populations we conducted Analysis of Molecular Variance (AMOVA) on different Brazilian population groups. The use of a 23 Y-STR DNA database and of an autosomal STR DNA database of samples from sexual assaults in a dual approach of a combined autosomal/Y chromosomal STR analysis played an important role in identifying perpetrators and serial rapists, highlighting the importance of its use in the investigation of sexual assaults.
    No preview · Conference Paper · Oct 2015
  • Iva Gomes · António Brehm · Leonor Gusmão · Peter M. Schneider
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    ABSTRACT: A great amount of population and forensic genetic data are available for X-STRs supporting the need for having a common and accurate nomenclature among laboratories allowing for better communication, data exchange, and data comparison. DXS10148, DXS10074 and DXS10134 are commonly used X-STRs particularly due to their inclusion in the commercial kit Investigator Argus X-12 (Qiagen). Samples from West Africa and Iraq were sequenced for all three X-STRs allowing the detection of new DNA sequence variants. At DXS10148, variation was detected at four bases downstream from the flanking region from the repeat motif. The sequence AAGG-AAAG has been detected for the first time as a varying (AAGG-AAAG)1-3 motif, in the present work. One additional string when compared to the common one (AAGG-AAAG)2 adds eight bases to the fragment size of the tetranucleotide STR. This means that 2 repeats are added in these cases to the fragment size of the allele, while the presence of only one copy will reduce the expected allele size by 2 repeats. At DXS10074 two varying stretches consisting of AC and AG dinucleotide repeats were observed in the upstream flanking region, six bases from the main repeat core that also influence the expected allele size. DXS10134 revealed a simpler nomenclature in the Guinea-Bissau sample set when compared to the previously described allele nomenclature. This detected new hidden variation also has impact on the actual allele nomenclature at this locus as it contributes to a new class of short alleles so far undetected in other studies.
    No preview · Article · Oct 2015 · Forensic Science International: Genetics
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    Full-text · Article · Sep 2015 · Forensic Science International: Genetics
  • A. Castillo · K. Rueda · A. Pico · A. Gil · C. Vargas · F. Rondón · L. Gusmão

    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series

  • No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: São Tomé and Príncipe are the two main islands of a small archipelago located in the Gulf of Guinea, western equatorial African coast. These islands were probably uninhabited at the time of the Portuguese discovery in 1471. After the Portuguese decree of expulsion, many new-Christians fled to São Tomé, since the inquisition was never established there. Several documents attest the continuous movement of new-Christians to these islands, which worked as a refuge from inquisitional prosecutions. To elucidate the genetic impact of the historical Jewish migrations to São Tomé, we selected a sample of unrelated individuals based on the following criteria: (a) sharing surnames with those included in the historical reports as Jewish migrants (b) showing cultural practices putatively related to the Jewish religion. Both maternal and paternal lineages were investigated using the complete mtDNA control region, along with 22 Y-SNPs and 23 Y-STR markers. Moreover, 83 autosomal insertion/deletion markers were analyzed.
    Full-text · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: The Philippines are a group of islands in the Asia-Pacific region harboring a high diversity of cultures, languages and people due to various migration waves and different degrees of admixture between neighboring groups. In this work we studied the most populous region of the country – Metropolitan Manila – with a set of small autosomal insertion deletion (indel) polymorphisms, to assess their genetic diversity and usefulness in forensic context. Using a single-tube multiplex reaction we characterized 38 indels in 195 individuals born in the National Capital Region, allowing to establish an allele frequency database for future reference in forensic applications. The genetic diversity observed was high (average heterozygosity = 0.40890), similar to previous studies in other East Asian populations, and the marker set reached good levels of informativeness, with a combined power of discrimination of 99.999999999997% and combined power of exclusion of 99.50%. In conclusion, our study showed that this simple indel multiplex can be useful for forensic applications in Metropolitan Manila Filipino population.
    Full-text · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: The pattern of human variation in Africa is the result of a complex series of demographic events. There are few databases related to the peoples of Africa, especially in western and central regions. In this study, 17 Y-STR and 31 Y-SNP loci were genotyped in a sample from Western Africa, which was compared with other representative populations of other African regions. The haplotype diversity observed in this region was 1.0000 (±0.0018) and that is similar to those values obtained in other African samples already studied. The most frequent haplogroup found in our sample belongs to E, showing the M2 derived allele. The haplogroup diversity was 0.6895 (±0.0200), very similar to that observed in countries where the Bantu groups are predominant (0.681 in Angola; 0.753 in Equatorial Guinea). Concerning the Western Africa, significant differences were observed between Guinea–Bissau and the remaining populations of this region. In addition, there was no significant difference between our sample and samples from Eastern and Central Africa. The genetic composition of the population studied was significantly different from that of Guinea–Bissau, although a genetic homogeneity was found among most countries belonging to West Africa.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: Currently, all agencies of conformity assessment testing laboratory favor the participation in proficiency testing as a mechanism for quality assurance. In Colombia, the Genes Laboratory has been designated, since 2008, to perform, design and implement the proficiency testing for all the interested laboratories. In this report, we show the results of Colombian exercises Inter-laboratory Quality Control for the years 2013 and 2014. In both years the exercise consisted of one practical component, one theoretical mandatory component and a theoretical optional component. The participants were 23 and 20 laboratories in 2013 and 2014, respectively, representing seven different countries of Latin America and the Caribbean. For the practical component each participant laboratory receive; (1) samples of blood, saliva and/or semen stains, in this part they should report the routine own laboratory markers for each sample, (2) three optional theoretical cases of varying complexity, (3) a simple theoretical approach consistent of paternity case (father, mother and son) (2013) and a complex paternity case with a deceased father (2014). In the last two components of the exercise they had to submit only the calculations. In both years, for the practical component the consensus of 70 STR markers, distributed between autosomal and linked to the sex chromosomes, was achieved with an error rate of 1.75% and 3.07% for 2013 and 2014, respectively. On the other hand, for mandatory theoretical exercise, error rates of 21.74% (2013) and 10.63% (2014) were detected. This inter-laboratory exercise has become an important mechanism for quality assurance in the region.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: Ancestry informative markers (AIMs) are useful to estimate individual and population ancestries, providing important information to forensic investigations. Several AIM sets were described and evaluated by comparison with data from GWAS. Taking into account that an efficient set of AIMs shall provide identical results between full brothers and GWAS are not easily performed, we aimed to see if the accuracy of the ancestry estimates are correlated to differences obtained in siblings. Pairs of siblings from Brazil were genotyped for 83 InDels; and values of African, European and Native American contributions were compared using diverse sets of markers. The comparison of the ancestry in siblings was only meaningful for markers with high inter-populations variation. The lowest average differences between brothers were obtained for the complete set of 83 InDels, even including markers with low inter-populations variation.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: Philippines is an archipelago in the Western Pacific Ocean. It is one of the most populated country in Southeast Asia, harboring multiple ethnic groups and cultures. Most of the non-indigenous population is composed by Chinese and Spanish immigrants. In order to characterize the Y-STR composition of Philippines, in the present study, we have collected 74 samples from unrelated males from the three main geographical divisions: Luzon, Visayas and Mindanao. These samples were typed for the 27 Y-STR loci included in the YFiler Plus kit. A high Y-STR haplotype diversity was found with all haplotypes being unique in our sample. Low diversity values were found for DYS391 and DYS438 (below 34%) and the multi-loci markers DYS385 and DYF387S1 were among the most diverse ones (above 95%). Since no data is available for the full set of YFiler Plus markers, a smaller set was used to calculate genetic distances between Philippines and other Southeast Asian populations. The results showed no significant differences between our samples and two other samples from Philippines, one from the general population and the other restricted to Luzon region. Significant differences were observed when comparing any of the three Philippines samples with Vietnam and Singapore populations.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: The current Colombian population is the result of genetic admixture between Native Americans, Europeans and Africans. Around 82% of the population is considered admixed, 15% are Afro-Colombians and just 3% are Native Americans. There are about 81 native groups in Colombia. In this work, a sample of 121 non-related individuals from three Native American groups were analysed for 46 ancestry informative InDel markers. One of these groups was the Pijaos that, because of their combative nature, was almost exterminated during European conquest and colonial times. The other two studied groups belong to communities that have been less subjected to admixture with non-Natives. The Barí, known as "Motilones" or "Dobukubi", is a Native group that inhabits the Serranía del Perija, Norte de Santander, since pre-Colombian times. They still keep their original language, the Barí-ara, which belongs to the Chibcha family. We have also studied a sample of Natives from Guainía, formed by different groups that migrated from the Amazonia and Orinoquian regions, including the Desana, Curripaco, Puinave, Cubeo, Guaunano and Tucano, all belonging to Tucano and Arawak linguistic groups. This study allow determining genotypic and allelic frequencies for 46 ancestry informative InDels and to estimate Native American, European and African admixture proportions in three Colombian native communities. The results showed a very low European and African admixture in the Barí and Guainia native groups in contrast to the high levels of admixture presented by the Pijao.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series
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    ABSTRACT: The South American country of Peru is composed by a highly admixed population, with Native American, European and African genetic contributions. Some Native American groups in Peru underwent low admixture with Europeans or Africans and they have kept much of their culture and their original language. In this work we have studied one of these groups called Ashaninka, for the 27 Y chromosome specific STR loci that were included in the recently released YFiler Plus kit. The samples have been collected from 58 unrelated males belonging to 41 different communities located in the margins of the Amazonian rivers Pichis and Palcazú, in the district of Puerto Bermúdez, Pasco region, Peru. A high Y-STR haplotype diversity was found (1.0000. ±. 0.0022) with all haplotypes being unique in the studied sample. Two markers that usually present a high diversity in European populations showed very low values of diversity in the Ashaninka Native Americans, namely the DYS635 (Het = 0.2263) and DYS437 (Het = 0.1325). On the other hand, the DYS438 showed a much higher diversity in Ashaninka (Het = 0.6582) group than that usually found in European populations. Apart from the multi-loci markers DYS385 and DYF387S1, more than one allele was also observed in one sample for DYS518 locus. This study represents the first report of haplotype frequencies for the YFiler Plus markers' set in a Native American population, showing a high diversity of haplotypes and, therefore, demonstrating their usefulness in forensic identification cases.
    No preview · Article · Sep 2015 · Forensic Science International Genetics Supplement Series

Publication Stats

5k Citations
697.67 Total Impact Points

Institutions

  • 1996-2016
    • University of Porto
      • • Institute of Molecular Pathology and Immunology (IPATIMUP)
      • • Institute of Molecular Pathology and Immunology of the University of Porto
      Oporto, Porto, Portugal
  • 2014
    • Rio de Janeiro State University
      Rio de Janeiro, Rio de Janeiro, Brazil
  • 2006
    • Universidad del País Vasco / Euskal Herriko Unibertsitatea
      Leioa, Basque Country, Spain
  • 2002
    • Universidade da Madeira
      • Centro de Estudos da Macaronésia
      Funchal, Madeira, Portugal
  • 2001
    • University of Coimbra
      Coímbra, Coimbra, Portugal
  • 1999-2000
    • University of Santiago de Compostela
      • Instituto de Medicina Legal
      Santiago, Galicia, Spain
  • 1995
    • Instituto Superior Manuel Teixeira Gomes
      Vila Nova de Portimão, Faro, Portugal