António Amorim

António Amorim
University of Porto | UP · FCUP Departamento de Biologia / IPATIMUP/ i3s

PhD

About

789
Publications
140,960
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13,231
Citations
Additional affiliations
January 2012 - present
Universidade Federal do Rio de Janeiro
January 2009 - December 2012
Universidade NOVA de Lisboa

Publications

Publications (789)
Article
Full-text available
Microsatellites (or short-tandem repeats (STRs)) are widely used in anthropology and evolutionary studies. Their extensive polymorphism and rapid evolution make them the ideal genetic marker for dating events, such as the age of a gene or a population. This usage requires the estimation of mutation rates, which are usually estimated by counting the...
Article
To overcome the multifactorial complexity associated with the analysis and interpretation of the capillary electrophoresis results of forensic mixture samples, probabilistic genotyping methods have been developed and implemented as software, based on either qualitative or quantitative models. The former considers the electropherograms’ qualitative...
Article
In the already identified quantitative trait loci (QTL), modulating Hb F levels are cis-acting haplotypes of the β-globin gene cluster itself, although the single nucleotide polymorphisms (SNPs) accounting more for the association, remain uncertain. In this study, the role in Hb F production of previously reported candidate SNPs within the β-globin...
Article
Full-text available
The so-called Prüm system made mandatory for all EU Member States to join the pan-European network for the exchange of fingerprints, DNA profiles and motor vehicle information for stepping up on cross-border cooperation, particularly in combating terrorism and cross-border crime. Taking into consideration the number of DNA profiles archived in the...
Article
Full-text available
In the past few years, there has been an increasing neuroscientific interest in understanding the function of mammalian chromodomains helicase DNA-binding (CHD) proteins due to their association with severe developmental syndromes. Mammalian CHDs include nine members (CHD1 to CHD9), grouped into subfamilies according to the presence of specific fun...
Article
Full-text available
A non-negligible proportion of human pathogenic variants are known to be present as wild type in at least some non-human mammalian species. The standard explanation for this finding is that molecular mechanisms of compensatory epistasis can alleviate the mutations’ otherwise pathogenic effects. Examples of compensated variants have been described i...
Article
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Understanding the role of common polymorphisms in modulating the clinical phenotype when they co-occur with a disease-causing lesion is of critical importance in medical genetics. We explored the impact of apparently neutral common polymorphisms, using the gene encoding the urea cycle enzyme, ornithine transcarbamylase (OTC), as a model system. Dis...
Article
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Recombination between the X and Y human sex chromosomes is limited to the two pseudoautosomal regions (PARs) that present quite distinct evolutionary origins. Despite the crucial importance for male meiosis, genetic diversity patterns and evolutionary dynamics of these regions are poorly understood. In the present study, we analyzed and compared th...
Article
Full-text available
Background The impairment of the hepatic enzyme phenylalanine hydroxylase (PAH) causes elevation of phenylalanine levels in blood and other body fluids resulting in the most common inborn error of amino acid metabolism (phenylketonuria). Persistently high levels of phenylalanine lead to irreversible damage to the nervous system. Therefore, early di...
Article
Full-text available
Forensic genetics is a fast-growing field that frequently requires DNA-based taxonomy, namely, when evidence are parts of specimens, often highly processed in food, potions, or ointments. Reference DNA-sequences libraries, such as BOLD or GenBank, are imperative tools for taxonomic assignment, particularly when morphology is inadequate for classifi...
Article
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Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness,...
Article
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San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque pare...
Article
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The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X...
Article
Full-text available
The gene encoding the cytosolic β-glucosidase GBA3 shows pseudogenization due to a truncated allele (rs358231) that is polymorphic in humans. Since this enzyme is involved in the transformation of many plant β-glycosides, this particular case of gene loss may have been influenced by dietary adaptations during evolution. In humans, apart from the in...
Article
Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications’ field, the major current difficulties result from the lack of standards and genetic databases as well as...
Article
Microbial Forensics is a field that continues to grow in interest and application among the forensic community. This review, divided into two sections, covers several topics associated with this new field. The first section presents a historic overview concerning the use of microorganisms (or its product, i.e. toxins) as harmful biological agents i...
Article
Full-text available
Genetic diversity of Mycobacterium tuberculosis affects immune responses and clinical outcomes of tuberculosis (TB). However, how bacterial diversity orchestrates immune responses to direct distinct TB severities is unknown. Here we study 681 patients with pulmonary TB and show that M. tuberculosis isolates from cases with mild disease consistently...
Preprint
Full-text available
Advancements in DNA methods and biotechnology have enabled forensic scientists to explore the DNA evidence found as part of a criminal investigation on a much more comprehensive and predictive level. This has led to a rise in research into DNA intelligence tools such as phenotypic prediction (i.e., eye and hair colour) and inference of biogeographi...
Poster
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One of the major sources of intra and inter-species mitochondrial genome (mtDNA) variation are genomic rearrangements. These genomic rearrangements can have implications in diseases and evolution and result from insertions, deletions, transpositions, and tandem duplication random loss (TDRL). The mtDNA rearrangements often contribute to highly debi...
Article
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Amphibians are the focus of a recent debate and public attention owing to the global decline in their populations worldwide. Amphibians are one of the most threatened and poorly known groups of vertebrates in several geographic areas, even though they play a central role in their own ecosystems. At different levels, amphibians make their contributi...
Article
African populations have higher genetic diversity representing an interesting continent for population genetic studies. A sample set from Nigeria, a West African country on the Gulf of Guinea, was genetically characterized using 10 X chromosomal short tandem repeat polymorphisms (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, D...
Article
Unbiased estimation of germinal mutation rates are essential for population and evolutionary genetic analyses and in any forensic kinship evaluation. A major source of bias in diploid or haplodiploid loci was identified – ‘hidden’ or ‘covert’ mutations (i.e. those not causing Mendelian incompatibilities) and ways to overcome it proposed. Morever, t...
Article
Short tandem repeats are extremely abundant in the human genome and widely used in population and forensic genetics. The conventional approach to estimate mutation rates for STRs involves the detection of Mendelian incompatibilities and their frequency quantification, in family duos or trios. In this work, we aim to measure the impact this estimati...
Article
Reference databases are indispensable tools for species identification in forensic context. Among the most widely used public databases stands GenBank or BOLD, aggregating genetic data and associated metadata of millions of specimens. Acquiring and collecting such amount of information requires a concerted effort of the scientific community. Detect...
Article
In the present paper, our main goal is focused in developing fast algorithms for human mtDNA sequence analyses, requiring minimum and explicit assumptions on mutation models and evolutionary pathways. We propose a new approach based on a construction of Dawson, a technique based on the ordering of the variable sites. In this approach, the first ste...
Article
Forensic genetics is the application of genetics to human and nonhuman material for the resolution (and prevention) of legal conflicts. Nonhuman DNA applications are increasing, from the ancillary role in criminalistics to the control of protected species and their products, microbial identification in bioterrorism or medical malpractice. We review...
Article
Full-text available
The identification of species in casework samples is of fundamental importance for forensic investigations. Laboratories are increasingly compelled to provide accurate and fast identifications in trace materials left on crime scenes, wildlife poaching, illegal trade of protected species, fraudulent food products cases, etc. However, the field of no...
Article
Y chromosome specific short tandem repeats (Y-STRs) are widely used in population genetics and forensics. Since these markers do not recombine, mutation is the only source of diversity. The primary mutational mechanism leading to length changes in STRs is thought to be polymerase template slippage, and the most common change is the gain or the loss...
Article
Body fluid identification has become a field of interest in forensic casework as it can add value to particular investigative scenarios. Identifying the source of the biological material is not always an upfront task using conventional methods; therefore, profiling of specific mRNA markers can provide the answer. The implementation of RNA based ana...
Article
Mutations on the HBB gene are a common cause of hemoglobinopathies, including sickle cell anemia, a severe genetic condition that constitutes a major public health concern. The aim of this study was to determine the prevalence of sickle cell anemia and β-globin haplotype distribution in newborns from the Bengo region. The first two exons of β-globi...
Article
Full-text available
Neurodevelopmental disorders (NDDs) represent a growing medical challenge in modern societies. Ever-increasing sophisticated diagnostic tools have been continuously revealing a remarkably complex architecture that embraces genetic mutations of distinct types (chromosomal rearrangements, copy number variants, small indels, and nucleotide substitutio...
Chapter
Application of genetics to forensics has been multifactorial, that is analysing various inherited characteristics (genes or gene products) in the same court case. However, only when DNA fast and cheap sequencing technologies became available can we speak of forensic genomics proper, that is the use of genome‐wide data to forensic applications. Thes...
Article
In 1994, a kindred from Yemen was described as the first Jewish family with Machado–Joseph disease (MJD/SCA3), a dominant ataxia caused by the expansion of a (CAG)n above 61 repeats, in ATXN3. MJD is spread worldwide due to an ancient variant of Asian origin (the Joseph lineage). A second, more recent, independent expansion arose in a distinct hapl...
Article
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The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit model...
Article
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At least 40 human diseases are associated with repeat expansions; yet, the mutational origin and instability mechanisms remain unknown for most of them. Previously, genetic epidemiology and predisposing backgrounds for the instability of some expanding loci have been studied in different populations through the analysis of diversity flanking the re...
Article
In kinship testing powerful statistical results are usually obtained when genetic information is required to be shared between a set of individuals, under the assumption of one of the hypotheses. This is the case when the hypotheses parenthood or identity are compared with the hypothesis of no relatedness, even when only a pair of individuals is an...
Article
Full-text available
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on...
Article
Full-text available
Background Aspergillus fumigatus is the species section Fumigati most frequently isolated from the respiratory tract of cystic fibrosis (CF) patients. Recent studies suggest that mutations in the Cyp51 gene, particularly TR34/L98H, are responsible for azole resistance. Objectives and Methods The focus of this study was on section Fumigati isolates...
Article
Full-text available
Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancill...
Article
Forensic laboratories frequently receive biological samples from crime scene investigations with limited DNA in terms of quantity and quality. Hair shafts are a common type of evidence constituting an ideal sample for DNA testing. Nevertheless, the majority of these hairs are rootless. In an attempt to facilitate the analyses of such samples, new D...
Article
The potential and difficulties of the application of genome wide data in forensics are analyzed. We argue that, besides statistical, computational, ethical, economic and technical validation problems, the state of the art of population genetics theory is insufficient to deal with the forensic use of this type of data. In order to keep the current s...
Article
Full-text available
Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TA...
Preprint
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the admixture of Native Americans, Europeans and Sub-Saharan Africans ¹ . Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry...
Article
Objectives: We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. Methods: A total of 110 males of Portugue...
Article
Obtaining a genetic profile from pieces of evidence collected at a crime scene is the primary objective of forensic laboratories. New procedures, methods, kits, software or equipment must be carefully evaluated and validated before its implementation. The constant development of new methodologies for DNA testing leads to a steady process of validat...
Article
One of the taxa suffering from intense poaching activities along its entire occurrence area, Dasypus represents a genus of armadillos that comprises seven living species: D. hybridus, D. kappleri, D. novemcinctus, D. pilosus, D. sabanicola, D. septemcinctus, and D. yepesi. The aim of this study is to analyze the genetic diversity of D. novemcinctus...
Article
During the Neolithic, human populations underwent cultural and technological developments that led to an agricultural revolution. Although the population genetics and evolution of European Neolithic populations have been extensively studied, little is known regarding the Neolithic expansion in North Africa with respect to Europe. One could expect t...
Article
Full-text available
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic...
Data
Illustrative examples of scenarios of nonhuman genetic material (NHGM) for main evidence in litigations not related with human identification. (PDF)
Data
Illustrative examples of scenarios using nonhuman genetic material (NHGM) for auxiliary evidence in litigations related with human identification. (PDF)
Data
Literature cited in the supplementary material. (PDF)
Article
Full-text available
Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all...