A. M. Bento

National Institute of Legal Medicine, Coímbra, Coimbra, Portugal

Are you A. M. Bento?

Claim your profile

Publications (31)17 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
    Forensic Science International: Genetics 06/2015; 19:56-67. DOI:10.1016/j.fsigen.2015.06.004 · 3.20 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The European DNA profiling group (EDNAP) organized a sixth collaborative exercise on RNA/DNA co-analysis for body fluid/tissue identification and STR profiling. The task was to identify skin samples/contact traces using specific RNA biomarkers and test three housekeeping genes for their suitability as reference genes. Eight stains, a skin RNA dilution series and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 22 participating laboratories using RNA extraction or RNA/DNA co-extraction methods. Two sets of previously described skin-specific markers were used: skin1 pentaplex (LCE1C, LCE1D, LCE2D, IL1F7 and CCL27) and skin2 triplex (LOR, KRT9 and CDSN) in conjunction with a housekeeping gene, HKG, triplex (B2M, UBC and UCE). The laboratories used different chemistries and instrumentation. All laboratories were able to successfully isolate and detect mRNA in contact traces (e.g., human skin, palm-, hand- and fingerprints, clothing, car interiors, computer accessories and electronic devices). The simultaneous extraction of RNA and DNA provides an opportunity for positive identification of the tissue source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling. The skin markers LCE1C and LOR and the housekeeping gene marker B2M were detected in the majority of contact traces. Detection of the other markers was inconsistent, possibly due to the low amounts and/or poor quality of the genetic material present in shed skin cells. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid/tissue identification method that can easily be combined with current STR typing technology. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, > 94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organized by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences.
    Forensic Science International: Genetics 04/2014; 11. DOI:10.1016/j.fsigen.2014.04.006 · 3.20 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract This work aimed to study the rapidly mutating Y-STRs in a population of Portugal Centre. The results showed that these markers are highly polymorphic, observing that each sample had a unique haplotype.
    Forensic Science International Genetics Supplement Series 12/2013; DOI:10.1016/j.fsigss.2013.10.042
  • [Show abstract] [Hide abstract]
    ABSTRACT: Abstract
    Forensic Science International Genetics Supplement Series 12/2013; 4(1-1):e152-e153. DOI:10.1016/j.fsigss.2013.10.079
  • [Show abstract] [Hide abstract]
    ABSTRACT: Samples analysed in this study suffered from afflictions, such as low level DNA, degradation and PCR inhibitors: samples with induced degraded conditions and real crime scene samples, from a wide range of crimes.Results obtained with NGM SElect™ PCR amplification kit and PowerPlex® ESI 17 system were compared, to verify the behaviour of both kits in the presence of challenging samples.
    Forensic Science International Genetics Supplement Series 12/2011; 3(1-1):e123 - e124. DOI:10.1016/j.fsigss.2011.08.061
  • [Show abstract] [Hide abstract]
    ABSTRACT: The identification of disaster victims through the use of DNA analysis is an integral part of DVI response, regardless of the scale and nature of the disaster. DNA analysis is performed to assist in the identification of victims through kinship (familial matching to relatives) or direct (self source sample) matching of DNA profiles. The exfoliated primary teeth can be an alternative self-sample used as an antemortem record for direct matching in DVI context.The main purpose of the study is to evaluate the possibility of DNA extraction in primary teeth with probative value for identification, despite being stored for long periods of time (until 18 years).
    Forensic Science International Genetics Supplement Series 12/2011; 3(1). DOI:10.1016/j.fsigss.2011.09.052
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A variety of challenging biological samples, including blood stains, saliva, semen, hair, bones, finger nails, among others, are often a part of our casework investigation. In this study, semen, blood samples and saliva swabs were extracted by several methods in order to optimize and validate the Prepfiler Express™ Extraction kit and the AutoMate Express DNA Extraction System. Results obtained with the robot (using silica-coated magnetic beads) were compared with methods based on a chelating resin, silica membranes and paramagnetic resin.
    Forensic Science International Genetics Supplement Series 12/2011; 3(1):e377 - e378. DOI:10.1016/j.fsigss.2011.09.050
  • [Show abstract] [Hide abstract]
    ABSTRACT: Samples of 70 individuals from 3 ethnic groups from Angola (Bakongos, Kimbundu and Ovimbundu) were studied analysing the polymorphisms of the entire mitochondrial control region in order to verify the genetic diversity. A total of 68 different haplotypes were identified, 66 being unique. Sequence diversity was estimated to be 1.0000. ±. 0.0113 and nucleotide diversity for Bakongo, Kimbundu and Ovimbundu ethnic groups were 0.015556. ±. 0.007970, 0.016772. ±. 0.008517 and 0.016020. ±. 0.008411, respectively. It was possible to include the majority of the mtDNA haplotypes into a specific African mtDNA haplogroup.
    Forensic Science International Genetics Supplement Series 12/2011; 3(1). DOI:10.1016/j.fsigss.2011.08.062
  • [Show abstract] [Hide abstract]
    ABSTRACT: AmpFlSTR® NGM™ is a 16-locus multiplex kit claiming improved robustness than earlier generation AppliedBiosystems kits; NGM-SElect™ was released recently as an equivalent to NGM loci plus SE33 so it was determined if NGM-SElect can be an asset compared to NGM in low-level DNA samples.
    Forensic Science International Genetics Supplement Series 12/2011; 3(1-1):e121 - e122. DOI:10.1016/j.fsigss.2011.08.060
  • Forensic Science International Genetics Supplement Series 12/2011; 3(1). DOI:10.1016/j.fsigss.2011.08.066
  • [Show abstract] [Hide abstract]
    ABSTRACT: The AmpFlSTR® Identifiler® Direct PCR Amplification Kit is a short tandem repeat (STR) multiplex assay, optimized to amplify 16 loci directly from biological material (blood or buccal cell samples) stored in FTA paper, without resorting to DNA extraction. However, preliminary experiences have shown the versatility and robustness of this amplification kit, when applied to other biological sample supports. The aim of this research work is to analyze the results of this kit when applied to non-FTA paper or other support for biological samples such as a buccal swab.
    Forensic Science International Genetics Supplement Series 12/2011; 3(1-1):e371 - e372. DOI:10.1016/j.fsigss.2011.09.047
  • [Show abstract] [Hide abstract]
    ABSTRACT: The aim of the present work was to study the origin of paternal and maternal lineages in Guinea-Bissau population, inferred by phylogeographic analyses of mtDNA and Y chromosome defined haplogroups. To determine the male lineages present in Guinea-Bissau, 33 unrelated males were typed using a PCR-SNaPshot multiplex based method including 24 Y-SNPs, which characterize the main haplogroups in sub-Saharan Africa and Western Europe. In the same samples, 17 Y-STRs (included in the YFiler kit, Applied Biosystems) were additionally typed. The most frequent lineages observed were E1b1a (xE1b1a4,7)-M2 (68%) and E1a-M33 (15%). The European haplogroup R1b1-P25 was represented with a frequency of 12%. The two hypervariable mtDNA regions were sequenced in 79 unrelated individuals from Guinea-Bissau, and haplogroups were classified based on control region motifs using mtDNA manager. A high diversity of haplogroups was determined in our sample being the most frequent haplogroups characteristic of populations from sub-Saharan Africa, namely L2a1 (15%), L3d (13%), L2c (9%), L3e4 (9%), L0a1 (8%), L1b (6%) and L1c1 (6%). None of the typical European haplogroups (H, J and T) were found in the present sample of Guinea-Bissau. From our results, it is possible to confirm that Guinea-Bissau presents a typically West African profile, marked by a high frequency of the Y chromosome haplogroup E1b1a(xE1b1a4,7)-M2 and a high proportion of mtDNA lineages belonging to the sub-Saharan specific sub-clusters L1 to L3 (89%). A small European influx has been also detected, although restricted to the male lineages.
    Forensic Science International: Genetics 11/2010; 5(2):114-6. DOI:10.1016/j.fsigen.2010.10.007 · 3.20 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Mitochondrial DNA analysis is very useful for the interpretation of the history of human migration and to estimate the frequency of a haplotype in the forensic context. From a human settlement perspective, La Paz area is greatly interesting since the first planned city of the region is located there. Samples from 110 individuals from La Paz were studied analyzing the polymorphisms in the D-loop, hypervariable region I (HVI) and hypervariable region II (HVII) in order to verify the genetic diversity. The aim of this study was to start the creation of a population database in order to obtain the genetic interpopulation variability and classify haplotypes into characteristic haplogroups of South America. A total of 97 different haplotypes were identified, 90 being unique, expressed by 122 polymorphic nucleotide positions. Nucleotide and sequence diversity were estimated to be 0.015 _ 0.0075 and 0.996, respectively. Haplogroup distribution in the samples was 57.27% B4, 19.09% C1, 10.00% A2, 3.64% D1, 2.73% D4h3, 1.82% H, and 0.91% for each of the haplogroups A4, B4c1a, CZ, D4J, M7a and M8/N9b. The rate of length heteroplasmy was 36.36% in HVI and 52.73% in HVII. Phylogenetic analysis reveals proximity to the Korean, Chilean aboriginal, Japanese and Australian populations. The estimated genetic variability of the studied population was high, suggesting an early settlement.
    Journal of Forensic and Legal Medicine 07/2010; 17:247e253. DOI:10.1016/j.jflm.2010.02.011 · 0.99 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A collaborative exercise on mRNA profiling for the identification of blood was organized by the European DNA Profiling Group (EDNAP). Seven blood samples and one blood dilution series were analyzed by the participating laboratories for the reportedly blood-specific markers HBB, SPTB and PBGD, using different kits, chemistries and instrumentation. The results demonstrate that HBB is expressed abundantly in blood, SPTB moderately and PBGD significantly less. All but one of the 16 participating laboratories were able to successfully isolate and detect RNA from the dried bloodstains even though a majority of the laboratories had no prior experience with RNA. Despite some expected variation in sensitivity between laboratories, the method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise support the potential use of mRNA profiling as an alternative to conventional serological tests.
    Forensic Science International: Genetics 02/2010; 5(1):21-6. DOI:10.1016/j.fsigen.2010.01.003 · 3.20 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Biallelic markers, Single Nucleotide Polymorphisms (SNPs), are nowadays a powerful tool in the analysis of degraded samples. Namely, Y chromosome SNPs allow to determine the gender of the analyzed sample and to establish its haplogroup, making possible to attribute the ethnicity of male individuals. The aim of this study is to obtain Y-SNPs in forensic samples without STRs results, checking methodologies previously used.
    Forensic Science International Genetics Supplement Series 12/2009; 2(1-1):206 - 207. DOI:10.1016/j.fsigss.2009.09.001
  • [Show abstract] [Hide abstract]
    ABSTRACT: Pets live with people and place biological samples everywhere, which may be useful in a forensic context linking suspects and victims, to an occurrence.The genetic diversity of canine microsatellite loci PEZ1, FHC2054, FHC2010, PEZ5, PEZ20, PEZ12, PEZ3, PEZ6, PEZ8 and FHC2079 was investigated in a population of 63 Portuguese dogs.Preliminary results show that the studied markers appeared to be polymorphic, thus contributing to increase the potential of forensic samples of animal origin. The number of alleles per locus, varied between five (FHC2010) to 20 (PEZ3) and allelic frequencies were estimated.
    Forensic Science International Genetics Supplement Series 12/2009; 2(1):288-289. DOI:10.1016/j.fsigss.2009.08.068
  • [Show abstract] [Hide abstract]
    ABSTRACT: Mitochondrial DNA (mtDNA) has enormous potential in forensic genetics, allowing identification of genetic material from degraded samples. Genetic testing can also be performed using mtDNA coding region SNPs. SNPs have a number of characteristics that make them unique for forensic analysis, allowing the successful analysis of degraded samples. The aim of the present study was to evaluate the effectiveness of a mtSNP typing assay on skeletal remains that were buried directly in soil for more than thirty years in adverse climate conditions.
    Forensic Science International Genetics Supplement Series 12/2009; 2:215-216. DOI:10.1016/j.fsigss.2009.08.075
  • [Show abstract] [Hide abstract]
    ABSTRACT: Study of mitochondrial DNA (mtDNA) control region is a current practice in forensic genetics. In our service, mtDNA analysis is performed in many evidentiary specimens. Evaluation of this methodology is important to improve quality, increase efficiency and decrease artefacts, in order to reduce costs and time consuming. A case with 12 reference samples (bucal swabs) and 190 telogenic hair specimens extracted with DNA IQ™ System Tissue and Hair Extraction Kit (Promega) is reported. HVS-1 and HVS-2 control regions were sequenced with BigDye® Terminator v1.1 Kit (Applied Biosystems), using BetterBuffer (Microzone Limited), followed by a simple bead purification method (XTerminator) to remove unincorporated terminators. Application of this procedure had success in 180 hair samples within a very short time comparing to dRhodamine/ethanolic precipitation sequencing strategy and also demonstrated that better results are achieved with clean sequence data closer to the primer. The quality of data produced by the BigDye/BetterBuffer/XTerminator (BDX) procedure has been demonstrated to be very high. Besides that the BDX procedure can significantly reduce overall processing time and cost per reaction. This new methodology has additional advantages like fewer reagent transfers and smaller amounts of DNA.
    Forensic Science International Genetics Supplement Series 12/2009; 2:97-98. DOI:10.1016/j.fsigss.2009.08.011
  • [Show abstract] [Hide abstract]
    ABSTRACT: Degraded human remains and crime scene evidences with small amounts of DNA typically reveal incomplete or null genetic profiles when using standard (large) STR amplicons. The technology of mini-STRs, using reduced-size STR amplicons, can help to recover information from these samples. In our Forensic Genetic Service several genetic profiles were obtained or completed using MiniFiler kit (Applied Biosystems) increasing the success rate in sample typing. In all studied cases no inconsistencies were found between profiles obtained with MiniFiler and Identifiler, suggesting that this mini-STR kit can be used to include low copy number (LCN) evidence profiles in STR databases.
    Forensic Science International Genetics Supplement Series 12/2009; 2(1):121-122. DOI:10.1016/j.fsigss.2009.08.064