Publications by authors named "Vânia Pereira"

30 Publications

  • Page 1 of 1

Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms.

Forensic Sci Int Genet 2021 Jan 2;50:102411. Epub 2020 Nov 2.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.

A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.
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http://dx.doi.org/10.1016/j.fsigen.2020.102411DOI Listing
January 2021

Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations.

Front Genet 2020 21;11:966. Epub 2020 Aug 21.

DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil.

Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.
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http://dx.doi.org/10.3389/fgene.2020.00966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472784PMC
August 2020

Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry.

Int J Legal Med 2020 Sep 9;134(5):1569-1579. Epub 2020 May 9.

DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.

Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.
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http://dx.doi.org/10.1007/s00414-020-02307-yDOI Listing
September 2020

Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study.

Forensic Sci Int Genet 2020 05 5;46:102258. Epub 2020 Feb 5.

Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Brazil.

The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.
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http://dx.doi.org/10.1016/j.fsigen.2020.102258DOI Listing
May 2020

Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel.

Forensic Sci Int Genet 2020 01 17;44:102154. Epub 2019 Oct 17.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; Department of Mathematical Sciences, Aalborg University, DK-9220 Aalborg East, Denmark.

We compared the efficiency of the freely available software GenoGeographer that includes a z-score based analysis with that of a naïve method based on the maximal likelihoods of 164 of the 165 ancestral informative markers (AIM) that are included in the commercially available kit Precision ID Ancestry Panel from Thermo Fisher Scientific. The AIM profiles were obtained by investigations with the Precision ID Ancestry Panel in our laboratory and from SNP data in the literature and publically available databases. We established eight well-defined AIM reference population data sets from 3603 AIM profiles. Six reference populations with profiles from multiple populations (Sub-Saharan Africa, North Africa, Middle East, Europe, South/Central Asia, East Asia), and two populations with individuals with admixed ancestry (Somalia and Greenland). By means of GenoGeographer and naïve calculations of the maximal likelihoods, 566 AIM profiles from individuals that were not included in the reference populations and expected to belong to one of the eight reference populations were tested. An initial standard z-score based test with GenoGeographer demonstrated that 22.4% of the individuals could not be assigned to any of the reference populations. Among the remaining 77.6% of the individuals, 83.6% were assigned to the reference population that was concordant with the specified populations of origin of the individuals, 8.2% had ambiguous assignments because they could belong to both the specified population of origin and one or more of the other populations, and 8.2% were assigned to a reference population that was discordant from the specified population of origin. A naïve assignment based on the maximal likelihood resulted in 78.1% concordant and 21.9% discordant assignments. The results demonstrate that the z-score analysis with GenoGeographer can reduce the error rate with a factor of almost three compared with that of the naïve estimation based on the maximal likelihoods of the AIM profiles. The Precision ID Ancestry Panel is a useful kit for the assignment of ancestry of the eight investigated populations that included two admixed populations. More AIMs with better discrimination and more data on the distribution of AIMs in relevant populations are needed to improve the efficiency of genogeographic prediction with AIMs on a worldwide basis.
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http://dx.doi.org/10.1016/j.fsigen.2019.102154DOI Listing
January 2020

Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs.

Eur J Hum Genet 2019 12 8;27(12):1885-1893. Epub 2019 Jul 8.

Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.

The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.
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http://dx.doi.org/10.1038/s41431-019-0466-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6871633PMC
December 2019

Sequencing of mitochondrial genomes using the Precision ID mtDNA Whole Genome Panel.

Electrophoresis 2018 11 6;39(21):2766-2775. Epub 2018 Aug 6.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Massively parallel sequencing offers a fast and cost-effective method for sequencing of the whole mtDNA genome. The Precision ID mtDNA Whole Genome Panel amplifies the entire mtDNA genome in two multiplex PCRs with 81 primer sets using the Ion AmpliSeq™ technology. In this study, the performance of the panel was evaluated by testing different amplification methods (two-in-one or conservative), the number of PCR cycles (21, 23, and 25), and different reaction volumes (recommended volume or half-volume). Furthermore, a dilution series, controlled mtDNA mixtures, and casework samples were also sequenced. The normalised read depths of the individual fragments were highly consistent irrespectively of the amplification methods or reaction volumes used. The sequencing output matched the mixture ratios of the controlled mtDNA mixtures indicating that the sequencing results were a loyal representation of the input DNA. Complete mtDNA profiles were generated from <10 pg genomic DNA. Seven fragments with relatively low read depths and large variations in read depth were identified. One of these fragments covered part of the control region and the hypervariable region II.
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http://dx.doi.org/10.1002/elps.201800088DOI Listing
November 2018

Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog vocalizations.

PeerJ 2018 31;6:e4813. Epub 2018 May 31.

Laboratório Multiusuário de Bioacústica (LMBio) e Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

Background: Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny.

Methods: Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions) for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, . We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties.

Results And Discussion: We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of is composed of 3-18 short unpulsed notes (mean of 13 ms long), presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature, while the second is usually related to species-recognition process. Here we review and expand the acoustic knowledge of the subfamily Lophyohylinae, highlighting areas and species for future research.
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http://dx.doi.org/10.7717/peerj.4813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985149PMC
May 2018

Oral Health of Portuguese Children with Type 1 Diabetes: A Multiparametric Evaluation.

J Clin Pediatr Dent 2018;42(3):231-235. Epub 2018 Apr 26.

Objective: To perform a multiparametric evaluation of the oral health of 36 children with type 1 diabetes.

Study Design: A group of type 1 diabetic children and a sex-age-matched control group were formed. Seven parameters were evaluated: probing depth, bleeding on probing, plaque index (O'Laery index), calculus index (according to Ramfjord), dental caries (using ICDAS), salivary pH and unstimulated salivary flow rate. Statistical analysis was performed and the significance level was set at 5%.

Results: Both groups consisted of 36 children with a mean age of 13 years. With regard to bleeding on probing, plaque index and calculus index, higher values were obtained in the diabetic group and the differences between groups were statistically significant for all three parameters. Concerning dental caries and salivary parameters, there were no significant differences between groups. However, a statistically significant correlation between salivary parameters and metabolic control was found.

Conclusion: This study suggests that type 1 diabetic children are associated with some risk factors related to periodontal disease and dental caries. The proven relationship between diabetes and oral health complications imposes the need for these patients to be integrated into preventive dental programs from a young age.
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http://dx.doi.org/10.17796/1053-4628-42.3.12DOI Listing
August 2018

Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel.

Forensic Sci Int Genet 2018 03 6;33:106-109. Epub 2017 Dec 6.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p<0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p<0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P<0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.
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http://dx.doi.org/10.1016/j.fsigen.2017.12.004DOI Listing
March 2018

Genomic and immunohistochemical characterisation of a lacrimal gland oncocytoma and review of literature.

Oncol Lett 2017 Oct 3;14(4):4176-4182. Epub 2017 Aug 3.

Department of Pathology, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark.

The aim of the present study was to report the genetic and immunohistochemical profile of a rare case of lacrimal gland oncocytoma. A 20-year-old male underwent magnetic resonance imaging (MRI) due to viral encephalitis. Notably, the MRI revealed a multicystic tumor in the left lacrimal gland. A lateral orbitotomy was performed and the tumor was completely excised. Four months following surgery, the patient was free of symptoms. Histopathologically, the tumor was composed of large, eosinophilic and polyhedral cells with small round nuclei. The tumor cells stained strongly for antimitochondrial antibody MU213-UC, cytokeratin (CK) 5/6, CK 7, CK 17, CK 8/18 and CK 19. The final diagnosis was an oncocytoma of the lacrimal gland without any signs of malignancy. Array-based comparative genomic hybridisation demonstrated a gain of one copy of chromosome 8 and loss of one copy of chromosome 22 as the sole genomic imbalances. These chromosomal alterations have not previously been identified in oncocytoma and may be specific to lacrimal gland oncocytoma. Sequencing of the mitochondrial genome demonstrated multiple alterations of the NADH-ubiquinone oxidoreductase chain 5 (ND5) gene involved in mitochondrial oxidative phosphorylation. This may support the notion of a common genetic background of oncocytic lesions in the lacrimal gland and other anatomical sites.
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http://dx.doi.org/10.3892/ol.2017.6713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604129PMC
October 2017

Perspectives on invasive amphibians in Brazil.

PLoS One 2017 22;12(9):e0184703. Epub 2017 Sep 22.

Laboratório Multiusuário de Bioacústica (LMBio) and Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

Introduced species have the potential to become invasive and jeopardize entire ecosystems. The success of species establishing viable populations outside their original extent depends primarily on favorable climatic conditions in the invasive ranges. Species distribution modeling (SDM) can thus be used to estimate potential habitat suitability for populations of invasive species. Here we review the status of six amphibian species with invasive populations in Brazil (four domestic species and two imported species). We (i) modeled the current habitat suitability and future potential distribution of these six focal species, (ii) reported on the disease status of Eleutherodactylus johnstonei and Phyllodytes luteolus, and (iii) quantified the acoustic overlap of P. luteolus and Leptodactylus labyrinthicus with three co-occurring native species. Our models indicated that all six invasive species could potentially expand their ranges in Brazil within the next few decades. In addition, our SDMs predicted important expansions in available habitat for 2 out of 6 invasive species under future (2100) climatic conditions. We detected high acoustic niche overlap between invasive and native amphibian species, underscoring that acoustic interference might reduce mating success in local frogs. Despite the American bullfrog Lithobates catesbeianus being recognized as a potential reservoir for the frog-killing fungus Batrachochytrium dendrobatidis (Bd) in Brazil, we did not detect Bd in the recently introduced population of E. johnstonei and P. luteolus in the State of São Paulo. We emphasize that the number of invasive amphibian species in Brazil is increasing exponentially, highlighting the urgent need to monitor and control these populations and decrease potential impacts on the locally biodiverse wildlife.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184703PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609743PMC
October 2017

Analysis of ancestry informative markers in three main ethnic groups from Ecuador supports a trihybrid origin of Ecuadorians.

Forensic Sci Int Genet 2017 11 14;31:29-33. Epub 2017 Aug 14.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Ancestry inference is traditionally done using autosomal SNPs that present great allele frequency differences among populations from different geographic regions. These ancestry informative markers (AIMs) are useful for determining the most likely biogeographic ancestry or population of origin of an individual. Due to the growing interest in AIMs and their applicability in different fields, commercial companies have started to develop AIM multiplexes targeted for Massive Parallel Sequencing platforms. This project focused on the study of three main ethnic groups from Ecuador (Kichwa, Mestizo, and Afro-Ecuadorian) using the Precision ID Ancestry panel (Thermo Fisher Scientific). In total, 162 Ecuadorian individuals were investigated. The Afro-Ecuadorian and Mestizo showed higher average genetic diversities compared to the Kichwa. These results are consistent with the highly admixed nature of the first two groups. The Kichwa showed the highest proportion of Native Amerindian (NAM) ancestry relative to the other two groups. The Mestizo had an admixed ancestry of NAM and European with a larger European component, whereas the Afro-Ecuadorian were highly admixed presenting proportions of African, Native Amerindian, and European ancestries. The comparison of our results with previous studies based on uniparental markers (i.e. Y chromosome and mtDNA) highlighted the sex-biased admixture process in the Ecuadorian Mestizo. Overall, the data generated in this work represent one important step to assess the application of ancestry inference in admixed populations in a forensic context.
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http://dx.doi.org/10.1016/j.fsigen.2017.08.012DOI Listing
November 2017

Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers.

Forensic Sci Int Genet 2017 05 24;28:138-145. Epub 2017 Feb 24.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.

The application of massive parallel sequencing (MPS) methodologies in forensic genetics is promising and it is gradually being implemented in forensic genetic case work. One of the major advantages of these technologies is that several traditional electrophoresis assays can be combined into one single MPS assay. This reduces both the amount of sample used and the time of the investigations. This study assessed the utility of the Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) in forensic genetics. This assay was developed for the Ion Torrent PGM™ System and genotypes 165 ancestry informative SNPs. The performance of the assay and the accompanying software solution for ancestry inference was assessed by typing 142 Danes and 98 Somalis. Locus balance, heterozygote balance, and noise levels were calculated and future analysis criteria for crime case work were estimated. Overall, the Precision ID Ancestry Panel performed well, and only minor changes to the recommended protocol were implemented. Three out of the 165 loci (rs459920, rs7251928, and rs7722456) had consistently poor performance, mainly due to misalignment of homopolymeric stretches. We suggest that these loci should be excluded from the analyses. The different statistical methods for reporting ancestry in forensic genetic case work are discussed.
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http://dx.doi.org/10.1016/j.fsigen.2017.02.013DOI Listing
May 2017

A study of the peopling of Greenland using next generation sequencing of complete mitochondrial genomes.

Am J Phys Anthropol 2016 12 24;161(4):698-704. Epub 2016 Aug 24.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark.

Objectives: The Greenlandic population history is characterized by a number of migrations of people of various ethnicities. In this work, the analysis of the complete mtDNA genome aimed to contribute to the ongoing debate on the origin of current Greenlanders and, at the same time, to address the migration patterns in the Greenlandic population from a female inheritance demographic perspective.

Methods: We investigated the maternal genetic variation in the Greenlandic population by sequencing the whole mtDNA genome in 127 Greenlandic individuals using the Illumina MiSeq platform.

Results: All Greenlandic individuals belonged to the Inuit mtDNA lineages A2a, A2b1, and D4b1a2a1. No European haplogroup was found.

Discussion: The mtDNA lineages seem to support the hypothesis that the Inuit in Greenland are descendants from the Thule migration. The results also reinforce the importance of isolation and genetic drift in shaping the genetic diversity in Greenlanders. Based on the mtDNA sequences, the Greenlandic Inuit are phylogenetically close to Siberian groups and Canadian Inuit.
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http://dx.doi.org/10.1002/ajpa.23074DOI Listing
December 2016

Importance of nonsynonymous OCA2 variants in human eye color prediction.

Mol Genet Genomic Med 2016 Jul 11;4(4):420-30. Epub 2016 Mar 11.

Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark.

Background: The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single-nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G.

Methods: In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region.

Results: We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R (2) = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R (2) = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008).

Conclusion: Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.
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http://dx.doi.org/10.1002/mgg3.213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947861PMC
July 2016

Mosaic maternal ancestry in the Great Lakes region of East Africa.

Hum Genet 2015 Sep 19;134(9):1013-27. Epub 2015 Jul 19.

Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
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http://dx.doi.org/10.1007/s00439-015-1583-0DOI Listing
September 2015

Peopling of the North Circumpolar Region--insights from Y chromosome STR and SNP typing of Greenlanders.

PLoS One 2015 30;10(1):e0116573. Epub 2015 Jan 30.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

The human population in Greenland is characterized by migration events of Paleo- and Neo-Eskimos, as well as admixture with Europeans. In this study, the Y-chromosomal variation in male Greenlanders was investigated in detail by typing 73 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 17 Y-chromosomal short tandem repeats (Y-STRs). Approximately 40% of the analyzed Greenlandic Y chromosomes were of European origin (I-M170, R1a-M513 and R1b-M343). Y chromosomes of European origin were mainly found in individuals from the west and south coasts of Greenland, which is in agreement with the historic records of the geographic placements of European settlements in Greenland. Two Inuit Y-chromosomal lineages, Q-M3 (xM19, M194, L663, SA01 and L766) and Q-NWT01 (xM265) were found in 23% and 31% of the male Greenlanders, respectively. The time to the most recent common ancestor (TMRCA) of the Q-M3 lineage of the Greenlanders was estimated to be between 4,400 and 10,900 years ago (y. a.) using two different methods. This is in agreement with the theory that the North Circumpolar Region was populated via a second expansion of humans in the North American continent. The TMRCA of the Q-NWT01 (xM265) lineage in Greenland was estimated to be between 7,000 and 14,300 y. a. using two different methods, which is older than the previously reported TMRCA of this lineage in other Inuit populations. Our results indicate that Inuit individuals carrying the Q-NWT01 (xM265) lineage may have their origin in the northeastern parts of North America and could be descendants of the Dorset culture. This in turn points to the possibility that the current Inuit population in Greenland is comprised of individuals of both Thule and Dorset descent.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116573PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312058PMC
October 2015

Nitrite reductase activity of rat and human xanthine oxidase, xanthine dehydrogenase, and aldehyde oxidase: evaluation of their contribution to NO formation in vivo.

Biochemistry 2015 Jan 8;54(3):685-710. Epub 2015 Jan 8.

UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal.

Nitrite is presently considered a NO "storage form" that can be made available, through its one-electron reduction, to maintain NO formation under hypoxia/anoxia. The molybdoenzymes xanthine oxidase/dehydrogenase (XO/XD) and aldehyde oxidase (AO) are two of the most promising mammalian nitrite reductases, and in this work, we characterized NO formation by rat and human XO/XD and AO. This is the first characterization of human enzymes, and our results support the employment of rat liver enzymes as suitable models of the human counterparts. A comprehensive kinetic characterization of the effect of pH on XO and AO-catalyzed nitrite reduction showed that the enzyme's specificity constant for nitrite increase 8-fold, while the Km(NO2(-)) decrease 6-fold, when the pH decreases from 7.4 to 6.3. These results demonstrate that the ability of XO/AO to trigger NO formation would be greatly enhanced under the acidic conditions characteristic of ischemia. The dioxygen inhibition was quantified, and the Ki(O2) values found (24.3-48.8 μM) suggest that in vivo NO formation would be fine-tuned by dioxygen availability. The potential in vivo relative physiological relevance of XO/XD/AO-dependent pathways of NO formation was evaluated using HepG2 and HMEC cell lines subjected to hypoxia. NO formation by the cells was found to be pH-, nitrite-, and dioxygen-dependent, and the relative contribution of XO/XD plus AO was found to be as high as 50%. Collectively, our results supported the possibility that XO/XD and AO can contribute to NO generation under hypoxia inside a living human cell. Furthermore, the molecular mechanism of XO/AO-catalyzed nitrite reduction was revised.
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http://dx.doi.org/10.1021/bi500987wDOI Listing
January 2015

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.

Biotechniques 2014 Aug 1;57(2):91-4. Epub 2014 Aug 1.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.
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http://dx.doi.org/10.2144/000114200DOI Listing
August 2014

Biodegradation of ochratoxin A by Pediococcus parvulus isolated from Douro wines.

Int J Food Microbiol 2014 Oct 23;188:45-52. Epub 2014 Jul 23.

CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.

Lactic acid bacteria (LAB) are a promising solution to reduce exposure to dietary mycotoxins because of the unique mycotoxin decontaminating characteristic of some LAB. Ochratoxin A (OTA) is one of the most prominent mycotoxins found in agricultural commodities. The present work reports on the ability of Pediococcus parvulus strains that were isolated from Douro wines that spontaneously underwent malolactic fermentation to detoxify OTA. These strains were identified and characterised using a polyphasic approach that employed both phenotypic and genotypic methods. When cultivated on OTA-supplemented MRS media, OTA was biodegraded into OTα by certain P. parvulus strains. The presence of OTα was confirmed using LC-MS/MS. The conversion of OTA into OTα indicates that the OTA amide bond was hydrolysed by a putative peptidase. The rate of OTA biodegradation was found to be dependent on the inoculum size and on the incubation temperature. Adsorption assays with dead P. parvulus cells showed that approximately 1.3%±1.0 of the OTA was adsorbed onto cells wall, which excludes this mechanism in the elimination of OTA by strains that degrades OTA. Under optimum conditions, 50% and 90% of OTA were degraded in 6 and 19h, respectively. Other LAB strains that belonged to different species were tested but did not degrade OTA. OTA biodegradation by P. parvulus UTAD 473 was observed in grape must. Because some P. parvulus strains have relevant probiotic properties, the strains that were identified could be particularly relevant to food and feed applications to counteract the toxic effects of OTA.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2014.07.019DOI Listing
October 2014

The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers.

Eur J Hum Genet 2015 Feb 7;23(2):245-51. Epub 2014 May 7.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø, Denmark.

The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.
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http://dx.doi.org/10.1038/ejhg.2014.90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297915PMC
February 2015

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers.

Am J Phys Anthropol 2012 Jul 11;148(3):389-94. Epub 2012 May 11.

Institute of Molecular Pathology and Immunology of the University of Porto, Portugal.

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.
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http://dx.doi.org/10.1002/ajpa.22061DOI Listing
July 2012

Analysis of 12 X-STRs in Greenlanders, Danes and Somalis using Argus X-12.

Int J Legal Med 2012 Jan 2;126(1):121-8. Epub 2011 Sep 2.

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

X-chromosome markers have become a useful set of markers of choice when certain complex kinship cases need to be unravelled. The Argus X-12 kit allows the co-amplification in a single PCR reaction of 12 X-chromosome short tandem repeats located in four linkage groups. A number of 507 unrelated individuals from Greenland, Denmark and Somalia together with two generation families were typed using the Argus X-12 kit. Silent alleles for the DXS10148 and DXS10146 systems were observed in males, mostly from Somalia. High levels of intrapopulation variability and therefore high forensic parameter values were calculated for the three studied populations. The population in Greenland showed a significantly lower intrapopulation variability and a high genetic differentiation compared with 13 other populations. Significant levels of linkage disequilibrium were observed between markers belonging to the same linkage group, mainly in the populations in Greenland and Somalia. Family studies allowed the calculation of mutation and recombination frequencies. A higher male versus female mutation rate was obtained, with an average value of 3.3 × 10(-3). Recombination fraction calculations performed on two generation families showed, as previously described, a not complete independence between X-chromosome linkage groups 3 and 4.
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http://dx.doi.org/10.1007/s00414-011-0609-yDOI Listing
January 2012

A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR.

Int J Legal Med 2012 Jan 30;126(1):97-105. Epub 2011 Jun 30.

Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.

Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers.
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http://dx.doi.org/10.1007/s00414-011-0593-2DOI Listing
January 2012

Study of 25 X-chromosome SNPs in the Portuguese.

Forensic Sci Int Genet 2011 Aug 30;5(4):336-8. Epub 2010 Oct 30.

Faculty of Sciences, University of Porto, Porto, Portugal.

The importance of X-chromosome markers in individual identifications, population genetics, forensics and kinship testing is getting wide recognition. In this work, we studied the distributions of 25 X-chromosome single nucleotide polymorphisms (X-SNPs) in population samples from Northern, Central and Southern Portugal (n=305). The data were also compared with previous data from the Mediterranean area confirming a general genetic homogeneity among populations in the region. The X-SNP distribution in the three Portuguese regional samples did not show any significant substructure and the X-SNP distributions did not differ significantly from those of the majority of Mediterranean populations.
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http://dx.doi.org/10.1016/j.fsigen.2010.10.004DOI Listing
August 2011

Genetic characterization of uniparental lineages in populations from Southwest Iberia with past malaria endemicity.

Am J Hum Biol 2010 Sep-Oct;22(5):588-95

Department of Zoology and Anthropology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal.

Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD--Coruche, Pias, and Alcacer do Sal--to evaluate if their present-day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty-five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y-chromosome markers. Results were then compared with data from other Portuguese and non-Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub-Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub-Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia.
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http://dx.doi.org/10.1002/ajhb.21049DOI Listing
January 2011

A framework for the development of STR genotyping in domestic animal species: characterization and population study of 12 canine X-chromosome loci.

Electrophoresis 2010 Jan;31(2):303-8

Instituto de Patologia e Imunologia da Universidade do Porto, Porto, Portugal.

This study reports the methodology used to search, select and characterize STR loci on the canine X chromosome using publicly available genome resources and following the current guidelines for human and non-human forensic testing. After several rounds of selection, 12 X-STR markers were optimized for simultaneous co-amplification in a single PCR, and genetic profiles were determined in a sample of 103 unrelated dogs. Mendelian inheritance was verified and mutation rates were assessed using family groups. Alleles that varied in size were sequenced to create a standardized nomenclature proposal based on the number of repeats. All loci conformed to Hardy-Weinberg expectations. The resulting panel showed high forensic efficiency, presenting high values of power of discrimination (in males and females) and mean exclusion chance, both in trios involving female offspring and in duos composed of dam and male offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal species. As an increasing number of reference genomes become available, convenient tools for individual identification and parentage testing based on STR loci selected from autosomes or sex chromosomes' sequences may be created following this strategy.
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http://dx.doi.org/10.1002/elps.200900389DOI Listing
January 2010

The Karimojong from Uganda: genetic characterization using an X-STR decaplex system.

Forensic Sci Int Genet 2009 Sep 19;3(4):e127-8. Epub 2008 Dec 19.

IPATIMUP, Institute of Pathology and Molecular Immunology, University of Porto, 4200-465 Porto, Portugal.

The Karimojong, an African group from the Karamoja region of Northeast Uganda, were genetically analysed using a decaplex system for X chromosome short tandem repeats (X-STRs). A total of 255 individuals (117 males and 138 females) were genotyped for the following loci: DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902 and DXS6789. Allele frequencies and parameters for forensic evaluation were calculated for each STR. No association was found between any pairs of loci studied. DXS6789 was the most polymorphic marker in this sample, followed by DXS6809, with gene diversities of 84.79% and 83.94%, respectively. The less discriminating locus observed was DXS7133, with a gene diversity of 39.79%. High overall values of power of discrimination were obtained for female (1 in 1.8 x 10(10)) and male samples (1 in 1.6 x 10(6)), as well as high power of exclusion in father/mother/daughter trios (99.9997%), in father daughter duos (99.9862%) and in half sisters with same father (99.0331%). These results confirm the potential of this 10-plex in parentage testing and in human identification.
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http://dx.doi.org/10.1016/j.fsigen.2008.10.009DOI Listing
September 2009

A new autosomal STR nineplex for canine identification and parentage testing.

Electrophoresis 2009 Jan;30(2):417-23

IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.

A single multiplex PCR assay capable of simultaneously amplifying nine canine-specific autosomal STR markers (FH3210, FH3241, FH2004, FH2658, FH4012, REN214L11, FH2010, FH2361 and the newly described C38) was developed for individual identification and parentage testing in domestic dogs. In order to increase genotyping efficiency, amplicon sizes were optimized for a 90-350 bp range, with fluorescently labelled primers for use in Applied Biosystems, Inc., platforms. The performance of this new multiplex system was tested in 113 individuals from a case-study population and 12 random dogs from mixed-breed origin. Co-dominant inheritance of STR alleles was investigated in 101 father, mother and son trios. Expected heterozygosity values vary between 0.5648 for REN214L11 and 0.9050 for C38. The high level of genetic diversity observed for most markers provides this multiplex with a very high discriminating power (matching probability=1.63/10(10) and matching probability among siblings=4.9/10(3)). Allele sequences and a proposal for standardized nomenclature are also herein presented, aiming at implementing the use of this system in forensic DNA typing and population genetic studies. This approach resulted in an optimized and well-characterized canine DNA genotyping system that is highly performing and straightforward to integrate and employ routinely. Although this STR multiplex was developed for use and tested in a case-study population, the Portuguese breed Cão de Gado Transmontano, it proved to be useful for general identification purposes or parentage testing.
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http://dx.doi.org/10.1002/elps.200800307DOI Listing
January 2009