Monteiro, B

Pontes, ML

Prata, MJ

Portuguese

Open Repository of the University of Porto

NGM Select STR markers in a population sample of Ukrainian immigrants living in Portugal.

Repositório Aberto da Universidade do Porto

See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/330468271NGM Select STR markers in a population sample of Ukrainian immigrantsliving in PortugalArticle · January 2019CITATIONS0READS873 authors:Some of the authors of this publication are also working on these related projects:Less is more – substrate reduction therapy for mucopolysaccharidoses through RNAi View projectAutosomal SNPs in Forensic Genetics View projectM Lurdes PontesNational Institute of Legal Medicine45 PUBLICATIONS   409 CITATIONS   SEE PROFILEBruno MonteiroUniversity of Porto1 PUBLICATION   0 CITATIONS   SEE PROFILEMaria PrataUniversity of Porto130 PUBLICATIONS   2,774 CITATIONS   SEE PROFILEAll content following this page was uploaded by Bruno Monteiro on 07 February 2019.The user has requested enhancement of the downloaded file.Introduction Since 2000, and especially during the  rst decade, the number of Ukrainian immigrants living in Portugal increased as much as 213%. In 2011, Ukrainian immigrants were the third biggest community of immigrants living in Portugal, constituting 9% (33 790 individuals) of the total immigrants recorded in the Portuguese 2011 Census [1]. Thus, the aim of this work was to characterize the Ukrainian community residing in Portugal for 16 autosomal STRs included in the NGM Select kit, to evaluate whether population structure could represent a concern in the forensic setting. Viewing that, population comparisons were further performed to evaluate how this sample of Ukrainians complied with the patterns of genetic diversity reported for other populations. Material/Methods Extraction: DNA was extracted from buccal cell swabs by the Chelex method [2].Quanti cation: DNA quanti cation was achieved by real-time PCR using the Quanti lerTM Human DNA Quanti cation Kit (AB) and the ABI PRISM® Sequence Detection System (AB). PCR Ampli cation: The extracted DNA was ampli ed using the NGM Select Ampli cation Kit (Applied Biosystem, Foster City, CA) according to the manufacturer's recommendations, in a GeneAmp 9700 PCR system (Applied Biosystem, Foster City, CA). Electrophoresis: PCR products were analyzed by capillary electrophoresis in an Applied Biosystems 3500 Genetic analyzer (Foster City, CA). All samples were analyzed at least twice and only results doubly con rmed were considered. Data analysis: Allele assignment and designation was carried out by comparison with reference sequenced ladders and was performed with the GeneMapper ID-X v1.4 analysis software. Arlequin software v.3.5.2.2 [3] was used to calculate allele frequencies, locus by locus population pairwise genetic distance (F ), expected heterozygosity ST(He), observed heterozygosity (Ho) and to test departures from Hardy–Weinberg equilibrium. Power of Discrimination and Matching Probability were calculated using GenAlEx v6.503 software package [4]. Probability of Exclusion, combined probability of paternity exclusion, polymorphic information content and paternity index were obtained with Exel using the formulas described in the literature [5]. Average pairwise genetic distance (FST) over all loci was calculated with the Poptrew software [6] and submitted to Multidimensional Scaling Analysis using the R v3.3.2 software [7], and then the yielded coordinates were used to construct the corresponding graphs in Excel. Populations used: The sample studied consisted in a total of 72 Ukrainian immigrants living in Portugal who gave informed consent to participate in the study under anonymized identi cation. The number of individuals analyzed is relatively small, however it is representative of the total of Ukrainian immigrants living in Portugal, since the number of individuals corresponds to 0,32% of the total population of 10.6 million Portuguese [1]. For the comparative analysis, frequency data regarding the loci included in the NGM Select kit was recruited from the literature for samples from Portugal [8] and 15 additional worldwide populations namely Lithuania, Albania, Slovenia, Iraq, Turkey [9], Bosnia and Herzegovina, Germany [10], Netherlands [11], Spain [12], Denmark, Greenland [13], Kazakhstan [14] and Somalia [13] as well as from the AmaXhosa, a bantu-speaking group of South Africa [15], and the Han from the Fujian province of China [16].Locus by locus F  comparisons for Ukraine with the other STpopulations were performed. The F  values and respective p vales, ST2the matrix of F  and (δμ)  distances for all the populations and the STMDS graph for F  data were also obtained (data not shown). STResults and discussion Allele frequencies, heterozygosities and forensic statistic parameters for the 16 STR loci investigated in the Ukrainians living in Portugal are shown in Figure 1.NGM SELECT STR MARKERS IN A POPULATION SAMPLE OF UKRAINIAN IMMIGRANTS LIVING IN PORTUGALOriginal Research PaperBruno Monteiro  Faculty of Sciences of the University of Porto, FCUP, Porto, PortugalMJ Prata*Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal and Institute of Molecular Pathology and Immunology of the University of Porto, IPATIMUP, Porto, Portugal *cL Pontes* National Institute of Legal Medicine and Forensic Sciences, INMLCF, Portugal *Corresponding AuthorForensic ScienceIn this work, a sample of Ukrainians living in Portugal was characterized for the autosomal markers included in the NGM Select kit, a kit primarily used in forensic casework analysis. The estimated values of heterozygosity, combined power of discrimination (PDc) and combined probability of paternity exclusion (PEc), demonstrated the high level of discrimination between Ukrainians afforded by this kit, thereby making it very informative and consequently an important asset in forensic routine. Interpopulation comparisons showed signi cant genetic differentiation between the sample of Ukrainians and populations from non-European regions. Within Europe, low population structure, modestly related with geography, was detected with this kit. These  ndings pinpoint the prospective use of the NGM Select kit mainly in population genetic studies addressing the genetic differentiation between continental populations. ABSTRACTKEYWORDS : Short Tandem Repeats; Population data; Ukrainians; Intrapopulation and interpopulation comparisons96X GJRA - GLOBAL JOURNAL FOR RESEARCH ANALYSISIF : 5.156 | IC Value : 85.78VOLUME-8, ISSUE-1, JANUARY-2019 • ISSN No 2277 - 8160Figure 1: Forensic and populational parameters obtained for a sample of Ukrainians living in Portugal (n=72)   X 97GJRA - GLOBAL JOURNAL FOR RESEARCH ANALYSISIF : 5.156 | IC Value : 85.78 VOLUME-8, ISSUE-1, JANUARY-2019 • ISSN No 2277 - 8160No signi cant deviations from the Hardy–Weinberg equilibrium were found, even for the locus D18S51 (p = 0.040), once after applying the Bonferroni´s correction for multiple testing (adjusted p = 0.0031) the associated p value lost statistical signi cance. The He values for each locus were all high, ranging from 0.7458 in the D10S1248 locus to as much as 0.9478 in the SE33. Accordingly, the PIC values were also very elevated, usually ≥0.7, except the D16S539 (0.65153), which was also one of the least heterozygous locus. The paternity index (PI) varied from 1.7 (not surprisingly at D10S1248) to 9 (at SE33, as predictable), while the 16 STR  loci afforded a combined  paternity index of 1.1 ×10⁸ . The combined power of discrimination (PDc) and the combined probability of paternity exclusion (PEc) for all the loci are 0.999999999999999999998 and 0.999999992, respectively, illustrating the usefulness of this 16-STR multiplex for kinship analysis in the population sample scrutinized.Here we present 5 additional STR loci (D10S1248, D22S1045, D2S441, D1S1656 and D12S391) from the European Standard Set STR (ESS), who were posteriorly added in 2009. These markers are designated of mini-STR, because of their amplicon size of 70-180 bp. They provide competitive ability when compared to SNPs or INDELs, for the analysis of degraded samples. The inclusion of these markers maximize the sensibility of degraded DNA analysis, improve the discrimination power and the quality of the results [17].These  ve loci have not been described in the literature until know, and their inclusion in this study contributes signi cantly to the observed high discrimination power. Two of these loci (D1S1656 and D12S391) have high vales of He and PD, being the most informative loci, after SE33. These loci are, inclusively, more informative than the ones, previously described in the literature (D21S11, FGA, D18S51 and D2S1338), as very informative [18]. The loci previously described in the literature, as very informative, were also very informative in our analysis. The SE33 locus was already described in the literature [18]; however, we present also the allelic frequencies and forensic parameters of the Ukrainian sample for the SE33 locus, who is the most informative locus of this kit. The computed locus-by-locus F  distances involving the Ukrainians STliving in Portugal and other populations, revealed the clear predominance of signi cant differences between Ukrainians and population from regions far from Europe, like Greenland, Asia (Kazakhstan, China) and Africa (South Africa, Somalia). Distances of Ukrainians comparatively to Middle Eastern populations (from Iraq and Turkey) were higher than compared to European populations, but still none of them reached statistical signi cance. The differentiation of Ukrainians relatively to other Europeans was very low and by large non-signi cant, including comparatively to the Portuguese, a result that alleviates the concerns that detection of substructure could pose from the forensic perspective.These  ndings translate the ability of the set of markers contained in NGM Select kit to discriminate sharply between continental populations, ability that, however, is overtly insufficient to discriminate between European populations, likely because overall Europe is characterized by high level of genetic homogeneity [19]. The Multidimensional Scaling graph based on the matrix of F  value STfor a total of 16 populations (Fig 2), captured well this wide pattern. They exhibit the clear clustering of European populations apart from non-European ones, while also reveal that within Europe the distribution of population diversity is barely structured and only modestly related to geography. Previously, the correspondence between genetic and geographic distances in Europe was clearly observed in studies based on both dense number of loci and dense geographic sampling [19]. Thus, is quite understandable that the resolution afforded by the limited set of markers here studied was not enough to apprehend the broad structure of special variation of diversity among European populations.Figure 2: Multidimensional scaling (MDS) graph for FST values obtained with the matrix of the genetic distance (for 15 of the 16 markers) for the populations compared. REFERENCES[1]  Instituto Nacional de Estatística, S. P. (2011). A população estrangeira em Portugal.[2]  Walsh, P. S., Metzger, D. A., & Higushi, R. (2013). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10(4): 506-13 (April 1991). Biotechniques, 54(3), 134-139. [3]  Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour, 10(3), 564-567. [4]  Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics, 28(19), 2537-2539. [5]  Huston, A. K. (1998). Statistical Analysis of STR Data1(3), 14-15. Delghandi, M., Branting, B. J., & Jorgensen, L. (2001). Evaluation of a Quadruplex Short Tandem Repeat System (HUMVWA31/A, HUMD11S554, HUMAPOI1, and HUMACTBP2 loci) for Forensic Identity Testing, Con dent Typing of Complex Alleles, and Population Databases. Croatian Medical Journal, 42(1), 33–44. [6]  Takezaki, N., Nei, M., & Tamura, K. (2014). POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol Biol Evol, 31(6), 1622-1624.[7]  Team, R. C. (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Retrieved from http://www.R-project.org/[8]   Pontes, M. L., & Pinheiro, M. F. (2012). Population data of the AmpFISTR(R) NGM STR loci in a North of Portugal sample. Forensic Sci Int Genet, 6(5), e127-128. [9]  Poulsen, L., Tomas, C., . . . Morling, N. (2016). NGMSElect and Investigator((R)) Argus X-12 analysis in population samples from Albania, Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet, 22, 110-112. [10]  Welch, L. A., . . . Bastisch, I. (2012). European Network of Forensic Science Institutes (ENFSI): Evaluation of new commercial STR multiplexes that include the European Standard Set (ESS) of markers. Forensic Sci Int Genet, 6(6), 819-826. [11] Westen, A. A., . . . de Knijff, P. (2014). Comparing six commercial autosomal STR kits in a large Dutch population sample. Forensic Science International: Genetics, 10, 55-63. [12]  Garcia, O., . . . Yurrebaso, I. (2012). Population genetic data and concordance study for the kits Identi ler, NGM, PowerPlex ESX 17 System and Investigator ESSplex in Spain. Forensic Sci Int Genet, 6(2), e78-79. [13]  Tomas, C., . . . Morling, N. (2014). Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex(R) ESI 17 and AmpFlSTR(R) NGM SElect in Somalis, Danes and Greenlanders. Forensic Sci Int Genet, 11, e18-21. [14]  Zhang, H., . . . Li, S. (2016). Population genetic analysis of the GlobalFiler STR loci in 748 individuals from the Kazakh population of Xinjiang in northwest China. Int J Legal Med, 130(5), 1187-1189. [15]  Ristow, P. G., Cloete, K. W., & D'Amato, M. E. (2016). GlobalFiler((R)) Express DNA ampli cation kit in South Africa: Extracting the past from the present. Forensic Sci Int Genet, 24, 194-201. [16]  Li, B., Ge, J., Wu, F., Ye, L., Budowle, B., & Chen, Y. (2013). Population genetic analyses of the STR loci of the AmpFlSTR NGM SElect kit for Han population in Fujian Province, China. Int J Legal Med, 127(2), 345-346. [17]  Schneider, P. M. (2009). Expansion of the European Standard Set of DNA database loci-the current situation. Pro les in DNA, 12(1), 6-7. [18] Delghandi, M., Branting, B. J., Jorgensen, L. (2001). Evaluation of a Quadruplex Short Tandem Repeat System (HUMVWA31/A, HUMD11S554, HUMAPOI1, and HUMACTBP2 loci) for Forensic Identity Testing, Con dent Typing of Complex Alleles, and Population Databases. Croatian Medical Journal, 42, 33-44. [19]  Seldin, M. F., . . . Gregersen, P. K. (2006). European Population Substructure: Clustering of Northern and Southern Populations. PLoS Genetics, 2(9), e143. IF : 5.156 | IC Value : 85.78VOLUME-8, ISSUE-1, JANUARY-2019 • ISSN No 2277 - 816098X GJRA - GLOBAL JOURNAL FOR RESEARCH ANALYSISView publication stats

Global Journal For Research Analysis

https://repositorio-aberto.up.pt/bitstream/10216/128649/2/413719.pdf

NGM Select STR markers in a population sample of Ukrainian immigrants living in Portugal.

Abstract

Similar works

Full text

Available Versions

Open Repository of the University of Porto

Repositório Aberto da Universidade do Porto