Weryfikacja markerów insercyjno-delecyjnych (InDels) i mikrosatelitarnych (STR) jako narzędzi pomocniczych do wnioskowania o pochodzeniu populacji słowiańskiej
cytuj
pobierz pliki
RIS BIB ENDNOTEWybierz format
RIS BIB ENDNOTEVerification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry
Data publikacji: 03.2023
Archiwum Medycyny Sądowej i Kryminologii, 2022, Vol. 72 (3), s. 120 - 137
https://doi.org/10.4467/16891716AMSIK.22.015.17393Autorzy
Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry
Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpose, we genotyped Slavic-speaking populations samples from Belarus, the Czech Republic, Poland, Serbia, Ukraine and Russia in 46 InDels and 15 STRs by PCR and capillary electrophoresis and analyzed for between-population differentiation with the use of distance-based methods (FST, principal component analysis and multidimensional scaling). Additionally, we studied a sample from a Polish individual of well-documented genealogy whose biogeographic ancestry had previously been inferred by commercial genomic services using autosomal single nucleotide polymorphisms (SNPs), mitochondrial DNA and Y-SNP markers. For comparative purposes, we used genotype data collected in the “forInDel” browser and allele frequencies from previously published papers. The results obtained for InDels and STRs show that the Slavic populations constitute a genetically homogeneous group, with the exception of the Czechs differing clearly from the other tested populations. The analysis of the known Polish sample in the Snipper application proves the usefulness of the InDel markers on the continental level only. Conversely, microsatellites not only improve prediction, but are also informative if considered as an independent set of ancestry markers.
Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA. Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 2003; 112(4): 387-99.
Phillips C, Prieto L, Fondevila M, Salas A, Gómez-Tato A, Alvarez-Dios J, Alonso A, Blanco-Verea A, Brión M, Montesino M, Carracedo A, Lareu MV. Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One 2009; 4(8): e6583.
Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR. Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 2014; 10: 23-32.
Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 2009; 30(1): 69-78.
Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Borsting C, Johansen P, Fondevila M, Morling N, Schneider P; EUROFORGEN-NoE Consortium, Carracedo A, Lareu MV. Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set. Forensic Sci Int Genet 2014; 11: 13-25.
Pereira V, Freire-Aradas A, Ballard D, Borsting C, Diez V, Pruszkowska-Przybylska P, Ribeiro J, Achakzai NM, Aliferi A, Bulbul O, Carceles MDP, Triki-Fendri S, Rebai A, Court DS, Morling N, Lareu MV, Carracedo Á; EUROFORGEN-NoE Phillips C. Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel. Forensic Sci Int Genet 2019; 42: 260-267.
Pereira R, Phillips C, Pinto N, Santos C, dos Santos SE, Amorim A, Carracedo Á, Gusmao L. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 2012; 7(1): e29684.
Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A; SNPforID Consortium. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 2007; 1: 273-80.
Phillips C, Fernandez-Formoso L, Garcia-Magarinos M, Porras L, Tvedebrink T, Amigo J, Fondevila M, Gomez-Tato A, Alvarez-Dios J, Freire-Aradas A, Gomez-Carballa A, Mosquera-Miguel A, Carracedo A, Lareu MV. Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. Forensic Sci Int Genet 2011; 5(3): 155-69.
Santos C, Phillips C, Oldoni F, Amigo J, Fondevila M, Pereira R, Carracedo Á, Lareu MV. Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. Forensic Sci Int Genet 2015; 17: 75-80.
Rice WR. Analyzing tables of statistical tests. Evolution 1989; 1: 223-225.
Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010; 10(3): 564-7.
Nei M. Molecular evolutionary genetics. New York. Columbia University Press; 1987.
Barbaro A, Phillips C, Formoso LF, Lareu MV, Carracedo Á. Distribution of allele frequencies of 20 STRs loci in a population sample from Calabria, Southern Italy. Forensic Sci Int Genet 2012; 6(5): e137-8.
Hill CR, Duewer DL, Kline MC, Coble MD, Butler JM. U.S. population data for 29 autosomal STR loci. Forensic Sci Int Genet 2013; 7(3): e82-3. Erratum in: Forensic Sci Int Genet 2017; Nov; 31: e36-e40.
García O, Alonso J, Cano JA, García R, Luque GM, Martín P, de Yuso IM, Maulini S, Parra D, Yurrebaso I. Population genetic data and concordance study for the kits Identifiler, NGM, PowerPlex ESX 17 System and Investigator ESSplex in Spain. Forensic Sci Int Genet 2012; Mar; 6(2): e78-9. Erratum in: Forensic Sci Int Genet 2014; 9: 192.
Yurrebaso I, Ajuriagerra JA, Alday A, Lezama I, Pérez JA, Romón E, Uriarte I, García O. Allele frequencies and concordance study between the Identifiler and the PowerPlex ESX17 systems in the Basque Country population. Forensic Sci Int Genet 2011; 5(3): e79-80.
Montelius K, Karlsson AO, Holmlund G. STR data for the AmpFlSTR Identifiler loci from Swedish population in comparison to European, as well as with non-European population. Forensic Sci Int Genet 2008; 2(3): e49-52.
Sánchez-Diz P, Menounos PG, Carracedo A, Skitsa I. 16 STR data of a Greek population. Forensic Sci Int Genet 2008; 2(4): e71-2.
Barbarić L, Ozretić P, Horjan I, Korolija M, Mršić G. Forensic evaluation of the 20 STR loci in the population of Croatia. Forensic Sci Int Genet 2017; 28: e49-e50.
Stanciu F, Popescu OR, Stoian IM. Allele frequencies of 15 STR loci in Moldavia region (NE Romania). Forensic Sci Int Genet 2009; 4(1): e39-40.
Fernandez-Formoso L, Phillips C, Rodriguez A, Calvo R, Barbaro A, Lareu MV, Carracedo Á. Allele frequencies of 20 STRs from Northwest Spain (Galicia). Forensic Sci Int Genet 2012; 6(5): e149-50.
Serga SV, Dombrovskyi IV, Maistrenko OM, Ostapchenko LI, Demydov SV, Krivda RG, Kozeretska IA. Allele frequencies for 15 STR loci in the Ukrainian population. Forensic Sci Int Genet 2017; 29: e40-e41.
Piatek J, Jacewicz R, Ossowski A, Parafiniuk M, Berent J. Population genetics of 15 autosomal STR loci in the population of Pomorze Zachodnie (NW Poland). Forensic Sci Int Genet 2008; 2(3): e41-3.
Hussing C, Bytyci R, Huber C, Morling N, Borsting C. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™DNA Signature Prep Kit. Int J Legal Med 2019; 133(2): 325-334.
Staadig A, Tillmar A. An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis. Forensic Sci Int Genet 2019; 39: 44-49.
Veselinović I, Kubat M, Furac I, Skavić J, Martinović Klarić I, Tasić M. Allele frequencies of the 15 AmpF lSTR Identifiler loci in the population of Vojvodina Province, Serbia and Montenegro. Int J Legal Med 2004; 118(3): 184-6.
Kubat M, Skavić J, Behluli I, Nuraj B, Bekteshi T, Behluli M, Klarić IM, Pericić M. Population genetics of the 15 AmpF lSTR Identifiler loci in Kosovo Albanians. Int J Legal Med 2004; 118(2): 115-8.
Novković T, Panić B, Banjac A, Dekić TK, Tomisić-Kosić I, Vucetić-Dragović A, Stamenković G, Blagojević J, Marjanović D, Pojskić N. Genetic polymorphisms of 15 AmpFlSTR Identifiler loci in a Serbian population. Forensic Sci Int Genet 2010; 4(5): e149-50.
Simková H, Faltus V, Marvan R, Pexa T, Stenzl V, Broucek J, Horínek A, Mazura I, Zvárová J. Allele frequency data for 17 short tandem repeats in a Czech population sample. Forensic Sci Int Genet 2009; 4(1): e15-7.
Ossowski A, Diepenbroek M, Szargut M, Zielińska G, Jędrzejczyk M, Berent J, Jacewicz R. Population analysis and forensic evaluation of 21 autosomal loci included in GlobalFiler™PCR Kit in Poland. Forensic Sci Int Genet 2017; 29: e38-e39.
Jacewicz R, Jedrzejczyk M, Ludwikowska M, Berent J. Population database on 15 autosomal STR loci in 1000 unrelated individuals from the Lodz region of Poland. Forensic Sci Int Genet 2008; 2(1): e1-3.
Petrić G, Drašković D, Zgonjanin-Bosić D, Budakov B, Veselinović I. Genetic variation at 15 autosomal STR loci in the Hungarian population of Vojvodina Province, Republic of Serbia. Forensic Sci Int Genet 2012; 6(6): e163-5.
Haliti N, Carapina M, Masić M, Strinović D, Klarić IM, Kubat M. Evaluation of population variation at 17 autosomal STR and 16 Y-STR haplotype loci in Croatians. Forensic Sci Int Genet 2009; 3(4): e137-8.
Devesse L, Ballard D, Davenport L, Riethorst I, Mason-Buck G, Syndercombe Court D. Concordance of the ForenSeq™system and characterisation of sequence-specific autosomal STR alleles across two major population groups. Forensic Sci Int Genet 2018; 34: 57-61.
Zhivotovsky LA, Malyarchuk BA, Derenko MV, Wozniak M, Grzybowski T. Developing STR databases on structured populations: the native South Siberian population versus the Russian population. Forensic Sci Int Genet 2009; 3(4): e111-6.
Westen AA, Kraaijenbrink T, Robles de Medina EA, Harteveld J, Willemse P, Zuniga SB, van der Gaag KJ, Weiler NEC, Warnaar J, Kayser M, Sijen T, de Knijff P. Comparing six commercial autosomal STR kits in a large Dutch population sample. Forensic Sci Int Genet 2014; 10: 55-63.
Sadam M, Tasa G, Tiidla A, Lang A, Axelsson EP, Pajnič IZ. Population data for 22 autosomal STR loci from Estonia. Int J Legal Med 2015; 129(6): 1219-20.
Soták M, Petrejčíková E, Bôžiková A, Bernasovská J, Bernasovský I, Sovičová A, Boroňová I, Svičková P, Gabriková D, Mačeková S, Carnogurská J, Rębała K, Vlček D. Population database of 17 autosomal STR loci from the four predominant Eastern Slovakia regions. Forensic Sci Int Genet 2011; 5(3): 262-3.
Carboni I, Nutini AL, Porfirio B, Genuardi M, Ricci U. Genetic STRs variation in a large population from Tuscany (Italy). Forensic Sci Int Genet 2007; 1(3-4): e10-1.
Informacje: Archiwum Medycyny Sądowej i Kryminologii, 2022, Vol. 72 (3), s. 120 - 137
Typ artykułu: Oryginalny artykuł naukowy
Tytuły:
Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry
Weryfikacja markerów insercyjno-delecyjnych (InDels) i mikrosatelitarnych (STR) jako narzędzi pomocniczych do wnioskowania o pochodzeniu populacji słowiańskiej
Katedra Medycyny Sądowej, Collegium Medicum im. Ludwika Rydygiera w Bydgoszczy, Uniwersytet Mikołaja Kopernika w Toruniu,
Polska
Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
Serbian Academy of Sciences and Arts, Belgrade, Serbia
Faculty of Biology, University of Belgrade, Belgrade, Serbia
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
Katedra Medycyny Sądowej, Zakład Genetyki Molekularnej i Sądowej, Wydział Lekarski, Collegium Medicum Uniwersytetu Mikołaja Kopernika
Polska
Publikacja: 03.2023
Otrzymano: 31.12.2022
Zaakceptowano: 07.02.2023
Status artykułu: Otwarte
Licencja: CC-BY-NC-SA
Udział procentowy autorów:
Korekty artykułu:
-Języki publikacji:
AngielskiLiczba wyświetleń: 493
Liczba pobrań: 384
Sugerowane cytowania: Nature