Int J Legal Med DOI 10.1007/s00414-014-1089-7
POPULATION DATA
Population data for 22 autosomal STR loci from Estonia M. Sadam & G. Tasa & A. Tiidla & A. Lang & E. Podovšovnik Axelsson & I. Zupanič Pajnič
Received: 18 August 2014 / Accepted: 26 September 2014 # Springer-Verlag Berlin Heidelberg 2014
Abstract Allele frequencies and forensically relevant population statistics of 22 short tandem repeat (STR) loci were determined from 303 unrelated Estonian individuals. The samples were amplified with three kits: the AmpFlSTR® Identifiler, the PowerPlex® ESI 16 and the PowerPlex® 16. No significant deviation from Hardy-Weinberg equilibrium was detected, except for locus D22S1045. Investigated loci are very discriminating in Estonian population, with a combined discrimination power of 0.9999999999999999999999999877. Furthermore, a comparison with previously published frequency data from other nearby populations is presented. Keywords Autosomal short tandem repeats . Population genetics . Estonia
Estonians are part of the Finno-Ugric language group and Ychromosome haplotype variation suggests an admixture of Electronic supplementary material The online version of this article (doi:10.1007/s00414-014-1089-7) contains supplementary material, which is available to authorized users. M. Sadam : G. Tasa : A. Tiidla Estonian Forensic Science Institute, Tervise 30, 13419 Tallinn, Estonia G. Tasa : A. Tiidla : A. Lang Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411 Tartu, Estonia E. P. Axelsson Turistica - Faculty of Tourism Studies, University of Primorska, Obala 11a, 6320 Portorož, Slovenia I. Z. Pajnič (*) Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia e-mail: [email protected]
Baltic and Finno-Ugric haplotypes [1]. The population in Estonia is about 1.3 million, and throughout the history, this value has been very unstable. Many times this number has decreased below 100,000 and increased very quickly, mainly due to immigration. The first settlers arrived from the eastern part of Central Europe or southern part of Eastern Europe. In the Middle Ages, the immigrants came from Finland, Russia, Latvia, Lithuania and Poland, whereas in the thirteenth century, people emigrated mainly from Germany and Sweden. Another extensive immigration period started at the end of the nineteenth century when the Russian industrialisation and the railway network creation brought large number of migrant workers from Russia to Estonia [2]. We investigated genetic polymorphism of 22 autosomal short tandem repeat (STR) loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391, D2S1338, D3S1358, D8S1179, D16S539, D18S51, D19S433, D21S11, FGA, TH01, vWA, CSF1PO, D5S818, D7S820, D13S317, TPOX, Penta E and Penta D) amplified with PowerPlex® ESI 16, Identifiler and PowerPlex® 16 kit. Peripheral blood samples were collected from 303 healthy, unrelated and randomly selected ethnical Estonians living in different rural parts of Estonia and their ancestors back at least to grandparents had Estonian nationality. This research project was approved by the Research Ethics Committee of the University of Tartu (protocol number 235/T-5). Furthermore, the DNA department of the Estonian Forensic Science Institute is accredited to ISO/IEC 17025 and regularly participates in the quality control proficiency testing provided by the German DNA Profiling group (GEDNAP). It is also important to note that this article follows the population data publication guidelines set by the journal. Genomic DNA was extracted from blood samples using a phenol/chloroform extraction. The multiplex-PCR amplification of the autosomal STRs with Identifiler, PowerPlex® 16 and PowerPlex® ESI 16 kit was performed for all samples
Int J Legal Med
using final reaction volume of 12.5 μl and 26 cycles in GeneAmp 9700 PCR System (Applied Biosystems). Simultaneously, the positive (9947A and 2800M) and negative PCR controls were amplified. Amplification products were separated in a 3130 Genetic Analyzer (Applied Biosystems) and the results analysed with GeneMapper ID v3.2 software (Applied Biosystems) according to the manufacturers’ instructions, apart from injection parameters for the ESI 16, which were set at 3 kV and 10 s. The peak high threshold was 50 RFU for heterozygous and 200 RFU for homozygous alleles. In order to determine allele frequencies, probability value of the Hardy-Weinberg equilibrium (HWE) exact test and interpopulation comparison, the Arlequin software (version 3.5) was used [3]. Taking into account Estonian’s immigration history [2], interpopulation comparison was conducted using previously published STR data from other nearby countries. We used population data from Sweden [4, 5], Russia [6], Poland [7, 8], Belarus [9] and North Germany [10]. PowerStats (version 12, Promega) was used to compute forensically important statistical parameters for each locus. The distributions of observed allele frequencies and the population statistical parameters for the 22 STR loci are shown in Supplementary Table 1. According to the results of the statistical analysis, no deviations from the HWE hypothesis were detected, except for the D22S1045 locus where deviation was significant even after Bonferroni’s correction for multiple analyses. This, however, can be explained by limited population size. Quantitative comparisons of allele frequencies between Estonian population and other nearby populations are summarised in Supplementary Table 2. There were some differences between Estonians and people from Sweden (in 55 % of the compared loci), Russia (in 41 % of the compared loci), Poland (in 45 % of the compared loci), Belarus (in 47 % of the compared loci) and North Germany (in 47 % of the compared loci) even after applying Bonferroni’s correction for the number of comparisons. The forensic efficiency values suggest that the investigated STR loci are very discriminating in
Estonian population, with a combined discrimination power of 0.9999999999999999999999999877. Due to the high informative value, the investigated markers can easily be applied when solving challenging forensic cases with degraded DNA samples, in complex kinship testing and in difficult chimerism analyses.
References 1. Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, Savontaus ML, Lahermo P (2008) Migration waves to the Baltic Sea region. Ann Hum Genet 72:337–348 2. Estonica - Encyclopedia about Estonia. http://www.estonica.org/en/ Society/Population/. Accessed 13 Aug 2013 3. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567 4. Albinsson L, Noren L, Hedell R, Ansell R (2011) Swedish population data and concordance for the kits PowerPlex1 ESX 16 System, PowerPlex1 ESI 16 System, AmpFlSTR1 NGMTM, AmpFlSTR1 SGM PlusTM and Investigator ESSplex. Forensic Sci Int Genet 5: e89–e92 5. Montelius K, Karlsson AO, Holmlund G (2008) 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 2:e49–e52 6. Zhivotovsky LA, Malyarchuk BA, Derenko MV, Wozniak M, Grzybowski T (2009) Developing STR databases on structured populations: the native South Siberian population versus the Russian population. Forensic Sci Int Genet 3:e111–e116 7. Jedrzejczyk M, Jacewicz R, Szram S, Berent J (2012) Genetic population studies on 15 NGMTM STR loci in central Poland population. Forensic Sci Int Genet 6:e119–e120 8. Piatek J, Jacewicz R, Ossowski A, Parafiniuk M, Berent J (2008) Population genetics of 15 autosomal STR loci in the population of Pomorze Zachodnie (NW Poland). Forensic Sci Int Genet 2:e41–e43 9. Zhivotovsky LA, Veremeichyk VM, Kuzub NN, Atramentova LA, Udina IG, Kartel NA, Tsybovsky IS (2009) A reference data base on STR allele frequencies in the Belarus population developed from paternity cases. Forensic Sci Int Genet 3:e107–e109 10. Poetsch M, Bayer K, Ergin Z, Milbrath M, Schwark T, von WurmbSchwark N (2011) First experiences using the new Powerplex® ESX17 and ESI17 kits in casework analysis and allele frequencies for two different regions in Germany. Int J Legal Med 125:733–739
POPULATION DATA
Population data for 22 autosomal STR loci from Estonia M. Sadam & G. Tasa & A. Tiidla & A. Lang & E. Podovšovnik Axelsson & I. Zupanič Pajnič
Received: 18 August 2014 / Accepted: 26 September 2014 # Springer-Verlag Berlin Heidelberg 2014
Abstract Allele frequencies and forensically relevant population statistics of 22 short tandem repeat (STR) loci were determined from 303 unrelated Estonian individuals. The samples were amplified with three kits: the AmpFlSTR® Identifiler, the PowerPlex® ESI 16 and the PowerPlex® 16. No significant deviation from Hardy-Weinberg equilibrium was detected, except for locus D22S1045. Investigated loci are very discriminating in Estonian population, with a combined discrimination power of 0.9999999999999999999999999877. Furthermore, a comparison with previously published frequency data from other nearby populations is presented. Keywords Autosomal short tandem repeats . Population genetics . Estonia
Estonians are part of the Finno-Ugric language group and Ychromosome haplotype variation suggests an admixture of Electronic supplementary material The online version of this article (doi:10.1007/s00414-014-1089-7) contains supplementary material, which is available to authorized users. M. Sadam : G. Tasa : A. Tiidla Estonian Forensic Science Institute, Tervise 30, 13419 Tallinn, Estonia G. Tasa : A. Tiidla : A. Lang Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411 Tartu, Estonia E. P. Axelsson Turistica - Faculty of Tourism Studies, University of Primorska, Obala 11a, 6320 Portorož, Slovenia I. Z. Pajnič (*) Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia e-mail: [email protected]
Baltic and Finno-Ugric haplotypes [1]. The population in Estonia is about 1.3 million, and throughout the history, this value has been very unstable. Many times this number has decreased below 100,000 and increased very quickly, mainly due to immigration. The first settlers arrived from the eastern part of Central Europe or southern part of Eastern Europe. In the Middle Ages, the immigrants came from Finland, Russia, Latvia, Lithuania and Poland, whereas in the thirteenth century, people emigrated mainly from Germany and Sweden. Another extensive immigration period started at the end of the nineteenth century when the Russian industrialisation and the railway network creation brought large number of migrant workers from Russia to Estonia [2]. We investigated genetic polymorphism of 22 autosomal short tandem repeat (STR) loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391, D2S1338, D3S1358, D8S1179, D16S539, D18S51, D19S433, D21S11, FGA, TH01, vWA, CSF1PO, D5S818, D7S820, D13S317, TPOX, Penta E and Penta D) amplified with PowerPlex® ESI 16, Identifiler and PowerPlex® 16 kit. Peripheral blood samples were collected from 303 healthy, unrelated and randomly selected ethnical Estonians living in different rural parts of Estonia and their ancestors back at least to grandparents had Estonian nationality. This research project was approved by the Research Ethics Committee of the University of Tartu (protocol number 235/T-5). Furthermore, the DNA department of the Estonian Forensic Science Institute is accredited to ISO/IEC 17025 and regularly participates in the quality control proficiency testing provided by the German DNA Profiling group (GEDNAP). It is also important to note that this article follows the population data publication guidelines set by the journal. Genomic DNA was extracted from blood samples using a phenol/chloroform extraction. The multiplex-PCR amplification of the autosomal STRs with Identifiler, PowerPlex® 16 and PowerPlex® ESI 16 kit was performed for all samples
Int J Legal Med
using final reaction volume of 12.5 μl and 26 cycles in GeneAmp 9700 PCR System (Applied Biosystems). Simultaneously, the positive (9947A and 2800M) and negative PCR controls were amplified. Amplification products were separated in a 3130 Genetic Analyzer (Applied Biosystems) and the results analysed with GeneMapper ID v3.2 software (Applied Biosystems) according to the manufacturers’ instructions, apart from injection parameters for the ESI 16, which were set at 3 kV and 10 s. The peak high threshold was 50 RFU for heterozygous and 200 RFU for homozygous alleles. In order to determine allele frequencies, probability value of the Hardy-Weinberg equilibrium (HWE) exact test and interpopulation comparison, the Arlequin software (version 3.5) was used [3]. Taking into account Estonian’s immigration history [2], interpopulation comparison was conducted using previously published STR data from other nearby countries. We used population data from Sweden [4, 5], Russia [6], Poland [7, 8], Belarus [9] and North Germany [10]. PowerStats (version 12, Promega) was used to compute forensically important statistical parameters for each locus. The distributions of observed allele frequencies and the population statistical parameters for the 22 STR loci are shown in Supplementary Table 1. According to the results of the statistical analysis, no deviations from the HWE hypothesis were detected, except for the D22S1045 locus where deviation was significant even after Bonferroni’s correction for multiple analyses. This, however, can be explained by limited population size. Quantitative comparisons of allele frequencies between Estonian population and other nearby populations are summarised in Supplementary Table 2. There were some differences between Estonians and people from Sweden (in 55 % of the compared loci), Russia (in 41 % of the compared loci), Poland (in 45 % of the compared loci), Belarus (in 47 % of the compared loci) and North Germany (in 47 % of the compared loci) even after applying Bonferroni’s correction for the number of comparisons. The forensic efficiency values suggest that the investigated STR loci are very discriminating in
Estonian population, with a combined discrimination power of 0.9999999999999999999999999877. Due to the high informative value, the investigated markers can easily be applied when solving challenging forensic cases with degraded DNA samples, in complex kinship testing and in difficult chimerism analyses.
References 1. Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, Savontaus ML, Lahermo P (2008) Migration waves to the Baltic Sea region. Ann Hum Genet 72:337–348 2. Estonica - Encyclopedia about Estonia. http://www.estonica.org/en/ Society/Population/. Accessed 13 Aug 2013 3. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567 4. Albinsson L, Noren L, Hedell R, Ansell R (2011) Swedish population data and concordance for the kits PowerPlex1 ESX 16 System, PowerPlex1 ESI 16 System, AmpFlSTR1 NGMTM, AmpFlSTR1 SGM PlusTM and Investigator ESSplex. Forensic Sci Int Genet 5: e89–e92 5. Montelius K, Karlsson AO, Holmlund G (2008) 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 2:e49–e52 6. Zhivotovsky LA, Malyarchuk BA, Derenko MV, Wozniak M, Grzybowski T (2009) Developing STR databases on structured populations: the native South Siberian population versus the Russian population. Forensic Sci Int Genet 3:e111–e116 7. Jedrzejczyk M, Jacewicz R, Szram S, Berent J (2012) Genetic population studies on 15 NGMTM STR loci in central Poland population. Forensic Sci Int Genet 6:e119–e120 8. Piatek J, Jacewicz R, Ossowski A, Parafiniuk M, Berent J (2008) Population genetics of 15 autosomal STR loci in the population of Pomorze Zachodnie (NW Poland). Forensic Sci Int Genet 2:e41–e43 9. Zhivotovsky LA, Veremeichyk VM, Kuzub NN, Atramentova LA, Udina IG, Kartel NA, Tsybovsky IS (2009) A reference data base on STR allele frequencies in the Belarus population developed from paternity cases. Forensic Sci Int Genet 3:e107–e109 10. Poetsch M, Bayer K, Ergin Z, Milbrath M, Schwark T, von WurmbSchwark N (2011) First experiences using the new Powerplex® ESX17 and ESI17 kits in casework analysis and allele frequencies for two different regions in Germany. Int J Legal Med 125:733–739
