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Belarusian population genetic database for 15 autosomal STR loci
Forensic Science International 173 (2007) 235–237 www.elsevier.com/locate/forsciint
Announcement of Population Data
Belarusian population genetic database for 15 autosomal STR loci Krzysztof Re˛bała a,*, Joanna Wysocka a, Ewa Kapin´ska a, Lidia Cybulska a, Alexei I. Mikulich b, Iosif S. Tsybovsky c, Zofia Szczerkowska a a
Department of Forensic Medicine, Medical University of Gdan´sk, Poland ul. De˛bowa 23, 80-204 Gdan´sk, Poland b Institute for the Study of Arts, Ethnography and Folklore, National Academy of Sciences, Minsk, Belarus c Institute of Problems of Criminology, Criminalistics and Forensic Expertise, Minsk, Belarus Received 4 October 2006; received in revised form 30 January 2007; accepted 3 February 2007 Available online 13 March 2007
Abstract Allele frequencies of 15 short tandem repeat loci included in the AmpFlSTR Identifiler kit (Applied Biosystems) were obtained from a sample set of unrelated individuals living in Belarus (n = 176). For all loci, no deviation from Hardy–Weinberg equilibrium was found. Results were compared with data available for the Belarusian minority residing in northeastern Poland and for other Slavic populations. Statistically significant differences were observed between Belarusians and all compared populations. The values of heterozygosity, polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), paternity index (PI) and matching probability (pM) were calculated. # 2007 Elsevier Ireland Ltd. All rights reserved. Keywords: AmpFlSTR Identifiler; PCR; Short tandem repeats (STRs); Population genetics
Population: DNA samples were obtained from 176 unrelated individuals from Belarus, residing in localities evenly distributed throughout the country. According to Chakraborty [1], such a sample size ensures that all common alleles (with frequency greater than 0.05) are represented in the sample with at least 99.99999% confidence. PCR: Multiplex PCR using 0.5 ng of target DNA was performed with the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions [2]. Typing: DNA typing was carried out on the 3130 Genetic Analyzer (Applied Biosystems). Results: See Tables 1 and 2. Quality control: Proficiency testing of the Polish Society of Forensic Medicine and Criminology and the Paternity Testing Workshop of the English Speaking Working Group of the International Society for Forensic Genetics. Analysis of data: Statistical parameters like PD, PIC, PE, PI, matching probability (pM), heterozygosity observed (Ho) and heterozygosity expected (He) were calculated using PowerStats Version 1.2 package. Possible divergence from Hardy–Weinberg
* Corresponding author. Tel.: +48 58 349 12 58; fax: +48 58 341 04 85. E-mail address: [email protected] (K. Re˛bała). 0379-0738/$ – see front matter # 2007 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2007.02.002
equilibrium was determined by chi-squared test using Utility Programs for Analysis of Genetic Linkage HWE Version 1.10 and by the exact test using Arlequin software [3–6]. Others remarks: The AmpFlSTR1IdentifilerTM has a combined power of discrimination greater than 0.9999999999999999 and a cumulative power of exclusion greater than 0.99999 in the Belarusian population. No deviation from Hardy–Weinberg equilibrium was observed for all loci tested. The obtained allele frequencies were compared with data available for the Belarusian minority residing in northeastern Poland [7] as well as the Polish [8], Serbian [9] and Macedonian [10] populations. No statistically significant differences in allele distribution were observed in comparison with Poles and Polish Belarusians, except for the D21S11 locus (P = 0.004 for comparison with Belarusians living in Poland, and P = 0.0001 for comparison with the Polish population). On the other hand, statistically significant differences were observed between Belarusian and Serbian populations in two loci (D7S820, P = 0.0024; D2S1338, P = 0.0340) and between Belarusian and Macedonian populations in five out of fifteen loci (TH01, P = 0.0050; D13S317, P = 0.0320; D2S1338, P = 0.000041; D18S51, P = 0.0180; D5S818, P = 0.0078). In conclusion, an allele frequency database for 15 autosomal STR loci of the AmpFlSTR Identifiler PCR Amplification Kit
236
K. Re˛bała et al. / Forensic Science International 173 (2007) 235–237
Table 1 Allele frequencies for AmpFlSTR1IdentifilerTM loci in the Belarusian population (n = 176) Locus allele D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 VWA TPOX D18S51 D5S818 FGA 6 7 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 19.2 20 21 22 22.2 23 23.2 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2
– – 0.006 0.011 – 0.040 0.051 0.193 0.330 – 0.247 – 0.097 – 0.017 – 0.009 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.003 – 0.020 0.153 0.222 0.003 0.224 0.071 0.088 0.057 0.020 0.088 0.006 0.045
– 0.009 0.148 0.148 – 0.250 0.307 0.108 0.031 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.003 – – 0.034 – 0.259 0.361 0.276 0.057 – 0.006 – 0.006 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.003 – – – 0.111 – 0.256 – 0.207 0.003 0.239 – 0.162 – 0.020 – – – – – – – – – – – – – – – – – – – – – – –
0.219 0.108 0.111 0.207 0.341 0.014 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.131 0.063 – 0.040 0.395 0.247 0.077 – 0.045 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.014 0.077 – 0.051 0.310 0.318 0.205 – 0.026 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.023 – 0.216 – 0.065 – 0.128 – 0.182 0.045 0.014 – 0.080 – 0.125 – 0.088 0.028 0.006 – – – – – – – – – – –
– – – – – – 0.003 0.085 0.227 0.017 0.392 0.026 0.168 0.020 0.028 0.020 0.006 0.003 – 0.006 – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.009 – 0.122 – 0.116 – 0.210 – 0.256 – 0.239 – 0.043 – 0.006 – – – – – – – – – – – – – – – – – – – – –
– 0.003 0.599 0.065 – 0.074 0.224 0.034 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.020 0.097 0.094 – 0.136 – 0.182 – 0.213 – 0.082 – 0.094 – 0.054 – 0.011 0.011 – – – – 0.003 – 0.003 – – – – – – – – – – – – –
– 0.006 0.003 0.060 – 0.082 0.378 0.318 0.139 – 0.011 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.003 – – – 0.009 – 0.085 – 0.142 0.193 0.216 0.020 0.114 0.009 0.119 0.003 0.077 0.009 0.003 – – – – – – – – – – –
H (ob) H (ex) x2 Exact test
0.750 0.781 0.347 0.545
0.801 0.852 0.053 0.096
0.824 0.823 0.854 0.468
0.733 0.724 0.350 0.855
0.852 0.799 0.804 0.299
0.767 0.783 0.677 0.263
0.761 0.757 0.083 0.052
0.699 0.754 0.278 0.053
0.858 0.858 0.688 0.788
0.744 0.760 0.728 0.267
0.824 0.824 0.638 0.148
0.557 0.581 0.211 0.050
0.875 0.868 0.090 0.051
0.705 0.704 0.293 0.139
0.824 0.858 0.581 0.382
Table 2 Statistical parameters of the usefulness of AmpFlSTR1IdentifilerTM in forensic medicine for the Belarusian population Statistical parameters locus
Power of discrimination, PD
Polymorphism information of content, PIC
Power of exclusion, PE
Matching probability, pM
Paternity index, PI
D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539
0.919 0.958 0.916 0.872 0.914 0.902 0.898 0.895
0.750 0.830 0.760 0.670 0.760 0.730 0.720 0.710
0.510 0.601 0.644 0.481 0.699 0.539 0.529 0.427
0.081 0.042 0.084 0.128 0.086 0.098 0.102 0.105
2.000 2.510 2.840 1.870 3.380 2.150 2.100 1.660
K. Re˛bała et al. / Forensic Science International 173 (2007) 235–237
237
Table 2 (Continued ) Statistical parameters locus
Power of discrimination, PD
Polymorphism information of content, PIC
Power of exclusion, PE
Matching probability, pM
Paternity index, PI
D2S1338 D19S433 VWA TPOX D18SS51 D5S818 FGA
0.966 0.899 0.928 0.766 0.962 0.873 0.960
0.850 0.720 0.770 0.530 0.850 0.680 0.840
0.711 0.500 0.644 0.242 0.745 0.435 0.644
0.034 0.101 0.072 0.234 0.038 0.127 0.040
3.520 1.960 2.840 1.130 4.000 1.690 2.840
has been established for the Belarusian population, and the high value of the combined power of discrimination proves their usefulness for forensic purposes in Belarus. This paper follows the guidelines for publication of population data requested by the journal [11]. References [1] R. Chakraborty, Sample size requirements for addressing the population genetic issues of forensic use of DNA typing, Hum. Biol. 64 (1992) 141– 159. [2] Applied Biosystems, AmpFlSTR Identifiler PCR Amplification Kit User’s Manual, Foster City, CA, P/N 4322288, 2001. [3] C. Brenner, J. Morris, Paternity index calculations in single locus hypervariable DNA probes: validation and other studies, in: Proceedings for the International Symposium on Human Identification, 1989, Promega Corporation Madison, WI, (1990), pp. 21–53. [4] J. Ott, Utility Programs for analysis of Genetic Linkage, Laboratory of Statistical Genetics, Rockefeller University, New York, 2001.
[5] R.E. Parker, Wprowadzenie do statystyki dla biologo´w, PWN, Warszawa, 1978. [6] S. Schneider, D. Roessli, L. Excoffier, Arlequin Ver 2.000: A Software for Population Genetics Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Switzerland, 2000. [7] W. Pepinski, A. Niemcunowicz-Janica, M. Skawrowska, E. Koc-Zorawska, J. Janica, I. Soltyszewski, Allele distribution of 15 STR loci in a population sample of Byelorussian minority residing in the northeastern Poland, Forensic Sci. Int. 139 (2004) 265–267. [8] Z. Szczerkowska, E. Kapin´ska, J. Wysocka, L. Cybulska, Northern Polish population data and forensic usefulness of 15 autosomal STR loci, Forensic Sci. Int. 144 (2004) 69–71. [9] I. Veselinovic´, M. Kubat, I. Furacˇ, J. Sˇkavic´, I. Martinovic´ Klaric´, M. Tasic´, Allele frequencies of the 15 AmpFISTR Identifiler loci in the population of Vojvodina Province, Serbia and Montenegro, Int. J. Legal Med. 118 (2004) 184–186. [10] Z. Jakovski, K. Nikolova, I. Furacˇ, M. Masic, B. Janeska, M. Kubat, Allele frequencies for 15 STR loci in a population from the Republic of Macedonia, Int. J. Legal Med. 120 (2006) 53–55. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of Population Data
Belarusian population genetic database for 15 autosomal STR loci Krzysztof Re˛bała a,*, Joanna Wysocka a, Ewa Kapin´ska a, Lidia Cybulska a, Alexei I. Mikulich b, Iosif S. Tsybovsky c, Zofia Szczerkowska a a
Department of Forensic Medicine, Medical University of Gdan´sk, Poland ul. De˛bowa 23, 80-204 Gdan´sk, Poland b Institute for the Study of Arts, Ethnography and Folklore, National Academy of Sciences, Minsk, Belarus c Institute of Problems of Criminology, Criminalistics and Forensic Expertise, Minsk, Belarus Received 4 October 2006; received in revised form 30 January 2007; accepted 3 February 2007 Available online 13 March 2007
Abstract Allele frequencies of 15 short tandem repeat loci included in the AmpFlSTR Identifiler kit (Applied Biosystems) were obtained from a sample set of unrelated individuals living in Belarus (n = 176). For all loci, no deviation from Hardy–Weinberg equilibrium was found. Results were compared with data available for the Belarusian minority residing in northeastern Poland and for other Slavic populations. Statistically significant differences were observed between Belarusians and all compared populations. The values of heterozygosity, polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), paternity index (PI) and matching probability (pM) were calculated. # 2007 Elsevier Ireland Ltd. All rights reserved. Keywords: AmpFlSTR Identifiler; PCR; Short tandem repeats (STRs); Population genetics
Population: DNA samples were obtained from 176 unrelated individuals from Belarus, residing in localities evenly distributed throughout the country. According to Chakraborty [1], such a sample size ensures that all common alleles (with frequency greater than 0.05) are represented in the sample with at least 99.99999% confidence. PCR: Multiplex PCR using 0.5 ng of target DNA was performed with the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions [2]. Typing: DNA typing was carried out on the 3130 Genetic Analyzer (Applied Biosystems). Results: See Tables 1 and 2. Quality control: Proficiency testing of the Polish Society of Forensic Medicine and Criminology and the Paternity Testing Workshop of the English Speaking Working Group of the International Society for Forensic Genetics. Analysis of data: Statistical parameters like PD, PIC, PE, PI, matching probability (pM), heterozygosity observed (Ho) and heterozygosity expected (He) were calculated using PowerStats Version 1.2 package. Possible divergence from Hardy–Weinberg
* Corresponding author. Tel.: +48 58 349 12 58; fax: +48 58 341 04 85. E-mail address: [email protected] (K. Re˛bała). 0379-0738/$ – see front matter # 2007 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2007.02.002
equilibrium was determined by chi-squared test using Utility Programs for Analysis of Genetic Linkage HWE Version 1.10 and by the exact test using Arlequin software [3–6]. Others remarks: The AmpFlSTR1IdentifilerTM has a combined power of discrimination greater than 0.9999999999999999 and a cumulative power of exclusion greater than 0.99999 in the Belarusian population. No deviation from Hardy–Weinberg equilibrium was observed for all loci tested. The obtained allele frequencies were compared with data available for the Belarusian minority residing in northeastern Poland [7] as well as the Polish [8], Serbian [9] and Macedonian [10] populations. No statistically significant differences in allele distribution were observed in comparison with Poles and Polish Belarusians, except for the D21S11 locus (P = 0.004 for comparison with Belarusians living in Poland, and P = 0.0001 for comparison with the Polish population). On the other hand, statistically significant differences were observed between Belarusian and Serbian populations in two loci (D7S820, P = 0.0024; D2S1338, P = 0.0340) and between Belarusian and Macedonian populations in five out of fifteen loci (TH01, P = 0.0050; D13S317, P = 0.0320; D2S1338, P = 0.000041; D18S51, P = 0.0180; D5S818, P = 0.0078). In conclusion, an allele frequency database for 15 autosomal STR loci of the AmpFlSTR Identifiler PCR Amplification Kit
236
K. Re˛bała et al. / Forensic Science International 173 (2007) 235–237
Table 1 Allele frequencies for AmpFlSTR1IdentifilerTM loci in the Belarusian population (n = 176) Locus allele D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 VWA TPOX D18S51 D5S818 FGA 6 7 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 19.2 20 21 22 22.2 23 23.2 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2
– – 0.006 0.011 – 0.040 0.051 0.193 0.330 – 0.247 – 0.097 – 0.017 – 0.009 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.003 – 0.020 0.153 0.222 0.003 0.224 0.071 0.088 0.057 0.020 0.088 0.006 0.045
– 0.009 0.148 0.148 – 0.250 0.307 0.108 0.031 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.003 – – 0.034 – 0.259 0.361 0.276 0.057 – 0.006 – 0.006 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.003 – – – 0.111 – 0.256 – 0.207 0.003 0.239 – 0.162 – 0.020 – – – – – – – – – – – – – – – – – – – – – – –
0.219 0.108 0.111 0.207 0.341 0.014 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.131 0.063 – 0.040 0.395 0.247 0.077 – 0.045 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.014 0.077 – 0.051 0.310 0.318 0.205 – 0.026 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.023 – 0.216 – 0.065 – 0.128 – 0.182 0.045 0.014 – 0.080 – 0.125 – 0.088 0.028 0.006 – – – – – – – – – – –
– – – – – – 0.003 0.085 0.227 0.017 0.392 0.026 0.168 0.020 0.028 0.020 0.006 0.003 – 0.006 – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.009 – 0.122 – 0.116 – 0.210 – 0.256 – 0.239 – 0.043 – 0.006 – – – – – – – – – – – – – – – – – – – – –
– 0.003 0.599 0.065 – 0.074 0.224 0.034 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.020 0.097 0.094 – 0.136 – 0.182 – 0.213 – 0.082 – 0.094 – 0.054 – 0.011 0.011 – – – – 0.003 – 0.003 – – – – – – – – – – – – –
– 0.006 0.003 0.060 – 0.082 0.378 0.318 0.139 – 0.011 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.003 – – – 0.009 – 0.085 – 0.142 0.193 0.216 0.020 0.114 0.009 0.119 0.003 0.077 0.009 0.003 – – – – – – – – – – –
H (ob) H (ex) x2 Exact test
0.750 0.781 0.347 0.545
0.801 0.852 0.053 0.096
0.824 0.823 0.854 0.468
0.733 0.724 0.350 0.855
0.852 0.799 0.804 0.299
0.767 0.783 0.677 0.263
0.761 0.757 0.083 0.052
0.699 0.754 0.278 0.053
0.858 0.858 0.688 0.788
0.744 0.760 0.728 0.267
0.824 0.824 0.638 0.148
0.557 0.581 0.211 0.050
0.875 0.868 0.090 0.051
0.705 0.704 0.293 0.139
0.824 0.858 0.581 0.382
Table 2 Statistical parameters of the usefulness of AmpFlSTR1IdentifilerTM in forensic medicine for the Belarusian population Statistical parameters locus
Power of discrimination, PD
Polymorphism information of content, PIC
Power of exclusion, PE
Matching probability, pM
Paternity index, PI
D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539
0.919 0.958 0.916 0.872 0.914 0.902 0.898 0.895
0.750 0.830 0.760 0.670 0.760 0.730 0.720 0.710
0.510 0.601 0.644 0.481 0.699 0.539 0.529 0.427
0.081 0.042 0.084 0.128 0.086 0.098 0.102 0.105
2.000 2.510 2.840 1.870 3.380 2.150 2.100 1.660
K. Re˛bała et al. / Forensic Science International 173 (2007) 235–237
237
Table 2 (Continued ) Statistical parameters locus
Power of discrimination, PD
Polymorphism information of content, PIC
Power of exclusion, PE
Matching probability, pM
Paternity index, PI
D2S1338 D19S433 VWA TPOX D18SS51 D5S818 FGA
0.966 0.899 0.928 0.766 0.962 0.873 0.960
0.850 0.720 0.770 0.530 0.850 0.680 0.840
0.711 0.500 0.644 0.242 0.745 0.435 0.644
0.034 0.101 0.072 0.234 0.038 0.127 0.040
3.520 1.960 2.840 1.130 4.000 1.690 2.840
has been established for the Belarusian population, and the high value of the combined power of discrimination proves their usefulness for forensic purposes in Belarus. This paper follows the guidelines for publication of population data requested by the journal [11]. References [1] R. Chakraborty, Sample size requirements for addressing the population genetic issues of forensic use of DNA typing, Hum. Biol. 64 (1992) 141– 159. [2] Applied Biosystems, AmpFlSTR Identifiler PCR Amplification Kit User’s Manual, Foster City, CA, P/N 4322288, 2001. [3] C. Brenner, J. Morris, Paternity index calculations in single locus hypervariable DNA probes: validation and other studies, in: Proceedings for the International Symposium on Human Identification, 1989, Promega Corporation Madison, WI, (1990), pp. 21–53. [4] J. Ott, Utility Programs for analysis of Genetic Linkage, Laboratory of Statistical Genetics, Rockefeller University, New York, 2001.
[5] R.E. Parker, Wprowadzenie do statystyki dla biologo´w, PWN, Warszawa, 1978. [6] S. Schneider, D. Roessli, L. Excoffier, Arlequin Ver 2.000: A Software for Population Genetics Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Switzerland, 2000. [7] W. Pepinski, A. Niemcunowicz-Janica, M. Skawrowska, E. Koc-Zorawska, J. Janica, I. Soltyszewski, Allele distribution of 15 STR loci in a population sample of Byelorussian minority residing in the northeastern Poland, Forensic Sci. Int. 139 (2004) 265–267. [8] Z. Szczerkowska, E. Kapin´ska, J. Wysocka, L. Cybulska, Northern Polish population data and forensic usefulness of 15 autosomal STR loci, Forensic Sci. Int. 144 (2004) 69–71. [9] I. Veselinovic´, M. Kubat, I. Furacˇ, J. Sˇkavic´, I. Martinovic´ Klaric´, M. Tasic´, Allele frequencies of the 15 AmpFISTR Identifiler loci in the population of Vojvodina Province, Serbia and Montenegro, Int. J. Legal Med. 118 (2004) 184–186. [10] Z. Jakovski, K. Nikolova, I. Furacˇ, M. Masic, B. Janeska, M. Kubat, Allele frequencies for 15 STR loci in a population from the Republic of Macedonia, Int. J. Legal Med. 120 (2006) 53–55. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.