- Email: [email protected]
STR data for the AmpFl STR SGM Plus loci from Warmia and Mazury (NE Poland)
Forensic Science International 141 (2004) 69–71
Announcement of population data
STR data for the AmpFlSTR SGM Plus loci from Warmia and Mazury (NE Poland) Ireneusz Soltyszewskib, Witold Pepinskia,*, Malgorzata Skawronskaa, Ewa Koc-Zorawskaa, Anna Niemcunowicz-Janicaa, Jerzy Janicaa a
Department of Forensic Medicine, Medical University of Bialystok, Bialystok, Poland b Central Forensic Laboratory of Police, Warsaw, Poland
Received 30 June 2003; received in revised form 22 December 2003; accepted 8 January 2004
Abstract Allele frequencies for the ten STRs included in the AmpFlSTR SGM Plus kit were determined in a sample of 320 unrelated individuals born in the region of Warmia and Mazury (NE Poland). All loci met Hardy–Weinberg expectations. Exact tests disequilibrium analysis revealed only one departure from independence out of 45 pair-wise comparisons of the 10 loci. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Population data; AmpFlSTR SGM Plus; Warmia and Mazury; Poland
Population: Buccal swabs were collected from 320 unrelated healthy donors living in the region of Warmia and Mazury (NE Poland). Extraction: Chelex 100 and proteinase K [1]. PCR: two nano grams of target DNA was amplified according to the manufacturer’s instructions (AmpFlSTR SGM Plus amplification kit, Applied Biosystems). Typing: ABI 310 and reference sequenced ladders (Applied Biosystems) following the manufacturer’s instructions. Results: See Tables 1 and 2. Quality control: Proficiency testing of the Polish Society of Forensic Medicine and Criminology, Hemogenetics Committee.
Analysis of data: GDA v1.2 [2] and PowerStats v1.2 packages [3]. Access to the data: upon request: [email protected]. Other remarks: No differences with European Caucasian populations [4–6] using a pairwise population comparison test (R C contingency test; G. Carmody, Ottawa, Canada). A departure from independence between D3S1358 and D8S1179 was detected (P ¼ 0:007188) using the exact tests disequilibrium analysis. The product rule may be used in a multiple-locus profile frequency estimations. The combined MP and PE for all 10 loci are 9:11 1013 and 0.99, respectively. This paper follows the guidelines for publication of population data requested by the journal [7].
* Corresponding author. Tel.: þ48-85-7485948; fax: þ48-85-7485985. E-mail address: [email protected] (W. Pepinski).
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.01.005
70
I. Soltyszewski et al. / Forensic Science International 141 (2004) 69–71
Table 1 Allele frequencies for AmpFlSTR SGM Plus loci in the population of Warmia and Mazury (NE Poland) Allele
D3S1358
VWA
D16S539
D2S1338
D8S1179
D21S11
D18S51
D19S433
TH01
FGA
6 7 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 18 18.2 19 19.2 20 20.2 21 22 22.2 23 23.2 24 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34.2
– – – – – – – – 0.008 – 0.136 – 0.202 – 0.266 – 0.221 0.152 – 0.016 – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.008 – 0.082 – 0.104 – 0.202 – 0.290 0.226 – 0.072 – 0.016 – – – – – – – – – – – – – – – – – – – – – –
– – 0.008 0.080 – 0.040 0.258 0.340 0.205 – 0.040 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.045 – 0.223 0.125 – 0.117 – 0.128 – 0.032 0.011 – 0.080 – 0.098 0.112 0.024 0.005 – – – – – – – – – – – –
– – 0.008 0.013 – 0.066 0.059 0.154 0.343 – 0.247 – 0.093 – 0.011 – 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.003 0.032 0.173 0.189 0.005 0.266 0.069 0.061 0.074 0.011 0.088 0.005 0.019 0.003
– – – – – 0.011 0.011 0.109 0.120 – 0.186 – 0.152 – 0.170 – 0.098 0.069 – 0.035 – 0.024 – 0.016 – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.005 0.072 0.226 0.008 0.359 0.019 0.189 0.045 0.029 0.027 0.003 0.003 0.008 – 0.005 – – – – – – – – – – – – – – – – – – – – – –
0.223 0.141 0.074 0.202 0.356 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – 0.016 – 0.080 – 0.154 0.003 0.189 0.202 0.013 0.122 0.011 0.104 0.069 0.037 – – – – – – – – – – – – –
Ho He P
0.771 0.800 0.185
0.830 0.803 0.358
0.766 0.753 0.913
0.883 0.874 0.059
0.771 0.783 0.738
0.830 0.843 0.886
0.872 0.887 0.868
0.840 0.778 0.111
0.755 0.759 0.340
0.878 0.863 0.830
MP PD PIC PE TPI
0.076 0.924 0.77 0.547 2.19
0.077 0.923 0.77 0.655 2.94
0.104 0.896 0.71 0.537 2.14
0.036 0.964 0.86 0.761 4.27
0.082 0.918 0.75 0.547 2.19
0.044 0.956 0.82 0.655 2.94
0.034 0.966 0.86 0.739 3.92
0.091 0.909 0.74 0.676 3.13
0.098 0.902 0.72 0.519 2.04
0.038 0.962 0.85 0.750 4.09
Ho: Heterozygosity observed; He: Heterozygosity expected; P: Hardy-Weinberg equilibrium, exact test based on 3200 shufflings; MP: Matching Probability; PD: Power of Discrimination; PIC: Polymorphism Information Content; PE: Power of Exclusion; TPI: Typical Paternity Index.
I. Soltyszewski et al. / Forensic Science International 141 (2004) 69–71
71
Table 2 Exact test for linkage disequlibrium P
Locus combination
P
Locus combination
0.245312 0.055938 0.324688 0.007188a 0.095937 0.574375 0.576250 0.244375 0.102813 0.554375 0.794375 0.935625 0.862187 0.427812 0.495312 0.479063 0.531250 0.535625 0.153750 0.465313 0.947500 0.440937 0.954688
D3S1358/VWA D3S1358/TH01 D3S1358/D21S11 D3S1358/D8S1179 D3S1358/D2S1338 VWA/TH01 VWA/D21S11 VWA/D8S1179 VWA/D2S1338 FGA/D16S539 FGA/D18S51 FGA/D19S433 TH01/D16S539 TH01/D18S51 TH01/D19S433 D16S539/D21S11 D16S539/D8S1179 D16S539/D2S1338 D21S11/D8S1179 D21S11/D2S1338 D18S51/D19S433 D8S1179/D19S433 D19S433/D2S1338
0.653750 0.265625 0.423750 0.369063 0.898438 0.184062 0.727500 0.640938 0.428125 0.843125 0.846562 0.741563 0.438125 0.190312 0.372500 0.231875 0.710625 0.537188 0.819063 0.053125 0.355000 0.250312
D3S1358/FGA D3S1358/D16S539 D3S1358/D18S51 D3S1358/D19S433 VWA/FGA VWA/D16S539 VWA/D18S51 VWA/D19S433 FGA/TH01 FGA/D21S11 FGA/D8S1179 FGA/D2S1338 TH01/D21S11 TH01/D8S1179 TH01/D2S1338 D16S539/D18S51 D16S539/D19S433 D21S11/D18S51 D21S11/D19S433 D18S51/D8S1179 D18S51/D2S1338 D8S1179/D2S1338
P: probability based on 3200 shufflings. a Departure from linkage equilibrium.
References [1] P. Wiegand, T. Bajanowski, B. Brinkmann, PCR typing of debris from fingernails, Int. J. Legal Med. 106 (1993) 81–84. [2] P.O. Lewis, D. Zaykin, Genetic Data Analysis: Computer Program For The Analysis of Allelic Data. Version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html. [3] A. Tereba, Tools for Analysis of Population Statistics. Profiles in DNA 3 (1999) Promega Corporation (http://www.promega. com/geneticidtools/powerstats/).
[4] B. Reichenpfader, U. Immel, M. Klintschar, Population data on the AmpFlSTR SGM plus PCR amplification kit in Germans and Austrians, Forensic Sci. Int. 132 (2003) 84–86. [5] W. Pepinski, J. Janica, M. Skawronska, A. NiemcunowiczJanica, I. Soltyszewski, Population genetics of 15 STR loci in the population of Podlasie (NE Poland), Forensic Sci. Int. 124 (2001) 226–227. [6] D. Vanek, R. Hradil, B. Budowle, Czech population data on 10 short tandem repeat loci of SGM Plus STR system kit using DNA purified in FTATM cards, Forensic Sci. Int. 119 (2001) 107–108. [7] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci Int. 110 (2000) 3–5.
Announcement of population data
STR data for the AmpFlSTR SGM Plus loci from Warmia and Mazury (NE Poland) Ireneusz Soltyszewskib, Witold Pepinskia,*, Malgorzata Skawronskaa, Ewa Koc-Zorawskaa, Anna Niemcunowicz-Janicaa, Jerzy Janicaa a
Department of Forensic Medicine, Medical University of Bialystok, Bialystok, Poland b Central Forensic Laboratory of Police, Warsaw, Poland
Received 30 June 2003; received in revised form 22 December 2003; accepted 8 January 2004
Abstract Allele frequencies for the ten STRs included in the AmpFlSTR SGM Plus kit were determined in a sample of 320 unrelated individuals born in the region of Warmia and Mazury (NE Poland). All loci met Hardy–Weinberg expectations. Exact tests disequilibrium analysis revealed only one departure from independence out of 45 pair-wise comparisons of the 10 loci. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Population data; AmpFlSTR SGM Plus; Warmia and Mazury; Poland
Population: Buccal swabs were collected from 320 unrelated healthy donors living in the region of Warmia and Mazury (NE Poland). Extraction: Chelex 100 and proteinase K [1]. PCR: two nano grams of target DNA was amplified according to the manufacturer’s instructions (AmpFlSTR SGM Plus amplification kit, Applied Biosystems). Typing: ABI 310 and reference sequenced ladders (Applied Biosystems) following the manufacturer’s instructions. Results: See Tables 1 and 2. Quality control: Proficiency testing of the Polish Society of Forensic Medicine and Criminology, Hemogenetics Committee.
Analysis of data: GDA v1.2 [2] and PowerStats v1.2 packages [3]. Access to the data: upon request: [email protected]. Other remarks: No differences with European Caucasian populations [4–6] using a pairwise population comparison test (R C contingency test; G. Carmody, Ottawa, Canada). A departure from independence between D3S1358 and D8S1179 was detected (P ¼ 0:007188) using the exact tests disequilibrium analysis. The product rule may be used in a multiple-locus profile frequency estimations. The combined MP and PE for all 10 loci are 9:11 1013 and 0.99, respectively. This paper follows the guidelines for publication of population data requested by the journal [7].
* Corresponding author. Tel.: þ48-85-7485948; fax: þ48-85-7485985. E-mail address: [email protected] (W. Pepinski).
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.01.005
70
I. Soltyszewski et al. / Forensic Science International 141 (2004) 69–71
Table 1 Allele frequencies for AmpFlSTR SGM Plus loci in the population of Warmia and Mazury (NE Poland) Allele
D3S1358
VWA
D16S539
D2S1338
D8S1179
D21S11
D18S51
D19S433
TH01
FGA
6 7 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 18 18.2 19 19.2 20 20.2 21 22 22.2 23 23.2 24 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34.2
– – – – – – – – 0.008 – 0.136 – 0.202 – 0.266 – 0.221 0.152 – 0.016 – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.008 – 0.082 – 0.104 – 0.202 – 0.290 0.226 – 0.072 – 0.016 – – – – – – – – – – – – – – – – – – – – – –
– – 0.008 0.080 – 0.040 0.258 0.340 0.205 – 0.040 – 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.045 – 0.223 0.125 – 0.117 – 0.128 – 0.032 0.011 – 0.080 – 0.098 0.112 0.024 0.005 – – – – – – – – – – – –
– – 0.008 0.013 – 0.066 0.059 0.154 0.343 – 0.247 – 0.093 – 0.011 – 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.003 0.032 0.173 0.189 0.005 0.266 0.069 0.061 0.074 0.011 0.088 0.005 0.019 0.003
– – – – – 0.011 0.011 0.109 0.120 – 0.186 – 0.152 – 0.170 – 0.098 0.069 – 0.035 – 0.024 – 0.016 – – – – – – – – – – – – – – – – – – – –
– – – – – – 0.005 0.072 0.226 0.008 0.359 0.019 0.189 0.045 0.029 0.027 0.003 0.003 0.008 – 0.005 – – – – – – – – – – – – – – – – – – – – – –
0.223 0.141 0.074 0.202 0.356 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – 0.016 – 0.080 – 0.154 0.003 0.189 0.202 0.013 0.122 0.011 0.104 0.069 0.037 – – – – – – – – – – – – –
Ho He P
0.771 0.800 0.185
0.830 0.803 0.358
0.766 0.753 0.913
0.883 0.874 0.059
0.771 0.783 0.738
0.830 0.843 0.886
0.872 0.887 0.868
0.840 0.778 0.111
0.755 0.759 0.340
0.878 0.863 0.830
MP PD PIC PE TPI
0.076 0.924 0.77 0.547 2.19
0.077 0.923 0.77 0.655 2.94
0.104 0.896 0.71 0.537 2.14
0.036 0.964 0.86 0.761 4.27
0.082 0.918 0.75 0.547 2.19
0.044 0.956 0.82 0.655 2.94
0.034 0.966 0.86 0.739 3.92
0.091 0.909 0.74 0.676 3.13
0.098 0.902 0.72 0.519 2.04
0.038 0.962 0.85 0.750 4.09
Ho: Heterozygosity observed; He: Heterozygosity expected; P: Hardy-Weinberg equilibrium, exact test based on 3200 shufflings; MP: Matching Probability; PD: Power of Discrimination; PIC: Polymorphism Information Content; PE: Power of Exclusion; TPI: Typical Paternity Index.
I. Soltyszewski et al. / Forensic Science International 141 (2004) 69–71
71
Table 2 Exact test for linkage disequlibrium P
Locus combination
P
Locus combination
0.245312 0.055938 0.324688 0.007188a 0.095937 0.574375 0.576250 0.244375 0.102813 0.554375 0.794375 0.935625 0.862187 0.427812 0.495312 0.479063 0.531250 0.535625 0.153750 0.465313 0.947500 0.440937 0.954688
D3S1358/VWA D3S1358/TH01 D3S1358/D21S11 D3S1358/D8S1179 D3S1358/D2S1338 VWA/TH01 VWA/D21S11 VWA/D8S1179 VWA/D2S1338 FGA/D16S539 FGA/D18S51 FGA/D19S433 TH01/D16S539 TH01/D18S51 TH01/D19S433 D16S539/D21S11 D16S539/D8S1179 D16S539/D2S1338 D21S11/D8S1179 D21S11/D2S1338 D18S51/D19S433 D8S1179/D19S433 D19S433/D2S1338
0.653750 0.265625 0.423750 0.369063 0.898438 0.184062 0.727500 0.640938 0.428125 0.843125 0.846562 0.741563 0.438125 0.190312 0.372500 0.231875 0.710625 0.537188 0.819063 0.053125 0.355000 0.250312
D3S1358/FGA D3S1358/D16S539 D3S1358/D18S51 D3S1358/D19S433 VWA/FGA VWA/D16S539 VWA/D18S51 VWA/D19S433 FGA/TH01 FGA/D21S11 FGA/D8S1179 FGA/D2S1338 TH01/D21S11 TH01/D8S1179 TH01/D2S1338 D16S539/D18S51 D16S539/D19S433 D21S11/D18S51 D21S11/D19S433 D18S51/D8S1179 D18S51/D2S1338 D8S1179/D2S1338
P: probability based on 3200 shufflings. a Departure from linkage equilibrium.
References [1] P. Wiegand, T. Bajanowski, B. Brinkmann, PCR typing of debris from fingernails, Int. J. Legal Med. 106 (1993) 81–84. [2] P.O. Lewis, D. Zaykin, Genetic Data Analysis: Computer Program For The Analysis of Allelic Data. Version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html. [3] A. Tereba, Tools for Analysis of Population Statistics. Profiles in DNA 3 (1999) Promega Corporation (http://www.promega. com/geneticidtools/powerstats/).
[4] B. Reichenpfader, U. Immel, M. Klintschar, Population data on the AmpFlSTR SGM plus PCR amplification kit in Germans and Austrians, Forensic Sci. Int. 132 (2003) 84–86. [5] W. Pepinski, J. Janica, M. Skawronska, A. NiemcunowiczJanica, I. Soltyszewski, Population genetics of 15 STR loci in the population of Podlasie (NE Poland), Forensic Sci. Int. 124 (2001) 226–227. [6] D. Vanek, R. Hradil, B. Budowle, Czech population data on 10 short tandem repeat loci of SGM Plus STR system kit using DNA purified in FTATM cards, Forensic Sci. Int. 119 (2001) 107–108. [7] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci Int. 110 (2000) 3–5.