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The distribution of allele frequencies of 15 STRs in Dominican population
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Forensic Science International: Genetics Supplement Series 1 (2008) 322–325 www.elsevier.com/locate/FSIGSS
Research article
The distribution of allele frequencies of 15 STRs in Dominican population Vilma Dı´az a,*, Patria Rivas a, Carmen Olivero a, Angel Carracedo b b
a Laboratorio Clinico Lic. Patria Rivas. Santo Domingo, Dominican Republic Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
Received 11 September 2007; accepted 11 October 2007
Abstract The most effective tools for individual and population genetic characterization that we will use today are STRs. This work presents the results of a population study of 15 autosomal STRs loci included in PowerPlex 16 (Promega Corporation) that has the aim of creating a local database. Buccal swabs and blood samples were obtained from more than two thousands unrelated individuals were born in Dominican Republic and lived there for at least two generations. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Autosomal Marker; PowerPlex 16; Dominican Republic; Database
1. Introduction In the latest years, many countries around the world began a plan studies whose purpose is to create national and local databases and to be acquainted with the expressions frequency of a great number of these DNA loci. Our research has the aim of creating the first Dominican Database according to the recommendations published by ISFG and truly recommended by AABB in relationship testing laboratories. Genetic analysis 15 autosomal STRs loci including the 13 CODIS core: CSF1PO (n = 2378), D3S1358 (n = 2563), D5S818 (n = 2097), D7S820 (n = 2526), D8S1179 (n = 2565), D13S317 (n = 2121), D16S539 (n = 2561), D18S51 (n = 2547), D21S11 (n = 2443), FGA (n = 2286), TH01 (n = 2553), TPOX (n = 2504), and vWA (n = 2386) and pentanucleotides STR loci Penta E (n = 2481) and Penta D (n = 2495) [1,2]. The Dominican Republic is located on the eastern two-thirds of the island of Hispaniola and is 18,816 square miles (48,734 km2). The Republic of Haiti occupies the western portion of the island. Hispaniola is near the center of the West Indies, a group of islands that extend from Florida to Venezuela. To the north of Hispaniola is the Atlantic Ocean, to the south the Caribbean Sea, to the east Puerto Rico, and to the west Cuba. Hispaniola,
Puerto Rico, Cuba, and Jamaica are referred to as the Greater Antilles. The capital, Santo Domingo, was the first permanent European settlement in the New World and was established by Spain in 1496. The population of the Dominican Republic is about 9,183,984 and is increasing at a rate of 1.6% per year [3]. 2. Materials and methods DNA Buccal swabs and blood were obtained from more than two thousands unrelated individuals, who were born in Dominican Republic and lived there for at least two generations. All DNA samples were extracted with DNA IQ System (Promega Corporation) [4]. The 15 autosomal loci specific STRs CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51 D21S11, FGA, TH01, TPOX, and vWA, and pentanucleotides STR loci Penta E and Penta D were amplified with PowerPlex1 16 System kit (Promega Corporation) [5], following the manufacture’s protocol. Fragment length analysis was done by electrophoresis capillary using 3130 Genetic Analyzer (Applied Bio-Systems). DNA View Software version 28.46 performed evaluation of statistical parameters. 3. Results and discussion
* Corresponding author. Tel.: +809 6850950; fax: +809 6876172. E-mail address: [email protected] (V. Dı´az). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.164
Table 2 shows some statistical values useful in forensic casework and paternity text: Homozigosity (HO),
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325
Observed Heterozygosity (OH), Power of Discrimination (PD), and Power of Exclusion (PE). All statistical values were calculated using DNA View Software version 28.46 [6]. 4. Conclusions Table 1 shows the allele frequencies obtained for every STR with the correspond frequencies in the Dominican population. The allelic range changes among the 9 alleles that present in two loci CSF1PO and TH01 and 21 alleles detected in the loci FGA and D21S11. In Table 2 our study Table 1 Allele frequencies for 15 autosomal STRs in Dominican population D3S1358, n = 2563 9 11 12 13 14 15 15.2 16 17 18 19 20 21
0.0004 0.0002 0.0031 0.0049 0.0954 0.2957 0.0002 0.2944 0.1968 0.0991 0.0086 0.0975 0.0002
a = 5126 TH01, n = 2553 4 5 6 7 8 9 9.3 10 11
0.0002 0.0012 0.1998 0.2683 0.1919 0.1594 0.1667 0.0123 0.0196
a = 5106 D18S51, n = 2547 10 10.2 11 12 13 13.2 14 14.2 15 15.2 16 17 18 19 20 21 21.2 22 23 24 27
0.0053 0.0006 0.0096 0.1029 0.0856 0.0022 0.1225 0.0014 0.1455 0.0008 0.1580 0.1500 0.0850 0.0705 0.0324 0.0186 0.0002 0.0065 0.0014 0.0010 0.0002
323
Table 1 (Continued ) a = 5094 PENTA E, n = 2481 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
0.0002 0.0691 0.0004 0.1177 0.1074 0.0181 0.0810 0.0931 0.1520 0.1125 0.0532 0.0617 0.0411 0.0437 0.0266 0.0073 0.0058 0.0075 0.0010 0.0006
a = 4962 D13S317, n = 2121 6 7 8 9 10 11 12 13 14 15
0.0004 0.0002 0.0659 0.0653 0.0473 0.2718 0.3658 0.1247 0.0576 0.0010
a = 4842 D7S820, n = 2526 6 7 8 9 10 11 12 13 14 15
0.0006 0.0107 0.1779 0.1089 0.3122 0.2278 0.1336 0.0228 0.0053 0.0002
a = 5052 D16S539, n = 2561 5 7 8 9 10 11 12 13 14 15 16
0.0008 0.0002 0.0207 0.1882 0.0853 0.2932 0.2310 0.1542 0.0238 0.0023 0.0002
a = 5122 PENTA D, n = 2495 2.2
0.0739
324
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325
Table 1 (Continued )
Table 1 (Continued )
3.2 5 6 7 8
0.0034 0.0194 0.0020 0.0206 0.0551
9 10 10.2 11 12 13 14 15 16 17 18
0.1585 0.1355 0.0002 0.1613 0.1673 0.1357 0.0505 0.0138 0.0020 0.0004 0.0002
a = 4990 vWA, n = 2386 11 12 13 14 15 15.2 16 17 18 19 20 21 22
0.0034 0.0034 0.0136 0.0824 0.1653 0.0004 0.2691 0.2249 0.1588 0.0591 0.0163 0.0029 0.0004
a = 4772 D8S1179, n = 2565 8 9 10 11 12 13 14 15 16 17
0.0035 0.0068 0.0583 0.0737 0.1172 0.2682 0.2632 0.1632 0.0382 0.0078
a = 5130 TPOX, n = 2504 5 6 7 8 9 10 11 12 13 14
0.0012 0.0329 0.0088 0.4127 0.1478 0.0715 0.2684 0.0545 0.0020 0.0002
a = 5008 FGA, n = 2286 17 18 18.2 19 19.2
0.0007 0.0064 0.0079 0.0825 0.0026
20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29
0.0895 0.0020 0.1478 0.0020 0.1619 0.0029 0.1473 0.0007 0.1586 0.0002 0.1029 0.0002 0.0433 0.0264 0.0101 0.0042
a = 4547 CSF1PO, n = 2378 7 8 9 10 11 12 13 14 15
0.0341 0.0376 0.0334 0.2597 0.2744 0.3045 0.0456 0.0095 0.0013
a = 4756 D21S11, n = 2443 24 24.2 25 25.2 26 27 27.2 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2
0.0002 0.0008 0.0010 0.0002 0.0004 0.0312 0.0002 0.1829 0.0419 0.2137 0.0008 0.2340 0.0302 0.0660 0.0855 0.0149 0.0825 0.0034 0.0429 0.0046 0.0042
a = 4774 D5S818, n = 2097 7 8 9 10 11 12 13 14 15 16 a = 4194
0.0083 0.0365 0.0343 0.0577 0.2799 0.3591 0.2053 0.0157 0.0019 0.0012
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325 Table 2 Statistical parameters for the 15 STR loci in Dominican population Locus
N
No. Alleles
Range (repeat units)
HO
OH
PD
PE
D3S1358 TH01 D18S51 PENTA E D13S317 D7S820 D16S539 PENTA D vWA D8S1179 TPOX FGA CSF1PO D21S11 D5S818
2563 2553 2547 2481 2121 2526 2561 2495 2386 2565 2504 2286 2378 2443 2097
13 9 21 20 10 10 11 17 13 10 10 21 9 21 10
11–12 5–10 9–27 5–21.2 815 6.3–14 8–15 2.2–18 12–24 8–18 6–12 17–28 7–16 24.2–35 7–15
0.227 0.204 0.130 0.106 0.249 0.219 0.206 0.130 0.161 0.191 0.290 0.133 0.260 0.151 0.259
0.887 0.898 0.935 0.947 0.876 0.891 0.897 0.935 0.920 0.905 0.855 0.934 0.870 0.925 0.871
0.909 0.928 0.976 0.984 0.911 0.924 0.927 0.970 0.94 0.937 0.855 0.973 0.902 0.961 0.894
0.54 0.60 0.764 0.811 0.53 0.58 0.59 0.739 0.62 0.61 0.47 0.751 0.52 0.70 0.50
presents the statistical parameters for the 15 STR loci in Dominican population. The observed and expected heterozygosity rates showed similar values. All 15 loci were in Hardy–Weinberg equilibrium and the loci were highly
325
polymorphism. The results indicate that these 15 loci are useful genetic markers for human identification and relationship testing in our Dominican population [5,6]. Conflict of interest None. References [1] M. Lancia, et al., Allele frequencies of 15 STR loci in an Italian population, Progress in Forensic Genetic, vol. II, Elsevier, 2006 , pp. 340–342. [2] AABB Guidance for Standards for Relationship Testing Laboratories, 7th edition, 2006 p. 74. [3] Torres-Saillant, Silvio , The tribulations of blackness: stages in Dominican racial identity, Latin American Perspectives, Issue 100, CUNY Dominican Studies Institute, May 1998. [4] Technical Manual, DNA IQ System Promega Corporation, Madison, WI, USA. [5] Technical Manual, PowerPlex 16 System Part TMD012, Promega Corporation, Madison, WI, USA. [6] Brenner, Ch., DNA View Software version 28.46, Copyright 1989–2007.
Forensic Science International: Genetics Supplement Series 1 (2008) 322–325 www.elsevier.com/locate/FSIGSS
Research article
The distribution of allele frequencies of 15 STRs in Dominican population Vilma Dı´az a,*, Patria Rivas a, Carmen Olivero a, Angel Carracedo b b
a Laboratorio Clinico Lic. Patria Rivas. Santo Domingo, Dominican Republic Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
Received 11 September 2007; accepted 11 October 2007
Abstract The most effective tools for individual and population genetic characterization that we will use today are STRs. This work presents the results of a population study of 15 autosomal STRs loci included in PowerPlex 16 (Promega Corporation) that has the aim of creating a local database. Buccal swabs and blood samples were obtained from more than two thousands unrelated individuals were born in Dominican Republic and lived there for at least two generations. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Autosomal Marker; PowerPlex 16; Dominican Republic; Database
1. Introduction In the latest years, many countries around the world began a plan studies whose purpose is to create national and local databases and to be acquainted with the expressions frequency of a great number of these DNA loci. Our research has the aim of creating the first Dominican Database according to the recommendations published by ISFG and truly recommended by AABB in relationship testing laboratories. Genetic analysis 15 autosomal STRs loci including the 13 CODIS core: CSF1PO (n = 2378), D3S1358 (n = 2563), D5S818 (n = 2097), D7S820 (n = 2526), D8S1179 (n = 2565), D13S317 (n = 2121), D16S539 (n = 2561), D18S51 (n = 2547), D21S11 (n = 2443), FGA (n = 2286), TH01 (n = 2553), TPOX (n = 2504), and vWA (n = 2386) and pentanucleotides STR loci Penta E (n = 2481) and Penta D (n = 2495) [1,2]. The Dominican Republic is located on the eastern two-thirds of the island of Hispaniola and is 18,816 square miles (48,734 km2). The Republic of Haiti occupies the western portion of the island. Hispaniola is near the center of the West Indies, a group of islands that extend from Florida to Venezuela. To the north of Hispaniola is the Atlantic Ocean, to the south the Caribbean Sea, to the east Puerto Rico, and to the west Cuba. Hispaniola,
Puerto Rico, Cuba, and Jamaica are referred to as the Greater Antilles. The capital, Santo Domingo, was the first permanent European settlement in the New World and was established by Spain in 1496. The population of the Dominican Republic is about 9,183,984 and is increasing at a rate of 1.6% per year [3]. 2. Materials and methods DNA Buccal swabs and blood were obtained from more than two thousands unrelated individuals, who were born in Dominican Republic and lived there for at least two generations. All DNA samples were extracted with DNA IQ System (Promega Corporation) [4]. The 15 autosomal loci specific STRs CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51 D21S11, FGA, TH01, TPOX, and vWA, and pentanucleotides STR loci Penta E and Penta D were amplified with PowerPlex1 16 System kit (Promega Corporation) [5], following the manufacture’s protocol. Fragment length analysis was done by electrophoresis capillary using 3130 Genetic Analyzer (Applied Bio-Systems). DNA View Software version 28.46 performed evaluation of statistical parameters. 3. Results and discussion
* Corresponding author. Tel.: +809 6850950; fax: +809 6876172. E-mail address: [email protected] (V. Dı´az). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.164
Table 2 shows some statistical values useful in forensic casework and paternity text: Homozigosity (HO),
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325
Observed Heterozygosity (OH), Power of Discrimination (PD), and Power of Exclusion (PE). All statistical values were calculated using DNA View Software version 28.46 [6]. 4. Conclusions Table 1 shows the allele frequencies obtained for every STR with the correspond frequencies in the Dominican population. The allelic range changes among the 9 alleles that present in two loci CSF1PO and TH01 and 21 alleles detected in the loci FGA and D21S11. In Table 2 our study Table 1 Allele frequencies for 15 autosomal STRs in Dominican population D3S1358, n = 2563 9 11 12 13 14 15 15.2 16 17 18 19 20 21
0.0004 0.0002 0.0031 0.0049 0.0954 0.2957 0.0002 0.2944 0.1968 0.0991 0.0086 0.0975 0.0002
a = 5126 TH01, n = 2553 4 5 6 7 8 9 9.3 10 11
0.0002 0.0012 0.1998 0.2683 0.1919 0.1594 0.1667 0.0123 0.0196
a = 5106 D18S51, n = 2547 10 10.2 11 12 13 13.2 14 14.2 15 15.2 16 17 18 19 20 21 21.2 22 23 24 27
0.0053 0.0006 0.0096 0.1029 0.0856 0.0022 0.1225 0.0014 0.1455 0.0008 0.1580 0.1500 0.0850 0.0705 0.0324 0.0186 0.0002 0.0065 0.0014 0.0010 0.0002
323
Table 1 (Continued ) a = 5094 PENTA E, n = 2481 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
0.0002 0.0691 0.0004 0.1177 0.1074 0.0181 0.0810 0.0931 0.1520 0.1125 0.0532 0.0617 0.0411 0.0437 0.0266 0.0073 0.0058 0.0075 0.0010 0.0006
a = 4962 D13S317, n = 2121 6 7 8 9 10 11 12 13 14 15
0.0004 0.0002 0.0659 0.0653 0.0473 0.2718 0.3658 0.1247 0.0576 0.0010
a = 4842 D7S820, n = 2526 6 7 8 9 10 11 12 13 14 15
0.0006 0.0107 0.1779 0.1089 0.3122 0.2278 0.1336 0.0228 0.0053 0.0002
a = 5052 D16S539, n = 2561 5 7 8 9 10 11 12 13 14 15 16
0.0008 0.0002 0.0207 0.1882 0.0853 0.2932 0.2310 0.1542 0.0238 0.0023 0.0002
a = 5122 PENTA D, n = 2495 2.2
0.0739
324
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325
Table 1 (Continued )
Table 1 (Continued )
3.2 5 6 7 8
0.0034 0.0194 0.0020 0.0206 0.0551
9 10 10.2 11 12 13 14 15 16 17 18
0.1585 0.1355 0.0002 0.1613 0.1673 0.1357 0.0505 0.0138 0.0020 0.0004 0.0002
a = 4990 vWA, n = 2386 11 12 13 14 15 15.2 16 17 18 19 20 21 22
0.0034 0.0034 0.0136 0.0824 0.1653 0.0004 0.2691 0.2249 0.1588 0.0591 0.0163 0.0029 0.0004
a = 4772 D8S1179, n = 2565 8 9 10 11 12 13 14 15 16 17
0.0035 0.0068 0.0583 0.0737 0.1172 0.2682 0.2632 0.1632 0.0382 0.0078
a = 5130 TPOX, n = 2504 5 6 7 8 9 10 11 12 13 14
0.0012 0.0329 0.0088 0.4127 0.1478 0.0715 0.2684 0.0545 0.0020 0.0002
a = 5008 FGA, n = 2286 17 18 18.2 19 19.2
0.0007 0.0064 0.0079 0.0825 0.0026
20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29
0.0895 0.0020 0.1478 0.0020 0.1619 0.0029 0.1473 0.0007 0.1586 0.0002 0.1029 0.0002 0.0433 0.0264 0.0101 0.0042
a = 4547 CSF1PO, n = 2378 7 8 9 10 11 12 13 14 15
0.0341 0.0376 0.0334 0.2597 0.2744 0.3045 0.0456 0.0095 0.0013
a = 4756 D21S11, n = 2443 24 24.2 25 25.2 26 27 27.2 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2
0.0002 0.0008 0.0010 0.0002 0.0004 0.0312 0.0002 0.1829 0.0419 0.2137 0.0008 0.2340 0.0302 0.0660 0.0855 0.0149 0.0825 0.0034 0.0429 0.0046 0.0042
a = 4774 D5S818, n = 2097 7 8 9 10 11 12 13 14 15 16 a = 4194
0.0083 0.0365 0.0343 0.0577 0.2799 0.3591 0.2053 0.0157 0.0019 0.0012
V. Dı´az et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 322–325 Table 2 Statistical parameters for the 15 STR loci in Dominican population Locus
N
No. Alleles
Range (repeat units)
HO
OH
PD
PE
D3S1358 TH01 D18S51 PENTA E D13S317 D7S820 D16S539 PENTA D vWA D8S1179 TPOX FGA CSF1PO D21S11 D5S818
2563 2553 2547 2481 2121 2526 2561 2495 2386 2565 2504 2286 2378 2443 2097
13 9 21 20 10 10 11 17 13 10 10 21 9 21 10
11–12 5–10 9–27 5–21.2 815 6.3–14 8–15 2.2–18 12–24 8–18 6–12 17–28 7–16 24.2–35 7–15
0.227 0.204 0.130 0.106 0.249 0.219 0.206 0.130 0.161 0.191 0.290 0.133 0.260 0.151 0.259
0.887 0.898 0.935 0.947 0.876 0.891 0.897 0.935 0.920 0.905 0.855 0.934 0.870 0.925 0.871
0.909 0.928 0.976 0.984 0.911 0.924 0.927 0.970 0.94 0.937 0.855 0.973 0.902 0.961 0.894
0.54 0.60 0.764 0.811 0.53 0.58 0.59 0.739 0.62 0.61 0.47 0.751 0.52 0.70 0.50
presents the statistical parameters for the 15 STR loci in Dominican population. The observed and expected heterozygosity rates showed similar values. All 15 loci were in Hardy–Weinberg equilibrium and the loci were highly
325
polymorphism. The results indicate that these 15 loci are useful genetic markers for human identification and relationship testing in our Dominican population [5,6]. Conflict of interest None. References [1] M. Lancia, et al., Allele frequencies of 15 STR loci in an Italian population, Progress in Forensic Genetic, vol. II, Elsevier, 2006 , pp. 340–342. [2] AABB Guidance for Standards for Relationship Testing Laboratories, 7th edition, 2006 p. 74. [3] Torres-Saillant, Silvio , The tribulations of blackness: stages in Dominican racial identity, Latin American Perspectives, Issue 100, CUNY Dominican Studies Institute, May 1998. [4] Technical Manual, DNA IQ System Promega Corporation, Madison, WI, USA. [5] Technical Manual, PowerPlex 16 System Part TMD012, Promega Corporation, Madison, WI, USA. [6] Brenner, Ch., DNA View Software version 28.46, Copyright 1989–2007.