- Email: [email protected]
Population data for 15 loci (Identifiler® Kit) in a sample from the Valley of Mexico
Legal Medicine 7 (2005) 331–333 www.elsevier.com/locate/legalmed
Announcement of Population Data
Population data for 15 loci (Identifilerw Kit) in a sample from the Valley of Mexico A. Luna-Vazqueza,*, G. Vilchis-Dorantesa, M.O. Aguilar-Ruiza, A. Bautista-Rivasa, A.L. Rojo-Navaa, E. Rios-Barriosa, H. Rangel-Villalobosb,* a
Laboratorio de Gene´tica Forense, Direccio´n de la Coordinacio´n General de Servicios Periciales de la Procuradurı´a General de la Republica (PGR), Me´xico D.F., Me´xico b Laboratorio de Gene´tica Molecular (CUCie´nega-UdeG), Universidad de Guadalajara, 47810 Ocotla´n, Jalisco, Me´xico Received 30 April 2005; revised 5 June 2005; accepted 6 June 2005 Available online 25 July 2005
Abstract We analyzed 242 individuals from the Valley of Mexico, including the larger and more cosmopolitan city of this country. They were PCRtyped for 15 STR loci with the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems). Allele frequencies for each STR were estimated and compared to previous reports. Genotype distribution by locus and by two-loci combination was in agreement with Hardy– Weinberg expectations for all fifteen STRs. This STR system in Mexican-mestizos presented a combined probability of exclusion (PE) and discrimination (PD) longer than 99.999%, respectively. q 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Identifiler; Forensic; Mexico
1. Population
4. Typing
242 unrelated individuals implicated in Parentage Tests from Mexico D.F. and satellite cities.
Samples were analyzed using the ABI Prisme 310 Genetic Analyzer (Applied Biosystems). Capillar electrophoresis were carried out for 28 min at 15 kV, 11 mA, 60 8C and a laser power of 9.9 mW.
2. Extraction DNA was extracted from fresh blood by standard phenol–chloroform method, and from buccal swabs by Chelexw 100 method (Sigma Chemical CO. St. Louis MO, USA, Cat. C-7901) 3. PCR
5. Results See Tables 1–2.
6. Quality control w
The AmpFlSTR Identifilere PCR amplification kit (Applied Biosystems, Foster City, Calif.) was used according to the manufacturer’s instructions. * Corresponding authors. Tel.: C392 92 50026; fax: C392 92 53099. E-mail addresses: [email protected] (H. Rangel-Villalobos), [email protected] (H. Rangel-Villalobos).
1344-6223/$ - see front matter q 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2005.06.002
Proficiency testing of the GITAD (http://www.gitad.org).
7. Analysis of data Genetic Data Analysis version 1.1 [1] PowerStats [2].
332
Table 1 Allele frequencies (%) in 242 individuals from the Valley of Mexico for 15 STR loci Allele
D21S11
D7S820
CSFIPO
1.04 0.83
0.83 7.64 4.34
0.62 0.62 1.45
8.70
23.76
28.72
D3S1358
THO1
D13S317
D16S539
27.69 37.81 5.79 6.4 20.66 1.65
6.4 26.03
0.83 10.12
12.6
24.17
3.73
33.88
24.79
16.94
23.14
11.80
24.79
36.57
20.25
31.61
34.37
4.34
6.8
1.03
10.33
9.30
28.99
0.21
0.4
5.99
7.44
0.62
9.52
0.21
49.59
D2S1338
D19S433
VWA
TPOX
D18S51
0.41 52.48 4.34 0.21
0.21
0.83
24.79
1.4
0.21
13.84 4.13 0.62
16.3 5.8 26.9 16.3
0.41 0.83 0.21 5.58 2.69 17.15 10.54 24.17 6.40 14.67 10.74 4.13 1.65 0.83
2.48
5.18
28.1
0.21
50.52
11.98
9.71
21.33
14.88
11.59
0.21
16.94
6.2
16.3
35.71
9.9
29.3 14.9 6.4 0.4
16.7 5.6 2.9 2.3
1.0 6.2
0.8 9.09 7.44 0.21 9.3 11.36 0.21 16.94 12.4 0.21 19.42 10.33 1.65 0.21 0.41
1.9 1.4 0.2 0.2
17.8 6.0 0.41 1.7 0.6
1.21
0.83 6.61 19.01 1.03 28.1 2.89 9.3 14.3 1.9 10.3 5.2 0.21 1.22
1.19
1.17
1.13
1.13
1.26
1.22
1.19
0.4
1.32
1.2
1.09
FGA
6.42 0.21 4.8 0.41
0.41 6.4
D5S818
1.29
1.1
1.33
A. Luna-Vazquez et al. / Legal Medicine 7 (2005) 331–333
6 7 8 9 9.3 10 10.2 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 20 20.2 21 22 22.2 23 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33.2 35 MAF
D8S1179
A. Luna-Vazquez et al. / Legal Medicine 7 (2005) 331–333
333
Table 2 Statistical parameters of forensic importance estimated for 15 STR Loci in a population sample from the Valley of Mexico STR
D8S1179
D21S11
D7S820
CSF1PO
D3S1358
THO1
D13S317
D16S539
PD PIC PE Typic PI Het (%) HWE P-value STR PD PIC PE Typic PI Het (%) HWE P-value
0.906 0.690 0.572 2.33 78.5 0.835 D2S1338 0.948 0.800 0.535 2.12 76.4 0.201
0.956 0.600 0.633 2.75 81.8 0.722 D19S433 0.965 0.830 0.775 4.17 88.0 0.055
0.904 0.700 0.535 2.1 76.4 0.908 vWA 0.898 0.710 0.5490 2.2 77.3 0.65
0.866 0.800 0.485 1.89 73.6 0.829 TPOX 0.858 0.570 0.3260 1.34 62.8 0.977
0.843 0.623 0.4069 1.5 68.6 0.205 D18S51 0.967 0.86 0.714 3.56 86.0 1
0.882 0.690 0.419 1.64 69.4 0.054 D5S818 0.856 0.64 0.354 1.42 64.9 0.068
0.955 0.800 0.673 3.1 83.9 0.218 FGA 0.971 0.86 0.772 4.48 88.8 0.537
0.903 0.700 0.587 2.42 79.3 0.149 Combined 0.999999 0.999997 77.05* 1
PI, Paternity Index; PD, Power of Discrimination; PE, Power of Exclusion; Het (%), Percentage of heterozygosity; HWE, Hardy–Weinberg equilibrium test; * Average estimated.
8. Access to the data Available upon request by e-mail ([email protected])
Acknowledgements This work was partially supported by the grant N8J33949-H of the Consejo Nacional de Ciencia y Tecnologı´a (CONACyT) to H.R-V.
9. Other remarks References A population sample from the Valley of Mexico, including the most important and cosmopolitan city from this country, was PCR-typed for fifteen STR loci with the Identifiler PCR amplification kit. Genotype distribution by locus and two loci combination were in agreement with Hardy–Weinberg expectations for all fifteen STRs. The statistical parameters estimated for this STR system were presented in Table 2. The combined power of exclusion (PE) and discrimination (PD) were longer than 0.999999. We detected genetic differentiation with regard to a previous report in Mestizos from Northeastern Mexico for most STR loci (P!0.05) [3]; especially at TH01 and D3S1358 (PZ0.0000). It could be explained by differences in admixture components (Amerindian, Caucasian and/or African), in agreement with the historical records and genetic structure previously noticed in our country [4]. These results justify the establishment of local databases in Mexico for reliable DNA profile interpretation at forensic casework. This is the first report from Mexico D.F. including all these fifteen STRs, in addition to other ones reported from Mexican populations analyzed with these and other different markers [3,5–7].
[1] Lewis PO, Zaykin D. 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; 2001. [2] Tereba A. Tools for analysis of population statistics. Profiles in DNA.: Promega Corp.; 1999. [3] Martı´nez-Gonza´lez LJ, Martı´nez-Espı´n E, Ferna´ndez-Rosado F, ´ lvarez C, Lorente JA, Budowle B. Mexican Moguel MA, Estrada C, A population data of fifteen STR Loci Identifilerw kit in a Chihuahua (North Central Mexico) sample. J Forensic Sci 2005;50:1–3. [4] Gorodesky C, Alaez C, Vazquez-Garcı´a MN, De la Rosa G, Infante E, Balladares S, Toribio R, Pe´rez-Luque E, Mun˜oz L. The genetic structure of Mexican mestizos of different locations: tracking back their origins through MHC genes, blood group systems, and microsatellites. Hum Immunol 2001;62:979–91. [5] Cerda-Flores R, Budowle B, Jin L, Barton SA, Deka R, Chakraborty R. Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci. Am J Hum Biol 2002;14:429–39. [6] Vilchis-Dorantes G, Pa´ez-Riberos LA, Gonza´lez-Martı´n A, Mun˜ozValle F, Rangel-Villalobos H. Genetic distribution of nine STRs in a Mexican Population. Forensic Sci Int 2003;136:96–8. [7] Rangel-Villalobos H, Rivas F, Torres-Rodrı´guez M, Jaloma-Cruz AR, Gallegos-Arreola MP, Lo´pez-Satow J, Cantu´ JM, Figuera LE. Allele frequency distribution of six Amp-FLPs (D1S80, APO-B, VWA, TH01, CSF1PO and Hprtb) in Mexican Population. Forensic Sci Int 1999;105:125–9.
Announcement of Population Data
Population data for 15 loci (Identifilerw Kit) in a sample from the Valley of Mexico A. Luna-Vazqueza,*, G. Vilchis-Dorantesa, M.O. Aguilar-Ruiza, A. Bautista-Rivasa, A.L. Rojo-Navaa, E. Rios-Barriosa, H. Rangel-Villalobosb,* a
Laboratorio de Gene´tica Forense, Direccio´n de la Coordinacio´n General de Servicios Periciales de la Procuradurı´a General de la Republica (PGR), Me´xico D.F., Me´xico b Laboratorio de Gene´tica Molecular (CUCie´nega-UdeG), Universidad de Guadalajara, 47810 Ocotla´n, Jalisco, Me´xico Received 30 April 2005; revised 5 June 2005; accepted 6 June 2005 Available online 25 July 2005
Abstract We analyzed 242 individuals from the Valley of Mexico, including the larger and more cosmopolitan city of this country. They were PCRtyped for 15 STR loci with the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems). Allele frequencies for each STR were estimated and compared to previous reports. Genotype distribution by locus and by two-loci combination was in agreement with Hardy– Weinberg expectations for all fifteen STRs. This STR system in Mexican-mestizos presented a combined probability of exclusion (PE) and discrimination (PD) longer than 99.999%, respectively. q 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Identifiler; Forensic; Mexico
1. Population
4. Typing
242 unrelated individuals implicated in Parentage Tests from Mexico D.F. and satellite cities.
Samples were analyzed using the ABI Prisme 310 Genetic Analyzer (Applied Biosystems). Capillar electrophoresis were carried out for 28 min at 15 kV, 11 mA, 60 8C and a laser power of 9.9 mW.
2. Extraction DNA was extracted from fresh blood by standard phenol–chloroform method, and from buccal swabs by Chelexw 100 method (Sigma Chemical CO. St. Louis MO, USA, Cat. C-7901) 3. PCR
5. Results See Tables 1–2.
6. Quality control w
The AmpFlSTR Identifilere PCR amplification kit (Applied Biosystems, Foster City, Calif.) was used according to the manufacturer’s instructions. * Corresponding authors. Tel.: C392 92 50026; fax: C392 92 53099. E-mail addresses: [email protected] (H. Rangel-Villalobos), [email protected] (H. Rangel-Villalobos).
1344-6223/$ - see front matter q 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2005.06.002
Proficiency testing of the GITAD (http://www.gitad.org).
7. Analysis of data Genetic Data Analysis version 1.1 [1] PowerStats [2].
332
Table 1 Allele frequencies (%) in 242 individuals from the Valley of Mexico for 15 STR loci Allele
D21S11
D7S820
CSFIPO
1.04 0.83
0.83 7.64 4.34
0.62 0.62 1.45
8.70
23.76
28.72
D3S1358
THO1
D13S317
D16S539
27.69 37.81 5.79 6.4 20.66 1.65
6.4 26.03
0.83 10.12
12.6
24.17
3.73
33.88
24.79
16.94
23.14
11.80
24.79
36.57
20.25
31.61
34.37
4.34
6.8
1.03
10.33
9.30
28.99
0.21
0.4
5.99
7.44
0.62
9.52
0.21
49.59
D2S1338
D19S433
VWA
TPOX
D18S51
0.41 52.48 4.34 0.21
0.21
0.83
24.79
1.4
0.21
13.84 4.13 0.62
16.3 5.8 26.9 16.3
0.41 0.83 0.21 5.58 2.69 17.15 10.54 24.17 6.40 14.67 10.74 4.13 1.65 0.83
2.48
5.18
28.1
0.21
50.52
11.98
9.71
21.33
14.88
11.59
0.21
16.94
6.2
16.3
35.71
9.9
29.3 14.9 6.4 0.4
16.7 5.6 2.9 2.3
1.0 6.2
0.8 9.09 7.44 0.21 9.3 11.36 0.21 16.94 12.4 0.21 19.42 10.33 1.65 0.21 0.41
1.9 1.4 0.2 0.2
17.8 6.0 0.41 1.7 0.6
1.21
0.83 6.61 19.01 1.03 28.1 2.89 9.3 14.3 1.9 10.3 5.2 0.21 1.22
1.19
1.17
1.13
1.13
1.26
1.22
1.19
0.4
1.32
1.2
1.09
FGA
6.42 0.21 4.8 0.41
0.41 6.4
D5S818
1.29
1.1
1.33
A. Luna-Vazquez et al. / Legal Medicine 7 (2005) 331–333
6 7 8 9 9.3 10 10.2 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 20 20.2 21 22 22.2 23 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33.2 35 MAF
D8S1179
A. Luna-Vazquez et al. / Legal Medicine 7 (2005) 331–333
333
Table 2 Statistical parameters of forensic importance estimated for 15 STR Loci in a population sample from the Valley of Mexico STR
D8S1179
D21S11
D7S820
CSF1PO
D3S1358
THO1
D13S317
D16S539
PD PIC PE Typic PI Het (%) HWE P-value STR PD PIC PE Typic PI Het (%) HWE P-value
0.906 0.690 0.572 2.33 78.5 0.835 D2S1338 0.948 0.800 0.535 2.12 76.4 0.201
0.956 0.600 0.633 2.75 81.8 0.722 D19S433 0.965 0.830 0.775 4.17 88.0 0.055
0.904 0.700 0.535 2.1 76.4 0.908 vWA 0.898 0.710 0.5490 2.2 77.3 0.65
0.866 0.800 0.485 1.89 73.6 0.829 TPOX 0.858 0.570 0.3260 1.34 62.8 0.977
0.843 0.623 0.4069 1.5 68.6 0.205 D18S51 0.967 0.86 0.714 3.56 86.0 1
0.882 0.690 0.419 1.64 69.4 0.054 D5S818 0.856 0.64 0.354 1.42 64.9 0.068
0.955 0.800 0.673 3.1 83.9 0.218 FGA 0.971 0.86 0.772 4.48 88.8 0.537
0.903 0.700 0.587 2.42 79.3 0.149 Combined 0.999999 0.999997 77.05* 1
PI, Paternity Index; PD, Power of Discrimination; PE, Power of Exclusion; Het (%), Percentage of heterozygosity; HWE, Hardy–Weinberg equilibrium test; * Average estimated.
8. Access to the data Available upon request by e-mail ([email protected])
Acknowledgements This work was partially supported by the grant N8J33949-H of the Consejo Nacional de Ciencia y Tecnologı´a (CONACyT) to H.R-V.
9. Other remarks References A population sample from the Valley of Mexico, including the most important and cosmopolitan city from this country, was PCR-typed for fifteen STR loci with the Identifiler PCR amplification kit. Genotype distribution by locus and two loci combination were in agreement with Hardy–Weinberg expectations for all fifteen STRs. The statistical parameters estimated for this STR system were presented in Table 2. The combined power of exclusion (PE) and discrimination (PD) were longer than 0.999999. We detected genetic differentiation with regard to a previous report in Mestizos from Northeastern Mexico for most STR loci (P!0.05) [3]; especially at TH01 and D3S1358 (PZ0.0000). It could be explained by differences in admixture components (Amerindian, Caucasian and/or African), in agreement with the historical records and genetic structure previously noticed in our country [4]. These results justify the establishment of local databases in Mexico for reliable DNA profile interpretation at forensic casework. This is the first report from Mexico D.F. including all these fifteen STRs, in addition to other ones reported from Mexican populations analyzed with these and other different markers [3,5–7].
[1] Lewis PO, Zaykin D. 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; 2001. [2] Tereba A. Tools for analysis of population statistics. Profiles in DNA.: Promega Corp.; 1999. [3] Martı´nez-Gonza´lez LJ, Martı´nez-Espı´n E, Ferna´ndez-Rosado F, ´ lvarez C, Lorente JA, Budowle B. Mexican Moguel MA, Estrada C, A population data of fifteen STR Loci Identifilerw kit in a Chihuahua (North Central Mexico) sample. J Forensic Sci 2005;50:1–3. [4] Gorodesky C, Alaez C, Vazquez-Garcı´a MN, De la Rosa G, Infante E, Balladares S, Toribio R, Pe´rez-Luque E, Mun˜oz L. The genetic structure of Mexican mestizos of different locations: tracking back their origins through MHC genes, blood group systems, and microsatellites. Hum Immunol 2001;62:979–91. [5] Cerda-Flores R, Budowle B, Jin L, Barton SA, Deka R, Chakraborty R. Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci. Am J Hum Biol 2002;14:429–39. [6] Vilchis-Dorantes G, Pa´ez-Riberos LA, Gonza´lez-Martı´n A, Mun˜ozValle F, Rangel-Villalobos H. Genetic distribution of nine STRs in a Mexican Population. Forensic Sci Int 2003;136:96–8. [7] Rangel-Villalobos H, Rivas F, Torres-Rodrı´guez M, Jaloma-Cruz AR, Gallegos-Arreola MP, Lo´pez-Satow J, Cantu´ JM, Figuera LE. Allele frequency distribution of six Amp-FLPs (D1S80, APO-B, VWA, TH01, CSF1PO and Hprtb) in Mexican Population. Forensic Sci Int 1999;105:125–9.