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Y-chromosome haplotype database in Venezuelan central region and its comparison with other Venezuelan populations
Forensic Science International: Genetics Supplement Series 2 (2009) 407–408
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Research article
Y-chromosome haplotype database in Venezuelan central region and its comparison with other Venezuelan populations Maritza Alvarez a,*, Claudia Marrero a, Airene Dictamen a, Maria Figuera a, Miguel Marrero a, Lisbeth Borjas b, Raul Ferreira a a b
Laboratorio Genomik, Maracay, Bolivarian Republic of Venezuela Laboratorio de Gene´tica, Universidad del Zulia, Maracaibo, Bolivarian Republic of Venezuela
A R T I C L E I N F O
A B S T R A C T
Article history: Received 13 August 2009 Accepted 14 August 2009
One hundred and fifteen unrelated male individuals were sampled and Y-STR genotypes were determined using the PowerPlexY-System (Promega Corp.) and the ABIPRISM 3130 Genetic Analyzer. Allele frequencies and gene diversity for each of the 11 markers analyzed are shown. One hundred and seven different haplotypes were found. Five of them were present in more than one individual, and 101 were not previously found in Caracas and Maracaibo populations [1]. When genetic distance between Central Region and Caracas was estimated, non-significant difference was found. Likewise, differences were not found in markers either. However, when Central Region and Maracaibo were compared, significant differences were found in both genetic distance and DYS385 and DYS438 allele distributions. ß 2009 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-choromosome STR markers Haplotypes Forensic Population genetics
1. Introduction
3. Results and discussion
Although haplotypes frequencies have been previously estimate in Venezuelan populations (Caracas and Maracaibo) [1] genetic homogeneity population have to be confirmed before considering them as a Data Base for others Venezuelan populations. We have characterized alleles for 11 Y-chromosome STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, and DYS439) in Central Region of Venezuela (Carabobo, Cojedes and Aragua States) in order to conform a Data Base for this Region and to compare this one with those previously reported in Venezuela.
Allele frequencies and gene diversity for these 11 Y-STR markers are shown in Table 1. AMOVA locus by locus comparison of markers between Central Region and Caracas showed no significant differences (p > 0.05). However, significant difference was revealed for DYS385 (p = 0.005) and DYS438 (p = 0.027) when comparing Central Region and Maracaibo. One hundred and seven (107) different haplotypes were detected in Central Region of Venezuela (full list available at http://www.labgenomik.com), being only 5 of them carried by more than one individual. Central Region shared 5 and 3 haplotypes with Caracas and Maracaibo, respectively, and only 2 haplotypes are present in all these three populations (Table 2). This set of combined markers presents an haplotype diversity value of 0.982, which means it is highly discriminating in Central Region, as well as in Caracas and Maracaibo populations [1]. genetic distance (pairwise Rst Slatkin’s distance) between Central Region and Caracas was not significative (p = 0.829), but difference was significant between Central Region and Maracaibo (p = 0.018). When a ‘‘chimerical’’ population was constructed joining haplotypes from Central Region and Caracas, Genetic distances between this one and both individual populations was no significant. However, comparison of this ‘‘chimerical’’ population with Maracaibo also has shown a significant difference (p = 0.009).
2. Materials and methods DNA from blood samples of 115 unrelated males living in Central Region of Venezuela were extracted and amplified using PowerPlexY-System (Promega Corp.) and analyzed with an ABIPRISM 3130 Genetic Analyzer, according to manufactures’ recommendations. Allele frequencies, gene and haplotype diversity, and genetic distances among populations were calculated using software ARLEQUIN 3.11 [2].
* Corresponding author. E-mail address: [email protected] (M. Alvarez). 1875-1768/$ – see front matter ß 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2009.08.100
M. Alvarez et al. / Forensic Science International: Genetics Supplement Series 2 (2009) 407–408
408
Table 1 Allele frequencies of Y-STR markers in Central Region of Venezuela (115 alleles). Allele 6 8 9 10 11 12 13 14 15 16 17 21 22 23 24 25 26 27 28 29 30 31 32 33 GD
DYS19
DYS389I
DYS389II
DYS390
DYS391
DYS392
DYS393
DYS437
DYS438
DYS439
0.009 0.078 0.522 0.374 0.017
0.009 0.174 0.564 0.226 0.027
0.183 0.565 0.157 0.078 0.017
0.009 0.044 0.391 0.052 0.426 0.061 0.017
0.130 0.713 0.148 0.009
0.662
0.457
0.009 0.009 0.087 0.356 0.400 0.113 0.026
0.061 0.330 0.157 0.452 0.009 0.496 0.356 0.130 0.009
0.078 0.096 0.235 0.452 0.130 0.009 0.113 0.417 0.304 0.130 0.027 0.009 0.622
0.604
0.709
0.714
0.587
0.615
0.664
0.698
DYS385 Genot
Frequency
Genot
Frequency
10–14 11–11 11–12 11–13 11–14 11–15 11–17 11–18 12–12 12–14 12–15 12–16 13–13 13–14 13–15 13–16 13–17
0.017 0.009 0.017 0.017 0.252 0.096 0.017 0.009 0.009 0.035 0.009 0.009 0.017 0.078 0.061 0.017 0.044
13–18 14–14 14–15 14–16 15–15 15–16 15–17 15–18 15–19 15–20 16–16 16–17 16–18 17–17 17–18 17–19 18–18
0.009 0.035 0.027 0.035 0.017 0.017 0.009 0.017 0.009 0.009 0.035 0.017 0.009 0.017 0.009 0.009 0.009
0.914 GD: Gene diversity. Table 2 Y-chromosome haplotypes shared by Central Region with at least other Venezuelan population. Code in Central Region
Hp015 Hp035 Hp047 Hp049 Hp058 Hp069 a b
Marker
No. individual who carry this haplotype
DYS 19
DYS 389I
DYS 389II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
RC
Ca
13 14 14 14 14 14
14 13 13 13 13 14
30 29 29 29 30 30
24 23 24 24 23 24
9 12 11 11 10 11
11 13 13 13 11 13
13 13 13 13 12 13
13–14 11–15 11–14 11–15 13–18 11–14
14 15 15 15 14 14
10 12 12 12 10 12
10 12 12 13 11 11
4 1 3 2 1 1
1 1 1 2 1b
Ma
2 1 4
Code asigned by Borjas et al (2008)
H15 H40 H53 H57 H65 H87
RC: Central Region (this paper); C: Caracas; M: Maracaibo (Borjas et al., 2008). It has been erroneusly asigned a different code in the original paper (H93, L. Borjas, personal communication).
Although these results allow considering genetic homogeneity between Central Region and Caracas, deeper studies have to be developed before considering this criteria. Conflict of interest None.
References [1] L. Borjas, L.P. Bernal, M.A. Chiurillo, et al., Usefulness of 12 Y-STRs for forensic genetics evaluation in two populations from Venezuela, Legal Med. (Tokyo) 10 (2) (2008) 107–112. [2] L. Excoffier, L.G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinformatics Online 1 (2005) 47–50.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Research article
Y-chromosome haplotype database in Venezuelan central region and its comparison with other Venezuelan populations Maritza Alvarez a,*, Claudia Marrero a, Airene Dictamen a, Maria Figuera a, Miguel Marrero a, Lisbeth Borjas b, Raul Ferreira a a b
Laboratorio Genomik, Maracay, Bolivarian Republic of Venezuela Laboratorio de Gene´tica, Universidad del Zulia, Maracaibo, Bolivarian Republic of Venezuela
A R T I C L E I N F O
A B S T R A C T
Article history: Received 13 August 2009 Accepted 14 August 2009
One hundred and fifteen unrelated male individuals were sampled and Y-STR genotypes were determined using the PowerPlexY-System (Promega Corp.) and the ABIPRISM 3130 Genetic Analyzer. Allele frequencies and gene diversity for each of the 11 markers analyzed are shown. One hundred and seven different haplotypes were found. Five of them were present in more than one individual, and 101 were not previously found in Caracas and Maracaibo populations [1]. When genetic distance between Central Region and Caracas was estimated, non-significant difference was found. Likewise, differences were not found in markers either. However, when Central Region and Maracaibo were compared, significant differences were found in both genetic distance and DYS385 and DYS438 allele distributions. ß 2009 Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-choromosome STR markers Haplotypes Forensic Population genetics
1. Introduction
3. Results and discussion
Although haplotypes frequencies have been previously estimate in Venezuelan populations (Caracas and Maracaibo) [1] genetic homogeneity population have to be confirmed before considering them as a Data Base for others Venezuelan populations. We have characterized alleles for 11 Y-chromosome STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, and DYS439) in Central Region of Venezuela (Carabobo, Cojedes and Aragua States) in order to conform a Data Base for this Region and to compare this one with those previously reported in Venezuela.
Allele frequencies and gene diversity for these 11 Y-STR markers are shown in Table 1. AMOVA locus by locus comparison of markers between Central Region and Caracas showed no significant differences (p > 0.05). However, significant difference was revealed for DYS385 (p = 0.005) and DYS438 (p = 0.027) when comparing Central Region and Maracaibo. One hundred and seven (107) different haplotypes were detected in Central Region of Venezuela (full list available at http://www.labgenomik.com), being only 5 of them carried by more than one individual. Central Region shared 5 and 3 haplotypes with Caracas and Maracaibo, respectively, and only 2 haplotypes are present in all these three populations (Table 2). This set of combined markers presents an haplotype diversity value of 0.982, which means it is highly discriminating in Central Region, as well as in Caracas and Maracaibo populations [1]. genetic distance (pairwise Rst Slatkin’s distance) between Central Region and Caracas was not significative (p = 0.829), but difference was significant between Central Region and Maracaibo (p = 0.018). When a ‘‘chimerical’’ population was constructed joining haplotypes from Central Region and Caracas, Genetic distances between this one and both individual populations was no significant. However, comparison of this ‘‘chimerical’’ population with Maracaibo also has shown a significant difference (p = 0.009).
2. Materials and methods DNA from blood samples of 115 unrelated males living in Central Region of Venezuela were extracted and amplified using PowerPlexY-System (Promega Corp.) and analyzed with an ABIPRISM 3130 Genetic Analyzer, according to manufactures’ recommendations. Allele frequencies, gene and haplotype diversity, and genetic distances among populations were calculated using software ARLEQUIN 3.11 [2].
* Corresponding author. E-mail address: [email protected] (M. Alvarez). 1875-1768/$ – see front matter ß 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2009.08.100
M. Alvarez et al. / Forensic Science International: Genetics Supplement Series 2 (2009) 407–408
408
Table 1 Allele frequencies of Y-STR markers in Central Region of Venezuela (115 alleles). Allele 6 8 9 10 11 12 13 14 15 16 17 21 22 23 24 25 26 27 28 29 30 31 32 33 GD
DYS19
DYS389I
DYS389II
DYS390
DYS391
DYS392
DYS393
DYS437
DYS438
DYS439
0.009 0.078 0.522 0.374 0.017
0.009 0.174 0.564 0.226 0.027
0.183 0.565 0.157 0.078 0.017
0.009 0.044 0.391 0.052 0.426 0.061 0.017
0.130 0.713 0.148 0.009
0.662
0.457
0.009 0.009 0.087 0.356 0.400 0.113 0.026
0.061 0.330 0.157 0.452 0.009 0.496 0.356 0.130 0.009
0.078 0.096 0.235 0.452 0.130 0.009 0.113 0.417 0.304 0.130 0.027 0.009 0.622
0.604
0.709
0.714
0.587
0.615
0.664
0.698
DYS385 Genot
Frequency
Genot
Frequency
10–14 11–11 11–12 11–13 11–14 11–15 11–17 11–18 12–12 12–14 12–15 12–16 13–13 13–14 13–15 13–16 13–17
0.017 0.009 0.017 0.017 0.252 0.096 0.017 0.009 0.009 0.035 0.009 0.009 0.017 0.078 0.061 0.017 0.044
13–18 14–14 14–15 14–16 15–15 15–16 15–17 15–18 15–19 15–20 16–16 16–17 16–18 17–17 17–18 17–19 18–18
0.009 0.035 0.027 0.035 0.017 0.017 0.009 0.017 0.009 0.009 0.035 0.017 0.009 0.017 0.009 0.009 0.009
0.914 GD: Gene diversity. Table 2 Y-chromosome haplotypes shared by Central Region with at least other Venezuelan population. Code in Central Region
Hp015 Hp035 Hp047 Hp049 Hp058 Hp069 a b
Marker
No. individual who carry this haplotype
DYS 19
DYS 389I
DYS 389II
DYS 390
DYS 391
DYS 392
DYS 393
DYS 385
DYS 437
DYS 438
DYS 439
RC
Ca
13 14 14 14 14 14
14 13 13 13 13 14
30 29 29 29 30 30
24 23 24 24 23 24
9 12 11 11 10 11
11 13 13 13 11 13
13 13 13 13 12 13
13–14 11–15 11–14 11–15 13–18 11–14
14 15 15 15 14 14
10 12 12 12 10 12
10 12 12 13 11 11
4 1 3 2 1 1
1 1 1 2 1b
Ma
2 1 4
Code asigned by Borjas et al (2008)
H15 H40 H53 H57 H65 H87
RC: Central Region (this paper); C: Caracas; M: Maracaibo (Borjas et al., 2008). It has been erroneusly asigned a different code in the original paper (H93, L. Borjas, personal communication).
Although these results allow considering genetic homogeneity between Central Region and Caracas, deeper studies have to be developed before considering this criteria. Conflict of interest None.
References [1] L. Borjas, L.P. Bernal, M.A. Chiurillo, et al., Usefulness of 12 Y-STRs for forensic genetics evaluation in two populations from Venezuela, Legal Med. (Tokyo) 10 (2) (2008) 107–112. [2] L. Excoffier, L.G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinformatics Online 1 (2005) 47–50.