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Allele distribution of three X-chromosome STR loci in an antioquian population sample
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Forensic Science International: Genetics Supplement Series 1 (2008) 140–141 www.elsevier.com/locate/FSIGSS
Research article
Allele distribution of three X-chromosome STR loci in an antioquian population sample J.J. Builes a,b,*, R.E. Martinez c,d, C. Espinal a, D. Aguirre a, M.L. Bravo a, L. Gusma˜o e a GENES Ltda., Medellı´n, Colombia Instituto de Biologı´a, Universidad de Antioquia, Medellı´n, Colombia c Laboratorio de Biologı´a Molecular y A´cidos Nucleicos, CIBN-UNMSM, Lima, Peru d ADN Institute, Lima, Peru e IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, R. Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal b
Received 21 August 2007; accepted 10 October 2007
Abstract The X-linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The aim of this study was to describe the polymorphism of three X-chromosomal STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian (Colombian) population sample. PCR products were separated in 4% acrylamide-bis-acrylamide denaturing gels followed by silver staining. Allele size determination and genotyping were performed according to recommendations of the DNA Commission of the International Society of Forensic Genetic using the allelic ladder manufactured at home and based on DNA controls including K562 and 9947A (Promega). Gene frequencies were calculated using ARLEQUIN version 3.11. Population genetic data were obtained by analyzing 127–400 unrelated males and 135 unrelated females from Antioquian (Colombian) population. Distribution of the allele frequencies of these systems for Antioquia population is similar to the European populations. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: X-chromosome; DXS6797; DXS6800; HPRTB; Antioquia; Colombia
1. Introduction The advantage of non-autosomal testing is that males transmit an X-chromosome to all their daughters and a Ychromosome to all of their sons, thus, father and daughters should share at least one allele at every X-linked locus. Xlinked STRs are powerful auxiliary system to autosomal STR, for human identification, kinship and paternity testing [1,2] mainly in deficiency paternity cases when the disputed child is a female, in these cases, investigations X-chromosome markers may yield the desired information, even higher than that of autosomal markers with comparable polymorphism information content (PIC) values [3].
* Corresponding author at: Genes Ltda., Carrera 48, No. 10-45, Cons. 611, Medellı´n, Colombia. Tel.: +57 4 268 48 75; fax: +57 4 318 52 70. E-mail addresses: [email protected], [email protected] (J.J. Builes). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.104
The aim of this study was to describe the polymorphism of three X-chromosome STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian population (Colombian) sample and add those markers to the panel of paternity testing and forensically used markers. 2. Materials and methods DNA samples were obtained from 127 to 400 unrelated males and 135 unrelated females healthy donors who were born in Antioquia (Colombia) and collected from the DNA bank from the paternity testing from Genes Ltda Laboratory. The primer sequences of loci and cycling conditions were as recommended [4–6]. Thermal cycling was conducted using PTC 100 (MJ Research Inc.). Alleles were identified based on the number of variable repeats and their attribution was made by comparison with an in-house constructed allelic ladder and following the published nomenclature and ISFG guidelines for STR analysis [7].
J.J. Builes et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 140–141 Table 1 Allelic frequencies and forensic interest parameters of DXS6797, DXS6800 and HPRTB loci in an Antioquian (Colombian) population sample Allele 6 7 8 9 10 11 12 16 17 18 19 20 21 22 23 24 25 26 27 28 MEC1 MEC2 PD1 PD2
DXS6797
DXS6800
HPRTB 0.1461 0.0126 0.1738 0.0529 0.3224 0.1914 0.1008
0.0428 0.0050 0.0176 0.1587 0.3149 0.2821 0.0982 0.0529 0.0227 0.0025 0.0025 0.7323 0.6282 0.9522 0.7802
0.5045 0.0134 0.1448 0.2507 0.0134 0.0701 0.0030
0.5299 0.4523 0.8813 0.6486
141
Analysis of DXS6797, DXS6800 and HPRTB loci in Antioquia population contributes to the establishment of data bases of X-Chromosome markers to be used like a powerful tool in the human identification, complicated kinship testing and paternity testing, specially in deficiency cases where alleged child is a female. Conflict of interest None. References
0.8951 0.8193 0.9908 0.9043
MEC1: mean exclusion chance in trios involving daughters. MEC2: mean exclusion chance in father/daughter duos lacking maternal genotype information. PD1: power of discrimination in females. PD2: power of discrimination in males.
Power of discrimination in females (PD1) and males (PD2) and mean exclusion chance in trios involving daughters (MEC1) and in father/daughter duos lacking maternal genotype information (MEC2) were determined as proposed by Desmarais [8]. 3. Results and discussion Table 1 shows the allele frequencies and parameters of interest for three STR loci DXS6797, DXS6800 and HPRTB in an Antioquian population sample. Comparison of these allele frequencies with some existing population data for these STR, resulted a significant difference with Japanese, Corea and China Populations [9,10] and are similar to German [11] and Spain population [12]. Power of discrimination (PD) in males and females and mean exclusion chance (MEC) for three X-linked STR are shown in the Table 1. DXS6797 has been proven to the most informative marker for Antioquia population, with PD (0.9522 and 0.7802) for males and females, respectively and MEC (0.7323 and 0.6282) in trios involving daughters and in father/ daughter duos lacking maternal genotype information, respectively.
[1] K.L. Ayres, W.M. Powley, Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure, Forensic Sci. Int. 149 (2005) 201–203. [2] R. Szibor, J. Edelmann, S. Hering, I. Plate, H. Wittig, L. Roewer, P. Wiegand, F. Calı`, V. Romano, M. Michael, Cell line DNA typing in forensic genetics—the necessity of reliable standards, Forensic Sci. Int. 138 (2003) 37–43. [3] H.Y. Lee, M.J. Park, C.K. Jeong, S.Y. Lee, J.-E. Yoo, U. Chun, J.-H. Choi, Ch.-Y. Kim, K.-J. Shin, Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898, Int. J. Legal Med. 118 (2004) 355–360. [4] A. Edwards, H.A. Hammond, L. Jin, C.T. Caskey, R. Chakraborty, Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups, Genomics 12 (1992) 241–253. [5] J. Edelmann, D. Deichsel, S. Hering, I. Plate, R. Szibor, Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377, Forensic Sci. Int. 129 (2002) 99–103. [6] S.H. Shin, J.S. Yu, S.W. Park, G.S. Min, K.W. Chung, Genetic analysis of 18 Xlinked short tandem repeat markers in Korean population, Forensic Sci. Int. 147 (2005) 35–41. [7] P. Gill, B. Brinkmann, E. d’Aloja, J. Andersen, W. Bar, A. Carracedo, B. Dupuy, B. Eriksen, M. Jangblad, V. Johnsson, A.D. Kloosterman, P. Lincoln, N. Morling, S. Rand, M. Sabatier, R. Scheithauer, P. Schneider, M.C. Vide, Considerations from the European DNA profiling group (EDNAP) concerning STR nomenclature, Forensic Sci. Int. 87 (1997) 185–192. [8] D. Desmarais, Y. Zhong, R. Chakraborty, C. Perreault, L. Busque, Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA), J. Forensic Sci. 43 (1998) 1046–1049. [9] S.H. Shin, J.S. Yu, S.W. Park, G.S. Min, K.W. Chung, Genetic analysis of 18 X-linked short tandem repeat markers in Korean population, Forensic Sci. Int. 147 (2005) 35–41. [10] H. Asamura, H. Sakai, M. Ota, H. Fukushima, Japanese population data for eight X-STR loci using two new quadruplex systems, Int. J. Legal Med. 120 (2006) 303–309. [11] J. Edelmann, S. Hering, M. Michael, R. Lessig, D. Deichsel, G. MeierSundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci frequency data from a German population, Forensic Sci. Int. 124 (2001) 215–218. [12] M.T. Zarrabeitia, A. Alonso, J. Martı´n, M.A. Gonza´lez-Gay, J.C. Martı´n-Escudero, M. Martı´nez de Pancorbo, P. Martı´n, F. Ruı´z-Cabello, J.A. Riancho, Analysis of six tetranucleotide polymorphisms of the Xchromosome in different Spanish regions, Int. J. Legal Med. 116 (2002) 368–371.
Forensic Science International: Genetics Supplement Series 1 (2008) 140–141 www.elsevier.com/locate/FSIGSS
Research article
Allele distribution of three X-chromosome STR loci in an antioquian population sample J.J. Builes a,b,*, R.E. Martinez c,d, C. Espinal a, D. Aguirre a, M.L. Bravo a, L. Gusma˜o e a GENES Ltda., Medellı´n, Colombia Instituto de Biologı´a, Universidad de Antioquia, Medellı´n, Colombia c Laboratorio de Biologı´a Molecular y A´cidos Nucleicos, CIBN-UNMSM, Lima, Peru d ADN Institute, Lima, Peru e IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, R. Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal b
Received 21 August 2007; accepted 10 October 2007
Abstract The X-linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The aim of this study was to describe the polymorphism of three X-chromosomal STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian (Colombian) population sample. PCR products were separated in 4% acrylamide-bis-acrylamide denaturing gels followed by silver staining. Allele size determination and genotyping were performed according to recommendations of the DNA Commission of the International Society of Forensic Genetic using the allelic ladder manufactured at home and based on DNA controls including K562 and 9947A (Promega). Gene frequencies were calculated using ARLEQUIN version 3.11. Population genetic data were obtained by analyzing 127–400 unrelated males and 135 unrelated females from Antioquian (Colombian) population. Distribution of the allele frequencies of these systems for Antioquia population is similar to the European populations. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: X-chromosome; DXS6797; DXS6800; HPRTB; Antioquia; Colombia
1. Introduction The advantage of non-autosomal testing is that males transmit an X-chromosome to all their daughters and a Ychromosome to all of their sons, thus, father and daughters should share at least one allele at every X-linked locus. Xlinked STRs are powerful auxiliary system to autosomal STR, for human identification, kinship and paternity testing [1,2] mainly in deficiency paternity cases when the disputed child is a female, in these cases, investigations X-chromosome markers may yield the desired information, even higher than that of autosomal markers with comparable polymorphism information content (PIC) values [3].
* Corresponding author at: Genes Ltda., Carrera 48, No. 10-45, Cons. 611, Medellı´n, Colombia. Tel.: +57 4 268 48 75; fax: +57 4 318 52 70. E-mail addresses: [email protected], [email protected] (J.J. Builes). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.104
The aim of this study was to describe the polymorphism of three X-chromosome STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian population (Colombian) sample and add those markers to the panel of paternity testing and forensically used markers. 2. Materials and methods DNA samples were obtained from 127 to 400 unrelated males and 135 unrelated females healthy donors who were born in Antioquia (Colombia) and collected from the DNA bank from the paternity testing from Genes Ltda Laboratory. The primer sequences of loci and cycling conditions were as recommended [4–6]. Thermal cycling was conducted using PTC 100 (MJ Research Inc.). Alleles were identified based on the number of variable repeats and their attribution was made by comparison with an in-house constructed allelic ladder and following the published nomenclature and ISFG guidelines for STR analysis [7].
J.J. Builes et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 140–141 Table 1 Allelic frequencies and forensic interest parameters of DXS6797, DXS6800 and HPRTB loci in an Antioquian (Colombian) population sample Allele 6 7 8 9 10 11 12 16 17 18 19 20 21 22 23 24 25 26 27 28 MEC1 MEC2 PD1 PD2
DXS6797
DXS6800
HPRTB 0.1461 0.0126 0.1738 0.0529 0.3224 0.1914 0.1008
0.0428 0.0050 0.0176 0.1587 0.3149 0.2821 0.0982 0.0529 0.0227 0.0025 0.0025 0.7323 0.6282 0.9522 0.7802
0.5045 0.0134 0.1448 0.2507 0.0134 0.0701 0.0030
0.5299 0.4523 0.8813 0.6486
141
Analysis of DXS6797, DXS6800 and HPRTB loci in Antioquia population contributes to the establishment of data bases of X-Chromosome markers to be used like a powerful tool in the human identification, complicated kinship testing and paternity testing, specially in deficiency cases where alleged child is a female. Conflict of interest None. References
0.8951 0.8193 0.9908 0.9043
MEC1: mean exclusion chance in trios involving daughters. MEC2: mean exclusion chance in father/daughter duos lacking maternal genotype information. PD1: power of discrimination in females. PD2: power of discrimination in males.
Power of discrimination in females (PD1) and males (PD2) and mean exclusion chance in trios involving daughters (MEC1) and in father/daughter duos lacking maternal genotype information (MEC2) were determined as proposed by Desmarais [8]. 3. Results and discussion Table 1 shows the allele frequencies and parameters of interest for three STR loci DXS6797, DXS6800 and HPRTB in an Antioquian population sample. Comparison of these allele frequencies with some existing population data for these STR, resulted a significant difference with Japanese, Corea and China Populations [9,10] and are similar to German [11] and Spain population [12]. Power of discrimination (PD) in males and females and mean exclusion chance (MEC) for three X-linked STR are shown in the Table 1. DXS6797 has been proven to the most informative marker for Antioquia population, with PD (0.9522 and 0.7802) for males and females, respectively and MEC (0.7323 and 0.6282) in trios involving daughters and in father/ daughter duos lacking maternal genotype information, respectively.
[1] K.L. Ayres, W.M. Powley, Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure, Forensic Sci. Int. 149 (2005) 201–203. [2] R. Szibor, J. Edelmann, S. Hering, I. Plate, H. Wittig, L. Roewer, P. Wiegand, F. Calı`, V. Romano, M. Michael, Cell line DNA typing in forensic genetics—the necessity of reliable standards, Forensic Sci. Int. 138 (2003) 37–43. [3] H.Y. Lee, M.J. Park, C.K. Jeong, S.Y. Lee, J.-E. Yoo, U. Chun, J.-H. Choi, Ch.-Y. Kim, K.-J. Shin, Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898, Int. J. Legal Med. 118 (2004) 355–360. [4] A. Edwards, H.A. Hammond, L. Jin, C.T. Caskey, R. Chakraborty, Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups, Genomics 12 (1992) 241–253. [5] J. Edelmann, D. Deichsel, S. Hering, I. Plate, R. Szibor, Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377, Forensic Sci. Int. 129 (2002) 99–103. [6] S.H. Shin, J.S. Yu, S.W. Park, G.S. Min, K.W. Chung, Genetic analysis of 18 Xlinked short tandem repeat markers in Korean population, Forensic Sci. Int. 147 (2005) 35–41. [7] P. Gill, B. Brinkmann, E. d’Aloja, J. Andersen, W. Bar, A. Carracedo, B. Dupuy, B. Eriksen, M. Jangblad, V. Johnsson, A.D. Kloosterman, P. Lincoln, N. Morling, S. Rand, M. Sabatier, R. Scheithauer, P. Schneider, M.C. Vide, Considerations from the European DNA profiling group (EDNAP) concerning STR nomenclature, Forensic Sci. Int. 87 (1997) 185–192. [8] D. Desmarais, Y. Zhong, R. Chakraborty, C. Perreault, L. Busque, Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA), J. Forensic Sci. 43 (1998) 1046–1049. [9] S.H. Shin, J.S. Yu, S.W. Park, G.S. Min, K.W. Chung, Genetic analysis of 18 X-linked short tandem repeat markers in Korean population, Forensic Sci. Int. 147 (2005) 35–41. [10] H. Asamura, H. Sakai, M. Ota, H. Fukushima, Japanese population data for eight X-STR loci using two new quadruplex systems, Int. J. Legal Med. 120 (2006) 303–309. [11] J. Edelmann, S. Hering, M. Michael, R. Lessig, D. Deichsel, G. MeierSundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci frequency data from a German population, Forensic Sci. Int. 124 (2001) 215–218. [12] M.T. Zarrabeitia, A. Alonso, J. Martı´n, M.A. Gonza´lez-Gay, J.C. Martı´n-Escudero, M. Martı´nez de Pancorbo, P. Martı´n, F. Ruı´z-Cabello, J.A. Riancho, Analysis of six tetranucleotide polymorphisms of the Xchromosome in different Spanish regions, Int. J. Legal Med. 116 (2002) 368–371.