- Email: [email protected]
Genetic diversity of 12 X-chromosomal short tandem repeats in Jewish populations
Forensic Science International: Genetics Supplement Series 5 (2015) e327–e329
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Genetic diversity of 12 X-chromosomal short tandem repeats in Jewish populations J.F. Ferragut, J.A. Castro, C. Ramon, A. Picornell* Institut Universitari d’Investigacions en Ciències de la Salut (IUNICS) and Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears. Palma de Mallorca, Spain
A R T I C L E I N F O
A B S T R A C T
Article history: Received 19 August 2015 Accepted 18 September 2015 Available online 21 September 2015
Haplotype and allele frequencies of 12 X-STRs included in the Investigator Argus X-12 kit were studied for 313 individuals, representing five populations with known Jewish ancestry. The high efficiency in forensic parameters in all the populations studied demonstrates that this set of markers provides a powerful tool for solving complex kinship cases in Jewish populations. ã 2015 Elsevier Ireland Ltd. All rights reserved.
Keywords: X-STRs X-chromosome Investigator Argus X-12 kit Jews Chuetas
1. Introduction X-Short Tandem Repeat (X-STR) markers have a series of special characteristics that justify their increasing interest in forensic practice, population genetics, and anthropology. Compared with autosomes, the X-chromosome has lower recombination and mutation rates and a smaller effective population size, resulting in faster genetic drift. Consequently, both linkage disequilibrium (LD) and population structure in the X-chromosome are expected to be stronger than in autosomes. X-STRs are particularly useful in paternity testing and kinship analysis, especially in deficient cases, such as grandmother–granddaughter, aunt–niece and cousins. Owing to the complexity of kinship investigation, a new approach of substituting single STRs for stable haplotypes of closely linked loci has been suggested. Jews can be traced back to populations occupying a small geographic area, in the Middle East, several thousand years ago and have maintained continuous cultural and religious traditions despite a series of Diasporas. Contemporary Jews comprise several communities that can be classified according to the location where each community developed. Among others, these include Middle Eastern Jews (Mizrahim) (Iran and Iraq), who have always resided in the Middle East, dating from Babylonian or Persian communities in the fourth to sixth centuries BCE; the Askenazim – the vast
* Corresponding author at: Cra. Valldemossa Km 7,5. 07122-Palma (Balearic Islands, Spain). Fax: +34 971173184. E-mail address: [email protected] (A. Picornell). http://dx.doi.org/10.1016/j.fsigss.2015.09.130 1875-1768/ ã 2015 Elsevier Ireland Ltd. All rights reserved.
majority of living Jews – who lived in communities in central and eastern Europe, but whose origins remain highly contested and enigmatic to this day; the Sephardim (“Spanish” in Hebrew) who, after their expulsion from the Iberian Peninsula in the late 15th century, lived in other Mediterranean countries (especially Bulgaria and Turkey), where they mixed with local Jewish communities formed during classical antiquity; and North African Jews, comprising both Sephardim and Mizrahim, as there exists evidence of Jewish communities in North Africa as early as the first centuries AD that were augmented as a consequence of the Spanish expulsion [1]. Chuetas are an isolated, inbred Spanish community, descending from Majorcan Sephardic Jews. Their peculiar history has kept the memory of their Jewish origin and has prevented their gradual assimilation into the general population [2]. The present study analyzed 474 X-chromosomes from five populations with Jewish ancestry, aiming to build an X-STR database, based on the markers included in the Investigator Argus X-12 kit (Qiagen, Hilden, Germany), for anthropological and forensic purposes. 2. Material and methods DNA samples were collected from 313 unrelated individuals (152 men and 161 women), with known ancestors until at least the third generation, from four Jewish populations (Middle Eastern, Ashkenazi, Sephardic and North African) and Chuetas. The 12 X-STR loci included in the Investigator Argus X-12 Kit were analyzed. PCR amplification for 12X-STR loci was performed using the Investigator Argus X-12 Kit (Qiagen) according to the
e328
J.F. Ferragut et al. / Forensic Science International: Genetics Supplement Series 5 (2015) e327–e329
Table 1 Characteristics of new alleles found in this study. Marker
General structure
DXS10134
PrI22-N8-A6-T-A9- (GAAA)3-GAGA-(GAAA)4-AA(GAAA)-GAGA-(GAAA)4-GAGA-N18-(GAAA)-GTAA(GAAA)3-AAA-[(GAAA)4-AAA]1-2-(GAAA)12-20-N5PrII19 (Edelmann et al.) [7] DXS10079 (AGAG)3-TGAA-AGAG-(AGAA)10-21-AGAG-(AGAA)3 (Hering et al.) [8] DXS10148 (GGAA)4-(AAGA)X-(AAAG)Y-N8-(AAGG)2 (Bekada et al.) [9] DXS10135 (AAGA)3-GAAAG-(GAAA)X-(GGAA)Y-(GAAA)Z 30 flanking region AGAGAATAGAAAA(GAA/-) GAGA (Sumita and Whittle) [10]
New allele
Structure of new allele
Genbank accession number
44.2
PrI22-N8-A6-T-A9- (GAAA)3-GAGA-(GAAA)4-AA-(GAAA)-GAGA-(GAAA)3GAGA-N18-(GAAA)-GTAA-(GAAA)3-AAA-[(GAAA)4-AAA]3-(GAAA)16-N5-PrII19
KC581793
20.1
(AGAG)3-TGAA-AGAG-(AGAA)2-AGAAA-(AGAA)13-AGAG-(AGAA)3
KC662329
22
(GGAA)4-(AAGA)10-(AAAG)4-N8-(AAGG)2
KC662330
25.3
0
(AAGA)3-GAAAG-(GAAA)19-(GGAA)4-(GAAA) 3 flanking region AGAGAA [–––––] AAGAAGAGA
KC737839
Table 2 Statistical parameters of haplotypes of 4-X chromosomal STR trios in 152 Jewish men.
N Haplotypes Unique haplotypes Haplotype Diversity Discrimination Capacity Match probability (%) Frequency of the most common haplotype
Linkage group 1
Linkage group 2
Linkage group 3
Linkage group 4
123 98 (79.7%) 0.9970 80.92% 0.0030 0.0263
95 62 (65.3%) 0.9917 62.50% 0.0083 0.0461
93 66 (71.0%) 0.9881 61.18% 0.0119 0.0592
108 77 (71.3%) 0.9948 71.05% 0.0052 0.0263
lg 1: DXS10148-DXS10135-DXS8378; lg 2: DXS7132-DXS10079-DXS10074; lg 3: DXS10103-HPRTB-DXS10101; lg 4: DXS10146-DXS10134-DXS7423.
manufacturer’s instructions [3]. For genetic typing, an ABIPrism 3130 DNA Genetic Analyzer along with GeneMapper ID3.2 software (Applied Biosystems, Foster City, CA) was used. Forensic parameters were calculated on the Chromosome X homepage (http://www.chrx-str.org). Allele frequencies, exact test of the Hardy–Weinberg equilibrium for the female samples (HWE), pairwise exact test of linkage disequilibrium (LD), and haplotype diversity for the male samples, were carried out using the Arlequin v.3.5 software [4]. 3. Results and discussion We analyzed the 12 X-STR loci included in the Investigator Argus X-12 Kit in five populations with Jewish ancestry: Mizrahim, Ashkenazim, Sephardim, North African, and Chuetas, using 474 Xchromosomes. The highest variability was found in DXS10146 and DXS10135 (29 and 28 alleles, respectively, and observed heterozygosities between 0.8077 and 0.9744), while DXS7423 was the least polymorphic one, with 6 alleles and observed heterozygosities between 0.5000 and 0.8000. No deviations from the Hardy– Weinberg equilibrium were observed after Bonferroni correction. New alleles were described in DXS10134, DXS10019, DXS10148 and DXS10135 markers (Table 1). Forensic parameters of interest were calculated for each X-STR and population. Overall values obtained for Power of Discrimination were high (>4.30E + 08) in both females and males and Power of Exclusion ranged from 1.25E + 05 (Mizrahim Jews) to 3.38E + 05 (North African Jews). Although values differed slightly between populations, the set of loci in the Argus X-12 kit was highly informative in all the Jewish populations studied. Amongst the 152 males analyzed, the 4 X-STR trios of linkage group (lg) 1–4 revealed 123, 95, 93 and 108 haplotypes, respectively (Table 2). Most of them were only observed once,
and the other haplotypes were shared by 2–9 men, displaying frequencies <0.059. Match probability ranged from 0.3% (lg 3) to 1.2% (lg 1). 4. Conclusion In short, the forensic efficiency parameters of the twelve X-STRs investigated in this work demonstrates that this set of markers is highly discriminating and, therefore, provides a powerful tool for solving complex kinship cases in Jewish populations. This study follows ISFG recommendations [5] and the guidelines for publication of population data proposed by the journal [6]. Conflict of interest The authors declare no conflicts of interest Acknowledgments This work was partially supported by grant AAEE24/2014 from the Direcció General de R+D+I (Comunitat Autònoma de les Illes Balears) and European regional Development Fund (ERDF). References [1] H.H. Ben-Sasson, A History of the Jewish People, Harvard Universtity Press, Cambridge, 1976. [2] E. Laub, J. Laub, El mito triunfante: Estudio antropológico-social de los Chuetas mallorquines, Editorial Miguel Font, Palma de Mallorca, 1987. [3] Qiagen, Investigator Argus 12 X STR Kit Handbook, Madrid, S.A, Spain, 2010. [4] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5. A new series of programs to perform population genetics analyses under Lynux and Windows, Mol. Ecol. Res. 10 (2010) 564–567. [5] B. Olaisen, W. Bar, B. Brinkmann, et al., DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1998) 61–63. [6] A. Carracedo, J.M. Butler, L. Gusmao, et al., New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220.
J.F. Ferragut et al. / Forensic Science International: Genetics Supplement Series 5 (2015) e327–e329 [7] J. Edelmann, S. Hering, C. Augustin, R. Szibor, Characterization of the STR markers DXS10146, DXS10134 and DXS10147 located within a 79.1kb región at Xq28, Forensic Sci. Int. 2 (2008) 41–46. [8] S. Hering, C. Augustin, J. Edelmann, et al., DXS10079, DXS10074 and DXS10075 are STRs located within a 280-kb región of Xq12 and provide stable haplotypes useful for complex kinship cases, Int. J. Legal Med. 120 (2006) 337–345.
e329
[9] A. Bekada, S. Benhamamouch, A. Boudjema, et al., Analysis of 21-Xchromosomal STRs in an Algerian population sample, Int. J. Legal Med. 124 (2010) 287–294. [10] D.R. Sumita, M.R. Whittle, Updated allelic structure of the DXS10135 and DXS10078 STR loci, Forensic Sci. Int. Genet. Suppl. Series 2 (2009) 51–52.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Genetic diversity of 12 X-chromosomal short tandem repeats in Jewish populations J.F. Ferragut, J.A. Castro, C. Ramon, A. Picornell* Institut Universitari d’Investigacions en Ciències de la Salut (IUNICS) and Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears. Palma de Mallorca, Spain
A R T I C L E I N F O
A B S T R A C T
Article history: Received 19 August 2015 Accepted 18 September 2015 Available online 21 September 2015
Haplotype and allele frequencies of 12 X-STRs included in the Investigator Argus X-12 kit were studied for 313 individuals, representing five populations with known Jewish ancestry. The high efficiency in forensic parameters in all the populations studied demonstrates that this set of markers provides a powerful tool for solving complex kinship cases in Jewish populations. ã 2015 Elsevier Ireland Ltd. All rights reserved.
Keywords: X-STRs X-chromosome Investigator Argus X-12 kit Jews Chuetas
1. Introduction X-Short Tandem Repeat (X-STR) markers have a series of special characteristics that justify their increasing interest in forensic practice, population genetics, and anthropology. Compared with autosomes, the X-chromosome has lower recombination and mutation rates and a smaller effective population size, resulting in faster genetic drift. Consequently, both linkage disequilibrium (LD) and population structure in the X-chromosome are expected to be stronger than in autosomes. X-STRs are particularly useful in paternity testing and kinship analysis, especially in deficient cases, such as grandmother–granddaughter, aunt–niece and cousins. Owing to the complexity of kinship investigation, a new approach of substituting single STRs for stable haplotypes of closely linked loci has been suggested. Jews can be traced back to populations occupying a small geographic area, in the Middle East, several thousand years ago and have maintained continuous cultural and religious traditions despite a series of Diasporas. Contemporary Jews comprise several communities that can be classified according to the location where each community developed. Among others, these include Middle Eastern Jews (Mizrahim) (Iran and Iraq), who have always resided in the Middle East, dating from Babylonian or Persian communities in the fourth to sixth centuries BCE; the Askenazim – the vast
* Corresponding author at: Cra. Valldemossa Km 7,5. 07122-Palma (Balearic Islands, Spain). Fax: +34 971173184. E-mail address: [email protected] (A. Picornell). http://dx.doi.org/10.1016/j.fsigss.2015.09.130 1875-1768/ ã 2015 Elsevier Ireland Ltd. All rights reserved.
majority of living Jews – who lived in communities in central and eastern Europe, but whose origins remain highly contested and enigmatic to this day; the Sephardim (“Spanish” in Hebrew) who, after their expulsion from the Iberian Peninsula in the late 15th century, lived in other Mediterranean countries (especially Bulgaria and Turkey), where they mixed with local Jewish communities formed during classical antiquity; and North African Jews, comprising both Sephardim and Mizrahim, as there exists evidence of Jewish communities in North Africa as early as the first centuries AD that were augmented as a consequence of the Spanish expulsion [1]. Chuetas are an isolated, inbred Spanish community, descending from Majorcan Sephardic Jews. Their peculiar history has kept the memory of their Jewish origin and has prevented their gradual assimilation into the general population [2]. The present study analyzed 474 X-chromosomes from five populations with Jewish ancestry, aiming to build an X-STR database, based on the markers included in the Investigator Argus X-12 kit (Qiagen, Hilden, Germany), for anthropological and forensic purposes. 2. Material and methods DNA samples were collected from 313 unrelated individuals (152 men and 161 women), with known ancestors until at least the third generation, from four Jewish populations (Middle Eastern, Ashkenazi, Sephardic and North African) and Chuetas. The 12 X-STR loci included in the Investigator Argus X-12 Kit were analyzed. PCR amplification for 12X-STR loci was performed using the Investigator Argus X-12 Kit (Qiagen) according to the
e328
J.F. Ferragut et al. / Forensic Science International: Genetics Supplement Series 5 (2015) e327–e329
Table 1 Characteristics of new alleles found in this study. Marker
General structure
DXS10134
PrI22-N8-A6-T-A9- (GAAA)3-GAGA-(GAAA)4-AA(GAAA)-GAGA-(GAAA)4-GAGA-N18-(GAAA)-GTAA(GAAA)3-AAA-[(GAAA)4-AAA]1-2-(GAAA)12-20-N5PrII19 (Edelmann et al.) [7] DXS10079 (AGAG)3-TGAA-AGAG-(AGAA)10-21-AGAG-(AGAA)3 (Hering et al.) [8] DXS10148 (GGAA)4-(AAGA)X-(AAAG)Y-N8-(AAGG)2 (Bekada et al.) [9] DXS10135 (AAGA)3-GAAAG-(GAAA)X-(GGAA)Y-(GAAA)Z 30 flanking region AGAGAATAGAAAA(GAA/-) GAGA (Sumita and Whittle) [10]
New allele
Structure of new allele
Genbank accession number
44.2
PrI22-N8-A6-T-A9- (GAAA)3-GAGA-(GAAA)4-AA-(GAAA)-GAGA-(GAAA)3GAGA-N18-(GAAA)-GTAA-(GAAA)3-AAA-[(GAAA)4-AAA]3-(GAAA)16-N5-PrII19
KC581793
20.1
(AGAG)3-TGAA-AGAG-(AGAA)2-AGAAA-(AGAA)13-AGAG-(AGAA)3
KC662329
22
(GGAA)4-(AAGA)10-(AAAG)4-N8-(AAGG)2
KC662330
25.3
0
(AAGA)3-GAAAG-(GAAA)19-(GGAA)4-(GAAA) 3 flanking region AGAGAA [–––––] AAGAAGAGA
KC737839
Table 2 Statistical parameters of haplotypes of 4-X chromosomal STR trios in 152 Jewish men.
N Haplotypes Unique haplotypes Haplotype Diversity Discrimination Capacity Match probability (%) Frequency of the most common haplotype
Linkage group 1
Linkage group 2
Linkage group 3
Linkage group 4
123 98 (79.7%) 0.9970 80.92% 0.0030 0.0263
95 62 (65.3%) 0.9917 62.50% 0.0083 0.0461
93 66 (71.0%) 0.9881 61.18% 0.0119 0.0592
108 77 (71.3%) 0.9948 71.05% 0.0052 0.0263
lg 1: DXS10148-DXS10135-DXS8378; lg 2: DXS7132-DXS10079-DXS10074; lg 3: DXS10103-HPRTB-DXS10101; lg 4: DXS10146-DXS10134-DXS7423.
manufacturer’s instructions [3]. For genetic typing, an ABIPrism 3130 DNA Genetic Analyzer along with GeneMapper ID3.2 software (Applied Biosystems, Foster City, CA) was used. Forensic parameters were calculated on the Chromosome X homepage (http://www.chrx-str.org). Allele frequencies, exact test of the Hardy–Weinberg equilibrium for the female samples (HWE), pairwise exact test of linkage disequilibrium (LD), and haplotype diversity for the male samples, were carried out using the Arlequin v.3.5 software [4]. 3. Results and discussion We analyzed the 12 X-STR loci included in the Investigator Argus X-12 Kit in five populations with Jewish ancestry: Mizrahim, Ashkenazim, Sephardim, North African, and Chuetas, using 474 Xchromosomes. The highest variability was found in DXS10146 and DXS10135 (29 and 28 alleles, respectively, and observed heterozygosities between 0.8077 and 0.9744), while DXS7423 was the least polymorphic one, with 6 alleles and observed heterozygosities between 0.5000 and 0.8000. No deviations from the Hardy– Weinberg equilibrium were observed after Bonferroni correction. New alleles were described in DXS10134, DXS10019, DXS10148 and DXS10135 markers (Table 1). Forensic parameters of interest were calculated for each X-STR and population. Overall values obtained for Power of Discrimination were high (>4.30E + 08) in both females and males and Power of Exclusion ranged from 1.25E + 05 (Mizrahim Jews) to 3.38E + 05 (North African Jews). Although values differed slightly between populations, the set of loci in the Argus X-12 kit was highly informative in all the Jewish populations studied. Amongst the 152 males analyzed, the 4 X-STR trios of linkage group (lg) 1–4 revealed 123, 95, 93 and 108 haplotypes, respectively (Table 2). Most of them were only observed once,
and the other haplotypes were shared by 2–9 men, displaying frequencies <0.059. Match probability ranged from 0.3% (lg 3) to 1.2% (lg 1). 4. Conclusion In short, the forensic efficiency parameters of the twelve X-STRs investigated in this work demonstrates that this set of markers is highly discriminating and, therefore, provides a powerful tool for solving complex kinship cases in Jewish populations. This study follows ISFG recommendations [5] and the guidelines for publication of population data proposed by the journal [6]. Conflict of interest The authors declare no conflicts of interest Acknowledgments This work was partially supported by grant AAEE24/2014 from the Direcció General de R+D+I (Comunitat Autònoma de les Illes Balears) and European regional Development Fund (ERDF). References [1] H.H. Ben-Sasson, A History of the Jewish People, Harvard Universtity Press, Cambridge, 1976. [2] E. Laub, J. Laub, El mito triunfante: Estudio antropológico-social de los Chuetas mallorquines, Editorial Miguel Font, Palma de Mallorca, 1987. [3] Qiagen, Investigator Argus 12 X STR Kit Handbook, Madrid, S.A, Spain, 2010. [4] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5. A new series of programs to perform population genetics analyses under Lynux and Windows, Mol. Ecol. Res. 10 (2010) 564–567. [5] B. Olaisen, W. Bar, B. Brinkmann, et al., DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1998) 61–63. [6] A. Carracedo, J.M. Butler, L. Gusmao, et al., New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220.
J.F. Ferragut et al. / Forensic Science International: Genetics Supplement Series 5 (2015) e327–e329 [7] J. Edelmann, S. Hering, C. Augustin, R. Szibor, Characterization of the STR markers DXS10146, DXS10134 and DXS10147 located within a 79.1kb región at Xq28, Forensic Sci. Int. 2 (2008) 41–46. [8] S. Hering, C. Augustin, J. Edelmann, et al., DXS10079, DXS10074 and DXS10075 are STRs located within a 280-kb región of Xq12 and provide stable haplotypes useful for complex kinship cases, Int. J. Legal Med. 120 (2006) 337–345.
e329
[9] A. Bekada, S. Benhamamouch, A. Boudjema, et al., Analysis of 21-Xchromosomal STRs in an Algerian population sample, Int. J. Legal Med. 124 (2010) 287–294. [10] D.R. Sumita, M.R. Whittle, Updated allelic structure of the DXS10135 and DXS10078 STR loci, Forensic Sci. Int. Genet. Suppl. Series 2 (2009) 51–52.