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Noseda PA, Kenline J, Manning S, Gangitano DA. Population data for DXS6800, DXS101 and DXS8377 loci from Buenos Aires (Argentina). J Forensic Leg Med 2013; 20:522-4. [PMID: 23756526 DOI: 10.1016/j.jflm.2013.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/11/2012] [Accepted: 03/03/2013] [Indexed: 10/27/2022]
Abstract
The X-chromosomal short tandem repeats (X-STRs) DXS6800, DXS101 and DXS8377 were analysed in a population sample from Buenos Aires (Argentina) using a polymerase chain reaction (PCR) multiplex approach with fluorescent detection. We present allele frequencies for these loci in a population comprising 113 women and 99 men. The Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were observed. The homogeneity of allele frequencies of men and women was compared by the Fisher's exact test and showed similar distributions. Linkage disequilibrium (LD) tests were performed in males for all pairs of loci and no significant associations were detected. Parameters of forensic interest were also estimated.
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Affiliation(s)
- Pablo A Noseda
- Secretaria Nacional de Ninez, Adolescencia y Familia (SENAF), Laboratorio de Huellas Digitales Geneticas, Paz Soldan 5200, Buenos Aires C1427DSJ, Argentina
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Laouina A, Aznar JM, Chbel F, de Pancorbo MM. Genetic data of X-chromosomal STRs in a Moroccan population sample (Casablanca) using an X-STR decaplex. Forensic Sci Int Genet 2013; 7:e90-2. [PMID: 23517901 DOI: 10.1016/j.fsigen.2013.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 01/30/2013] [Accepted: 02/23/2013] [Indexed: 11/28/2022]
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3
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García B, Crespillo M, Paredes M, Valverde JL. Population data for 10 X-chromosome STRs from north-east of Spain. Forensic Sci Int Genet 2012; 6:e13-5. [DOI: 10.1016/j.fsigen.2010.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 10/29/2010] [Accepted: 12/24/2010] [Indexed: 11/29/2022]
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Łuczak S, Rogalla U, Malyarchuk BA, Grzybowski T. Diversity of 15 human X chromosome microsatellite loci in Polish population. Forensic Sci Int Genet 2011; 5:e71-7. [DOI: 10.1016/j.fsigen.2010.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 12/20/2010] [Accepted: 12/24/2010] [Indexed: 11/25/2022]
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Ribeiro-Rodrigues EM, Palha TDJBF, Bittencourt EA, Ribeiro-Dos-Santos A, Santos S. Extensive survey of 12 X-STRs reveals genetic heterogeneity among Brazilian populations. Int J Legal Med 2011; 125:445-52. [PMID: 21404027 DOI: 10.1007/s00414-011-0561-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
Abstract
The admixed Brazilian population shows high levels of genetic variability, which resulted from the contribution of three main ethnicities, Amerindian, European, and African. However, due to its huge territory, admixing has been asymmetrical, i.e., the relative contribution from each ethnicity has been unequal in the five geopolitical regions of the country. The aim of this study was to describe genetic variability using a panel of short-tandem repeats on the X chromosome (X-STR) in order to perform a comprehensive evaluation of the usefulness of such markers for forensic purposes in Brazil. Twelve X-STR (DXS9895, DXS7132, DXS6800, DXS9898, DXS6789, DXS7133, GATA172D05, DXS7130, HPRTB, GATA31E08, DXS7423, and DXS10011) were chosen and tested in a sample of 2,234 individuals belonging to 16 out of the 27 Brazilian States, representing all of its five geopolitical regions. No markers showed significant deviation from the Hardy-Weinberg equilibrium, even when analyses were partitioned to represent geopolitical regions. Genetic diversity per locus ranged from 67% (DSX7133) to 95% (DXS10011), and the State of Ceará showed the highest average genetic diversity (79% for all 12 X-STR markers). Considering the Brazilian population as a whole, the power of discrimination of the 12 X-STR panel in females (PDF) was 0.999999999999994, while the power of discrimination in males (PDM) was 0.9999999969. Such high values suggest the potential of that panel to be used in forensic applications and relatedness tests among individuals. Comparisons among the Brazilian populations investigated revealed significant differences when they were compared among each other, a pattern that was maintained when additional populations from Europe and Latin America were compared to Brazilians. Our results highlight the need and usefulness of specific genetic database for forensic purposes in Brazilian populations.
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Affiliation(s)
- Elzemar Martins Ribeiro-Rodrigues
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Cidade Universitária Prof. José da Silva Netto, Av. Augusto Corrêa, 01, Belém, PA, Brazil
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6
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Sixteen X-chromosomal STRs in two octaplex PCRs in Japanese population and development of 15-locus multiplex PCR system. Int J Legal Med 2010; 124:405-14. [PMID: 20512346 DOI: 10.1007/s00414-010-0467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
X-chromosome short tandem repeat (STR) polymorphisms are a useful tool in the fields of human population genetics and personal identification and are indispensable in investigating complex kinship or deficiency cases in circumstances where information on mtDNA or Y-chromosome polymorphisms is unavailable. The purpose of this study was to construct a multiplex polymerase chain reaction (PCR) system capable of analyzing a large number of X-STR loci and establish a 16-X-STR database in the Japanese population We developed two octaplex X-STR systems, one including the DXS7424, GATA172D05, HPRTB, DXS8377, GATA31E08, DXS9895, DXS7423, and DXS981 loci and the other the DXS6803, DXS6789, DXS6800, DXS6809, DXS7133, DXS7132, DXS101, and DXS6807 loci, and conducted a population study in 512 Japanese individuals comprising 339 men and 173 women. A 16-locus multiplex system produced unwanted PCR products due to mixture of the DXS9895 primer with the primers of two other loci. However, a 15-locus multiplex system exclusive of the DXS9895 locus did not. The 15-locus multiplex system amplified the largest number of loci among the X-STR multiplex systems used and afforded a power of discrimination of 0.99999999999997 in women and 0.999999997 in men.
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Hwa HL, Lee JCI, Chang YY, Yin HY, Chen YH, Tseng LH, Su YN, Ko TM. Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system. Int J Legal Med 2010; 125:33-7. [DOI: 10.1007/s00414-009-0414-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 12/21/2009] [Indexed: 10/19/2022]
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Li H, Tang H, Zhang Q, Jiao Z, Bai J, Chang S. A multiplex PCR for 4 X chromosome STR markers and population data from Beijing Han ethnic group. Leg Med (Tokyo) 2009; 11:248-50. [DOI: 10.1016/j.legalmed.2009.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 02/08/2009] [Accepted: 03/25/2009] [Indexed: 11/25/2022]
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Machado FB, Medina-Acosta E. Genetic map of human X-linked microsatellites used in forensic practice. Forensic Sci Int Genet 2009; 3:202-4. [DOI: 10.1016/j.fsigen.2008.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 09/30/2008] [Accepted: 10/20/2008] [Indexed: 11/27/2022]
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10
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Nomenclature discrepancies in the HPRTB short tandem repeat. Int J Legal Med 2009; 123:185-6. [DOI: 10.1007/s00414-008-0314-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 12/18/2008] [Indexed: 10/21/2022]
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11
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Hwa HL, Chang YY, Lee JCI, Yin HY, Chen YH, Tseng LH, Su YN, Ko TM. Thirteen X-chromosomal short tandem repeat loci multiplex data from Taiwanese. Int J Legal Med 2009; 123:263-9. [DOI: 10.1007/s00414-008-0310-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 11/24/2008] [Indexed: 10/21/2022]
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12
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Fracasso T, Schürenkamp M, Brinkmann B, Hohoff C. An X-STR meiosis study in Kurds and Germans: allele frequencies and mutation rates. Int J Legal Med 2008; 122:353-6. [DOI: 10.1007/s00414-008-0231-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 03/06/2008] [Indexed: 11/29/2022]
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Genetic profile characterization and segregation analysis of 10 X-STRs in a sample from Santander, Colombia. Int J Legal Med 2008; 122:347-51. [DOI: 10.1007/s00414-007-0215-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 10/17/2007] [Indexed: 11/25/2022]
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Ribeiro Rodrigues EM, Leite FPDN, Hutz MH, Palha TDJBF, Ribeiro dos Santos ÂKC, dos Santos SEB. A multiplex PCR for 11 X chromosome STR markers and population data from a Brazilian Amazon Region. Forensic Sci Int Genet 2008; 2:154-8. [DOI: 10.1016/j.fsigen.2007.10.179] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 09/25/2007] [Accepted: 10/16/2007] [Indexed: 11/29/2022]
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Aler M, Sánchez-Diz P, Gomes I, Gisbert M, Carracedo A, Amorim A, Gusmão L. Genetic data of 10 X-STRs in a Spanish population sample. Forensic Sci Int 2007; 173:193-6. [PMID: 17320320 DOI: 10.1016/j.forsciint.2006.10.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 10/11/2006] [Indexed: 11/27/2022]
Abstract
In this work, we present population genetic data of 10 X-chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) obtained from sample of 145 unrelated female individuals belonging to Valencia (Spain), a region located in the east of the Iberian Peninsula. All the markers studied present high genetic diversities, similar to those previously reported in other European population samples. No deviations from Hardy-Weinberg equilibrium were observed, with the exception of DXS101 locus. Allele frequencies and parameters of forensic interest for each X-STR were calculated. High mean exclusion chance and power of discrimination values were obtained by combining these 10 X-linked markers. Population comparisons (exact test of population differentiation; pairwise genetic distances) were carried out and low genetic distances were found between our sample and those from other Spanish or European regions.
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Affiliation(s)
- M Aler
- Forensic Genetics U.D. Legal Medicine, University of Valencia E.G., Valencia, Spain
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16
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Zarrabeitia MT, Mijares V, Riancho JA. Forensic efficiency of microsatellites and single nucleotide polymorphisms on the X chromosome. Int J Legal Med 2007; 121:433-7. [PMID: 17436009 DOI: 10.1007/s00414-007-0169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
Polymorphisms located on the X chromosome are being increasingly used in forensic studies. However, they have not been studied as extensively as the autosomal and Y-linked polymorphisms. Therefore, we planned to study the population genetics of two sets of X-linked markers, including short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), and particularly analyze the differences at the microgeographical level. Six X-linked STRs (DXS 9895, DXS 7132, DXS 9898, DXS 6789, GATA 172D05, and DXS 7130) and ten SNPs (rs1229078, rs1544545, rs4442270, rs1874111, rs5968332, rs1166756, rs12849634, rs5932595, rs203648, and rs611711) were studied in two population samples from Cantabria, northern Spain, a mixed coastal population and a relatively isolated small population in the Pas valley. There were statistically significant differences in allelic frequencies of the six STRs studied between both populations. On the other hand, only one out of ten SNPs studied showed between-population differences. Overall Fst values were 0.4-2.9% and 1.8-2.2% for the STRs and the SNPs, respectively. The overall power of discrimination for female samples was higher than 99.99% for both groups of markers. Therefore, these sets of X-linked STRs and SNPs seem to be potentially useful in forensic genetics, but care should be taken when interpreting results from cases that originate from small and relatively isolated populations.
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Affiliation(s)
- María T Zarrabeitia
- Unit of Legal Medicine, University of Cantabria, Av. Herrera Oria sn, 39011, Santander, Spain.
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Gomes I, Prinz M, Pereira R, Meyers C, Mikulasovich RS, Amorim A, Carracedo A, Gusmão L. Genetic analysis of three US population groups using an X-chromosomal STR decaplex. Int J Legal Med 2007; 121:198-203. [PMID: 17237948 DOI: 10.1007/s00414-006-0146-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 11/27/2006] [Indexed: 11/29/2022]
Abstract
An X-chromosomal multiplex amplifying ten short tandem repeats (STRs) in one single PCR reaction was developed and optimized in this work. The X-STRs included were DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101, and DXS6789. Decaplex performance was tested on 377 male samples from three United States population groups, namely, 130 African Americans, 104 Asians, and 143 Hispanics. DXS8377 was the most polymorphic locus across all three populations, whereas DXS7423 was the least informative marker. Genetic distance analysis (R (ST) and F (ST)) performed for the three populations residing in New York showed significant genetic distances between population groups for most pairwise comparisons, except for HPRTB, DXS6809, and DXS7132. When testing linkage disequilibrium for all pairs of loci in the three groups, no significant association was found between any pair of the loci studied, after applying Bonferroni correction. The high values for the average probability of excluding a random man obtained in all three populations when both mother and daughter are tested or when father/daughter relationships are evaluated support the potential of this decaplex system in kinship analysis. Also, the overall high power of discrimination values for samples of female and male origin, confirms the usefulness of this decaplex system in identification analysis. As expected, results also support the use of independent databases comprising these ten X-linked loci for the three US populations evaluated.
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Affiliation(s)
- Iva Gomes
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
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Pereira R, Gomes I, Amorim A, Gusmão L. Genetic diversity of 10 X chromosome STRs in northern Portugal. Int J Legal Med 2007; 121:192-7. [PMID: 17206433 DOI: 10.1007/s00414-006-0144-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 11/27/2006] [Indexed: 11/24/2022]
Abstract
Genetic data of 10 X chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) were obtained in a sample of unrelated males born in the five northern Portuguese districts. In a global sample of 347 individuals, no shared haplotypes were found for this set of markers and single locus gene diversities were high, varying between 0.678 for DXS7423 and 0.921 for DXS8377. Linkage disequilibrium analysis did not reveal consistent evidence of association between the X-STRs used. Population comparisons of northern Portuguese districts (exact test of population differentiation; pairwise genetic distances) and analysis of molecular variance supported genetic homogeneity of this region and therefore a common genetic database was considered. In comparisons with other European data, the only population samples showing statistically significant differences to northern Portugal were Germany and Latvia. The present work demonstrates that these genetic markers are highly discriminating and therefore useful for human identification purposes and anthropological research.
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Affiliation(s)
- Rui Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias, Portugal.
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Robino C, Giolitti A, Gino S, Torre C. Development of two multiplex PCR systems for the analysis of 12 X-chromosomal STR loci in a northwestern Italian population sample. Int J Legal Med 2006; 120:315-8. [PMID: 16862443 DOI: 10.1007/s00414-006-0115-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 06/19/2006] [Indexed: 11/27/2022]
Abstract
Two multiplex polymerase chain reaction systems for the automated profiling of 12 X-chromosomal short tandem repeat (STR) markers were developed. Multiplex A consisted of DXS6789, DXS6809, GATA172D05, DXS101, DXS8378, and DXS8377. Multiplex B consisted of DXS7132, DXS6800, DXS6801, DXS7424, HPRTB, and DXS10011. The set of amplified X-STRs was designed to include groups of closely linked markers (DXS101-DXS7424 and DXS6789-DXS6801-DXS6809) to generate highly informative haplotypes for kinship testing. A population genetics study of the 12 X-STRs was conducted in a northwestern Italian population sample (n=160, 80 women and 80 men). A diallelic pattern at locus DXS6789 was observed in one man.
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Affiliation(s)
- C Robino
- Department of Anatomy, Pharmacology and Legal Medicine, University of Turin, c.so Galileo Galilei 22, 10126, Turin, Italy.
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