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Genetic data of 10 X-STR in an Afro-descendant population sample of the Department of Chocó—Colombia

Published:September 23, 2015DOI:https://doi.org/10.1016/j.fsigss.2015.09.200

      Abstract

      In this study, 10 X-STRs: DXS6809, DXS7423, GATA172D05, DXS6789, DXS9902, DXS7132, GATA31E08, DXS7133, DXS9898 and DXS8378 were analyzed in a population sample of Afro-descendants of the Department of Chocó—Colombia. A total of 285 individuals not biologically related were analyzed. All loci studied were in Hardy–Weinberg equilibrium and the markers presented high levels of discrimination power (DP) in men and women, and a power of exclusion (PE) set higher than 99.99% for both trios (father–mother–daughter) and duos (father–daughter).

      Keywords

      1. Introduction

      In the last two decades the use of X-chromosomal markers (X-STRs) in forensics science has increased worldwide [
      • Edelmann J.
      • Hering S.
      • Kuhlisch E.
      • et al.
      Validation of the STR DXS7424 and the linkage situation on the X-chromosome.
      ,
      • Szibor R.
      • Krawczak M.
      • Henring S.
      • et al.
      Use of X-linked markers for forensic purposes.
      ,
      • Builes J.J.
      • Martinez R.
      • Espinal C.
      • et al.
      Allele distribution of three X-chromosome STR loci in an Antioquian population sample.
      ,
      • Gusmão L.
      • Sanchez-Diz P.
      • Alves C.
      • et al.
      A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.
      ]. The X-STRs play an important role in the complex paternity cases and in estimation of genetic distances, moreover, these markers are used in human identification when the STRs located on the autosomal chromosomes (A-STRs) are insufficient, in particular cases of relationship analysis, when the offspring is female [
      • Szibor R.
      • Krawczak M.
      • Henring S.
      • et al.
      Use of X-linked markers for forensic purposes.
      ]. The usefulness of X-STR in forensic practice and in paternity cases is mainly to establish the relation between father and daughter, grandmother and granddaughter, father–mother–daughter and sibling relationship of paternal origin between women [
      • Szibor R.
      • Krawczak M.
      • Henring S.
      • et al.
      Use of X-linked markers for forensic purposes.
      ]. The use of X-chromosomal markers allows the elucidation of complex cases, such as the ones mentioned before, that currently are increasing worldwide.

      2. Materials and methods

      For this study, we used DNA of 285 not biologically related individuals who were born in Chocó—Colombia. The DNA was extracted from whole blood by the method of salting-out [
      • Miller S.A.
      • Dykes D.D.
      • Polesky H.F.
      A single salting out procedure for extracting DNA from human nucleated cells.
      ]. The X-STRs were amplified using an MJ Research thermal cycler PTC-100 in two multiplex reactions, one comprising seven systems (DXS6789, DXS9902, DXS7132, GATA31E08, DXS7133, DXS9898 and DXS8378) and the other three systems (DXS6809, GATA172D05 and DXS7423). The primers and conditions of PCR were performed as recommended by the GHEP-ISFG [
      • Gusmão L.
      • Sanchez-Diz P.
      • Alves C.
      • et al.
      A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.
      ]. Genotyping was performed through comparison with allelic ladders donated by Dra Leonor Gusmão and DNA control reference samples 9947A, K562 (Promega Corporation, Madison, WI, USA). Allelic frequencies, Hardy–Weinberg equilibrium test in female samples and linkage disequilibrium test in male samples were calculated using software ARLEQUIN ver. 3.0 [
      • Excoffier L.
      • Laval G.
      • Schneider S.
      Arlequin ver. 3.0: an integrated software package for population genetics data analysis.
      ]. Statistics for forensic efficiency evaluation of each locus, namely MEC in trios involving daughters (MECT) as well as in father/daughter duos (MECD), and power of discrimination in females (PDF) and in males (PDM) were calculated according to Desmarais et al. [
      • Desmarais D.
      • Zhong Y.
      • Chakraborty R.
      • et al.
      Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA).
      ].

      3. Results and discussion

      Allelic frequencies for the 10 X-STR and the parameters of forensic interest for the population sample of Choco—Colombia are shown in Table 1. The sample population presented great genetic diversity within the 10 X-STR studied. Although DXS6789 and DXS6809 markers showed the highest values for forensic parameters, in general, all the markers used in this study exhibit appropriate values for these parameters to be used in forensic genetics. The absence of linkage disequilibrium that was found in all the X-STR loci in this study, suggesting no significant associations between them and therefore can be considered as loci of independent segregation with high probability of recombination [
      • Gusmão L.
      • Sanchez-Diz P.
      • Alves C.
      • et al.
      A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.
      ]. The study of these X-STRs in the population of Chocó—Colombia allow us to establish a database for X chromosome markers, that can be used in human identification and in the establishment of complex biological relations, especially in cases where the disputed child is female.
      Table 1Allele frequency distribution in an Afro-descendant population sample of the Department of Chocó—Colombia and forensic parameters; expected probability of exclusion in trios involving daughters (MECT), expected probability of exclusion in mother/son duos (MECD), power of discrimination in females (PDF) and power of discrimination in males (PDM). Minimum frequency (MF), observed (Ho) and expected (He) heterozygosity and p values for Hardy Weinberg test (P-HW) in female samples.
      AllelesDXS 8378DXS 9898DXS 7133GATA31E08GATA172D05DXS 7423DXS 6809DXS 7132DXS 9902DXS 6789
      60.00240.1726
      70.00470.01420.0355
      80.00470.03550.17020.0024
      8.30.0686
      90.00240.01650.17020.14890.29310.0449
      100.31910.09930.16790.17020.14180.0520
      110.37350.11110.57450.09460.13480.00950.3168
      120.27660.42320.07330.28840.05200.04490.3593
      12.10.0024
      130.02840.18680.00950.17020.06620.30970.21510.0024
      13.30.0118
      140.07330.06860.42320.36410.00950.0189
      14.30.0024
      150.00950.37830.21990.1560
      160.08510.03070.1206
      16.30.0047
      170.04490.00950.0095
      180.00710.0307
      190.0638
      200.2459
      210.2057
      220.1324
      230.0095
      240.0047
      270.0024
      280.0142
      290.0307
      300.0591
      310.1111
      320.1608
      330.2813
      340.1678
      350.1135
      360.0426
      370.0165
      MF0.02030.02140.01860.02060.02190.01930.02160.02090.02140.0221
      He0.68490.77740.61470.82950.82220.66400.84550.72000.71720.8345
      Ho0.76090.76810.62320.78260.85510.68840.84060.79710.82610.8623
      P-HW0.07750.63860.63430.38220.53790.96550.52280.09110.45140.8015
      PDM0.68130.75330.60740.82150.81310.66420.83490.72000.71940.8353
      PDF0.79740.87930.70350.93630.93020.77590.94550.84360.84290.9457
      MECT0.58030.69350.46510.78970.77820.55290.80770.64200.64110.8081
      MECD0.46840.59200.41440.68140.66690.45930.70410.52870.52720.7022

      Conflict of interest

      None.

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