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Genetic variation of 23 STR loci in a Northeast Colombian population (department of Santander)

Published:October 03, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.015

      Abstract

      The most efficient markers to solve filiation cases are the STRs, including complex cases that require the analysis of a greater number of markers. In this study samples from 123 unrelated individuals from the department of Santander (northeast Colombia) were typed for 23 autosomal STRs included in VeriFiler express kit (Thermo Fisher Scientific),and their allele frequencies and parameters of forensic relevance were determined. Results demonstrate independence within and between the loci analyzed, and the accumulate power of exclusion for the full set of markers was high (99.9996%), as well as the match probability, which was 1 in 8.77E + 29. Therefore, this northeast Colombian population database can be used in forensic to estimate the frequency of the genetic profile using of a multiple locus including in this DNA kit.

      Keywords

      1. Introduction

      Colombia is a country divided into 32 departments, one of which is Santander located on the Northeast region of the country. There are many groups in the territory, with contributions from different continents, thus being considered a multi-ethnic country. The high diversity of the Colombian populations has been confirmed by the analysis of different type of genetic markers, namely autosomal STRs [
      • Castillo A.
      • Gil A.
      • Pico A.
      • Vargas C.
      • Yurrebaso I.
      • García O.
      Genetic variation for 20 STR loci in a northeast Colombian population (Department of Santander).
      ], X-chromosomal Indels [
      • Ibarra A.
      • Restrepo T.
      • Rojas W.
      • Castillo A.
      • Amorim A.
      • et al.
      Evaluating the X Chromosome-Specific diversity of colombian populations using Insertion/Deletion polymorphisms.
      ], Y-chromosome specific STRs, among others [
      • Castillo A.
      • Rueda K.
      • Pico A.
      • Gil A.
      • Vargas C.
      • Rondón F.
      • Gusmão L.
      Comparing Different population groups in Santander – colombia through Y-STR haplotype analysis.
      ].
      Some of these markers are routinely usedin kinship cases, where it is necessary to perform a statistical evaluating of the genetic evidences. For this purpose, it is necessary to establish population allele frequencies in the concerned population.
      The development of new technologies prompt the need to resolve complex cases, where there are no direct relatives, using an increasing number of markers. Therefore, kits are being developed for large marker sets, which need to be evaluated and frequencies must be calculated for the new additional markers.
      Therefore, the 23 autosomal STRs included in the Verifiler Express kit were genotyped in a population sample from Santander, Colombia. Based on the observed allele frequencies, forensically relevant parameters were calculated for each marker and for the complete marker set.

      2. Materials and methods

      A total of 123 blood samples were collected from unrelated individuals born in different places of department of Santander, under informed consent signed by the participants. DNA was extracted with Chelex ® 100 (BioRad) as described by Walsh and col. [
      • Walsh P.S.
      • Metzger D.A.
      • Higuchi R.
      Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.
      ].
      These samples were genotyped for the 23 STRs included in the PCR Amplification multiplex VeriFiler Express kit (Thermo Fisher Scientific), namely D3S1358, vWA, D16S539, CSF1PO, TPOX, Y indel, Amelogenin, D8S1179, D21S11, D18S51, Penta E, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D6S1043, D10S1248, D1S1656, D12S391, D2S1338 and Penta D. Amplified products were separated and detected using an ABI 3500 sequencer, and alleles were assigned with the GeneMapper IDX v.1.5. Statistical analysis included Hardy-Weinberg tests [
      • Excoffier L.
      • Lischer H.E.
      Arlequin suite v 3.5: a new program to perform population genetics analyses under Linux and Windows.
      ] and calculation of parameters of forensic relevance: observed and expected heterozygosities, mean exclusion chance, discrimination power and possible associations between loci, using the software Familias [
      • Kling D.
      • Tillmar A.O.
      • Egeland T.
      Familias 3 – extensions and new functionality.
      ].

      3. Results and discussion

      Allelic frequencies for each marker and the statistical parameters of forensic relevance are presented in Table 1. All markers showed to be in Hardy-Weinberg equilibrium (exact p-values ≥ 0.0716). The locus Penta E presented the highest power of discrimination (PD = 0.9810), and D2S1338 and D6S1043 loci showed the highest power of exclusion (PE = 0.8004). The accumulate power of exclusion for the full set of 23 STR marker-set was high (99.9996%), as well as the match probability, which was 1 in 8.77E + 29.
      Table 1Allelic frequencies of 23 autosomal STR markers and statistical parameters of forensic relevance.
      AllelesD3S1358vWAD16S539CSF1POTPOXD8S1179D21S11D18S51PentaED2S441D19S433TH01
      40,004
      50,028
      60,0120,0040,394
      70,0040,1140,195
      80,0040,0080,4670,0040,0200,061
      90,1060,0240,0770,0040,0160,159
      9,30,0040,175
      100,1950,2600,0240,0570,0120,0280,3820,016
      110,2240,3050,3050,0770,0040,1060,2970,004
      11,20,012
      11,30,061
      120,3090,3410,1060,1380,0930,1340,0410,081
      12,20,012
      130,0080,0040,1460,0570,3370,1380,0730,0120,252
      13,20,0040,106
      140,0810,0690,0120,2600,1710,0980,1870,240
      14,20,0040,020
      150,3580,1100,0040,1060,1420,0810,0160,183
      15,20,033
      160,2970,3900,0160,1380,0810,045
      16,20,004
      170,1420,2560,1750,0370,008
      180,1020,1140,0490,037
      190,0120,0570,0280,024
      200,0280,065
      210,0080,037
      220,008
      230,008
      240,004
      270,0280,004
      280,114
      290,199
      300,313
      30,20,033
      310,065
      31,20,073
      320,016
      32,20,110
      33,20,045
      34,20,004
      N246246246246246246246246246246246246
      Ho0,7320,7240,7970,7070,6750,7970,8290,8940,8860,7480,8780,772
      He0,7500,7520,7870,7220,6730,7820,8270,8720,9220,7280,8270,750
      HWE p-value0,6260,5310,8540,4880,0720,9770,8550,5390,0960,4950,1540,115
      PIC0,7070,7140,7510,6670,6190,7480,8040,8550,9130,6800,8010,710
      PE0,4790,4660,5930,4400,3900,5930,6540,7840,7670,5060,7510,549
      PD0,9000,9040,9160,8640,8240,9210,9230,9610,9810,8710,9320,891
      AllelesFGAD22S1045D5S818D13S317D7S820D6S1043D10S1248D1S1656D12S391D2S1338PentaD
      2,20,008
      30,004
      70,0530,0120,004
      80,0040,1020,1100,0040,020
      90,0530,1260,0650,199
      100,0080,0650,0650,2850,0080,0040,232
      110,0330,3900,2400,2890,1590,0450,199
      120,0040,3050,2640,1910,2110,0240,1020,0040,122
      130,0040,1060,1300,0450,1020,2240,0930,0040,130
      140,0200,0200,0730,0040,1380,4190,0890,073
      14,30,004
      150,4270,0040,0160,2400,1590,0410,012
      15,30,045
      160,4190,0040,0810,1260,0410,012
      16,30,053
      170,0040,0770,0370,0040,0690,0850,211
      17,30,1500,008
      180,0080,0080,0850,0080,2240,049
      18,30,0040,0410,004
      190,0770,1140,0040,2360,146
      19,30,0040,016
      200,0690,0410,1380,150
      20,30,008
      210,1140,0160,0730,049
      21,20,004
      21,30,033
      220,1100,0240,0570,114
      22,20,008
      230,1100,0370,110
      240,1420,0040,0160,073
      250,1950,0120,077
      260,0890,0040,008
      270,045
      280,008
      300,012
      310,004
      N246246246246246246246246246246246
      Ho0,8620,6670,7150,8940,8370,9020,6670,8290,8290,9020,764
      He0,8870,6370,7360,8230,7840,8790,7130,9000,8570,8740,833
      HWE p-value0,1700,9530,4480,5190,2490,4900,1680,2180,4460,7350,302
      PIC0,8720,5660,6940,7960,7480,8630,6620,8870,8390,8560,807
      PE0,7180,3790,4530,7840,6700,8000,3790,6540,6540,8000,534
      PD0,9670,7790,8800,9150,9060,9630,8680,9710,9540,9610,944
      N (sample size); Ho (observed heterozygosity); He (expected heterozygosity); HWE p-value (Hardy–Weinberg equilibrium); PIC (polymorphic information content); PE (probability of paternity exclusion); PD (power of discrimination).

      4. Conclusion

      The results obtained showed that all studied markers have high values of diversity in the population of Santander, and the VeriFiler Express kit seems to be a useful tool for forensic identification and complex kinship analysis in this region.

      Financial resources

      Own resources of Genetic laboratory of the Industrial University of Santander (UIS). LG was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq (ref. 305330/2016-0) and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro – FAPERJ (CNE-2018).

      Declaration of Competing Interest

      None.

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