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. 2020 May 22;31:105746. doi: 10.1016/j.dib.2020.105746

Population dataset for 21 simple tandem repeat loci in the Akan population of Ghana

Abban Edward Kofi a,b, Hashom Mohd Hakim c, Hussein Omar Khan c, Siti Afifah Ismail c, Anita Ghansah d, Abd Rashid Nur Haslindawaty a, Shaharum Shamsuddin a, Mohd Yusmaidie Aziz e, Geoffrey Keith Chambers f, Hisham Atan Edinur a,g,h,⁎
PMCID: PMC7262416  PMID: 32490095

Abstract

Short tandem repeat (STR) loci are widely used as genetic marker for ancestral and forensic analyses. The latter application includes for paternity testing and DNA profiling of samples collected from scenes of crime and suspects. This survey provides the first dataset for 21 STR loci across the Akan population in Ghana by genotyping of 109 unrelated healthy individuals using Investigator 24plex kit. None of the STR loci screened deviated from Hardy-Weinberg equilibrium after applying Bonferroni correction. Overall, 224 unique alleles were observed with allele frequencies ranging from 0.005 to 0.518. The combined match probability, combined power of exclusion and combined power discrimination were 1 in 4.07 × 10−25, 0.999999999 and 1, respectively. Principal coordinate analysis carried out using 21 STR allele frequency data mapped the Akans with Nigerian subpopulation groups (Hausa, Igbo and Yoruba), but separated from Thais of Thailand, Chechen of Jordan and Tijuana of Mexico.

Keywords: STR, Investigator 24plex, Akan, Ghana

Specifications Table

Subject Genetics
Specific subject area DNA profiling
Type of data Tables and figure
How data were acquired Capillary electrophoresis of STR polymerase chain reaction amplified products on 3500XL Genetic Analyser (Applied Biosystems, USA)
Data format Raw and analyzed
Parameters for data collection Genomic DNA samples extracted from cheek cells were used as templates for amplification of 21 STR loci using Investigator 24plex QS kits (Qiagen, Germany)
Description of data collection Comparison of separated STR fragments with standard allelic ladder included in the Investigator 24plex QS kit using the GeneMapper IDx v4.1 software (Applied Biosystems, USA).
Data source location Forensic Science Program, School of Health Sciences, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
Data accessibility Data available in this article
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Value of the data

  • •

    In the Sub-Saharan region of Africa, population data for these 21 STR loci are only available for Nigerian subpopulations. The 21 STR dataset for the Akans of Ghana reported in this article is thus the first from a different country.

  • •

    Our 21 locus STR dataset provides an important source of information to estimate their statistical value as DNA evidence (match probability, power of exclusion power etc.) for this population group

  • •

    Data from this survey also supports the general value of STR loci for population studies across the region; allele frequencies of the 21 STR loci can be used to examine the past history of population events in Akans including gene flow, natural selection and migration patterns.

  • •

    The population genetic data and forensic statistics reported for the Akans can be used as a reference standard in future studies of other sub-population groups in Ghana; Ewe, Mole-Dagbon, Ga-Dangbe and Guang.

1. Data description

The allelic scores for the 21 STR loci examined across 109 unrelated Akan individuals are shown in Supplementary Table 1. Their allele frequency data and forensic parameters are shown in Table 1. A total of 224 unique alleles were observed with corresponding allele frequency ranging from 0.005 to 0.518. The observed heterozygosity (Ho) ranged from 0.725 (THO1, DS5818 and D7S820 loci) to 0.917 (SE33 locus) while the expected heterozygosity (He) ranged from 0.669 (TH01 locus) to 0.927 (SEE33 locus). After applying Bonferroni correction (p = 0.05/21, at 95% significance level), no deviation from Hardy-Weinberg equilibrium (HWE)were observed. The highest power of discrimination (PD) and polymorphic information content (PIC) were 0.982 and 0.917 (respectively), recorded for the SE33 locus. Locus TH01 showed the lowest PIC (0.628) and PD (0.824) values. The combined matching probability (CMP), combined probability of exclusion (CPE) and combined discriminating power (CPD) were 1 in 4.07 × 10−25, 0.999999999 and 1, respectively.

Table 1.

Allele frequency data and forensic parameters for Akans of Ghana (n=109)

Allele TH01 D3S1358 VWA D21S11 TPOX D1S1656 D12S391 SE33 D10S1248 D22S1045 D19S433 D8S1179 D2S1338 D2S441 D18S51 FGA D16S539 CSF1PO D13S317 D5S818 D7S820
5 0.009
6 0.087 0.087
7 0.518 0.023 0.096 0.009
8 0.211 0.271 0.005 0.009 0.014 0.078 0.023 0.055 0.220
9 0.101 0.257 0.005 0.009 0.220 0.028 0.009 0.005 0.119
9.3 0.055
10 0.018 0.110 0.014 0.005 0.032 0.009 0.009 0.023 0.124 0.252 0.009 0.060 0.358
11 0.220 0.037 0.050 0.096 0.110 0.028 0.362 0.009 0.358 0.239 0.252 0.234 0.239
11.3 0.128
12 0.005 0.023 0.069 0.005 0.138 0.064 0.101 0.133 0.124 0.083 0.138 0.239 0.472 0.353 0.055
12.2 0.041
13 0.028 0.005 0.133 0.014 0.174 0.303 0.147 0.106 0.009 0.147 0.174 0.257
13.2 0.050
14 0.064 0.050 0.005 0.239 0.005 0.046 0.312 0.174 0.179 0.339 0.225 0.041 0.069 0.050 0.032
14.2 0.064
15 0.298 0.280 0.188 0.087 0.050 0.220 0.197 0.037 0.257 0.032 0.211 0.009
15.2 0.069
15.3 0.023
16 0.427 0.220 0.115 0.069 0.050 0.078 0.179 0.046 0.064 0.156 0.005
16.2 0.032
16.3 0.087
17 0.161 0.220 0.028 0.133 0.092 0.018 0.206 0.028 0.073 0.170 0.005
17.3 0.023
18 0.041 0.110 0.005 0.257 0.124 0.037 0.005 0.023 0.115 0.028
18.2 0.009
18.3 0.032 0.005
19 0.005 0.055 0.009 0.183 0.138 0.005 0.151 0.106 0.055
19.2 0.014
20 0.032 0.138 0.096 0.050 0.060 0.018
20.2 0.014
21 0.005 0.050 0.060 0.174 0.023 0.083
21.2 0.009
22 0.050 0.028 0.133 0.005 0.206
22.2 0.009 0.009
23 0.005 0.101 0.009 0.142
23.2 0.018 0.014
24 0.005 0.018 0.119 0.005 0.165
24.2 0.018 0.005
25 0.087 0.087
25.2 0.055 0.005
26 0.005 0.014 0.073
26.2 0.060
27 0.018 0.009 0.037
27.2 0.069
28 0.303 0.018
28.2 0.032
29 0.202 0.005
29.2 0.023
30 0.165
30.2 0.014 0.014
31 0.083
31.2 0.028
32 0.028
32.2 0.073
33 0.014
33.2 0.014
34 0.009
35 0.037
36 0.005
N 7 7 9 16 9 14 12 20 9 10 12 10 12 7 14 21 6 7 8 8 6
MP 0.176 0.149 0.066 0.052 0.089 0.039 0.050 0.018 0.091 0.052 0.055 0.087 0.029 0.099 0.050 0.033 0.093 0.082 0.149 0.109 0.112
PD 0.824 0.851 0.934 0.948 0.911 0.961 0.950 0.982 0.909 0.948 0.945 0.913 0.971 0.901 0.950 0.967 0.907 0.918 0.851 0.891 0.888
PIC 0.628 0.648 0.778 0.804 0.760 0.846 0.828 0.917 0.767 0.820 0.822 0.744 0.873 0.743 0.851 0.873 0.733 0.773 0.631 0.706 0.709
PE 0.468 0.514 0.530 0.530 0.665 0.665 0.756 0.831 0.630 0.630 0.701 0.530 0.701 0.665 0.812 0.756 0.579 0.683 0.370 0.468 0.468
TPI 1.817 2.019 2.096 2.096 3.028 3.028 4.192 6.056 2.725 2.725 3.406 2.096 3.406 3.028 5.450 4.192 2.370 3.206 1.473 1.817 1.817
Ho 0.725 0.752 0.761 0.761 0.835 0.835 0.881 0.917 0.817 0.817 0.853 0.761 0.853 0.835 0.908 0.881 0.789 0.844 0.661 0.725 0.725
He 0.669 0.701 0.809 0.828 0.795 0.864 0.850 0.927 0.800 0.844 0.842 0.779 0.888 0.777 0.869 0.887 0.771 0.805 0.683 0.750 0.753
p-HWE 0.008 0.876 0.252 0.756 0.634 0.296 0.596 0.818 0.127 0.470 0.446 0.183 0.774 0.006 0.034 0.162 0.427 0.348 0.521 0.249 0.036
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N, number of loci; MP, matching probability; PD, power of discrimination; PIC, polymorphic information content; PE, power of exclusion; TPI, typical paternity index; Ho, observed heterozygosity; He, expected heterozygosity; p-HWE, p-value for Hardy-Weinberg equilibrium.

Principal coordinate (PCO) mapping performed using the allele frequency data across all 21 STR loci in the Akans and 7 other previously reported STR datasets (Supplementary Table 2) is shown in Fig. 1. The first and second axes accounted for 59.43% and 12.71% of genetic variability between datasets. The populations from Asia and North America are clustered in the upper left-hand quadrant. In contrast, the populations of Middle Eastern origin are plotted on the lower left quadrant. The Akans plotted closely with the Nigerian subpopulations in the lower right quadrant.

Fig. 1.

Fig 1

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PCO plot of 21 STR loci allele frequency data obtained from present survey of Akans and other reference populations.

2. Experimental design, materials, and methods

2.1. Ethical clearance

This research was reviewed and approved by the Institutional Review Board of Nugochi Memorial Institute of Medical Research (NMIMR), University of Ghana (permit no: NMIMR-IRB CPN 118/15-16 revd. 2019) and the Human Ethics Committee of University Sains Malaysia (USMKK), Health Campus, Kelantan, Malaysia (permit no: USM/JEPeM/16050188).

2.2. Sample collection

A total of 109 healthy unrelated individuals of Akan ethnicity aged between 18 to 45 years were recruited for this research. Each individual provided written informed consent and have at least three generations of un-admixed history. The sampling locations included Accra, Koforidua and Kumasi of Ghana.

2.3. DNA isolation and STR amplification

Cheek cells were collected using buccal swab sticks and genomic DNA was extracted from them using Invisorb® Spin Forensic kit (STRATEC Molecular GmbH, Germany). Total genomic DNA was quantified using Investigator Quantiplex Hyres kit according to manufacturer's recommendation (Qiagen, Hilden, Germany). The Investigator 24plex QS amplification kits (Qiagen, Germany) was utilized to amplify the sex-determining marker Amelogenin, 1 Y-STR locus, 2 quality sensors and 21 autosomal STR loci namely CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, TPOX, D19S433, D1S1656, D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, FGA, D8S1179, SE33, TH01 and vWA on the GeneAmp PCR System 9700 thermal cycler (Applied Biosytems, USA) in total of 12.5 ul reaction volume. PCR products were separated by multi-capillary electrophoresis in 3500XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). The STR alleles were systematically called using the GeneMapper IDx v4.1 software (Applied Biosystems, USA). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided in the kit.

2.4. Statistical analysis

The HWE and the expected heterozygosity (He) values were calculated using Arlequin v3.5.2.2 [1,2]. The significance level for deviation from HWE (<0.05) was adjusted to p > 0.00238 after Bonferroni correction (p = 0.05/21 = 0.00238, where 21 is the number of loci and 0.05 is the standard HWE significance value). Allele frequencies for the 21 STR loci, PD, power of exclusion (PE), MP, typical paternity index (TPI), PIC and Ho values were computed using the Powerstats software version 1.2 [3]. PCO data mapping was used to compare and visualize genetic relatedness between Akans (Ghana), Thais [4], Tijuanans [5], Chechens living in Jordan [6], Saudis [7], and Nigerians [8]). The PCO analysis was performed using the MVSP software version 3.22 [9] and STR datasets for PCO analysis are provided as Supplementary table 2.

Declaration of Competing Interest

The authors declare that they have no known competing interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

The authors acknowledge with thanks donors and volunteers who have provided their samples and contributed to sample collections. We extend our earnest appreciation to the Inspector General of Police of Ghana and Malaysia for supporting this research. Special thanks to the DNA Databank Division, Royal Malaysian Police and Institute for Research in Molecular Medicine, Universiti Sains Malaysia Health Campus, Kubang Kerian for research facilities. This research was supported financially by the Ghana Education Trust Fund (304/PPSK/6150145/G112 and 304/PPSK/6150159) and Universiti Sains Malaysia (Short Term: 304/PPSK / 6315142). Geoff Chambers thanks Victoria University of Wellington for Alumnus Scholar support.

Footnotes

Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.dib.2020.105746.

Appendix. Supplementary materials

mmc1.xml (364B, xml)
mmc2.xlsx (28.3KB, xlsx)
mmc3.xlsx (29.6KB, xlsx)

References

  • 1.Guo S.W., Thompson E.A. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics. 1992;48:361–372. doi: 10.2307/2532296. [DOI] [PubMed] [Google Scholar]
  • 2.Excoffier L., Lischer H.E. Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 2010;10:564–567. doi: 10.1111/j.1755-0998.2010.02847.x. [DOI] [PubMed] [Google Scholar]
  • 3.Tereba A. Tools for analysis of population statistics, Profiles in DNA 2, Promega Corporation. Madison. 1999:14–16. [Google Scholar]
  • 4.Boonderm N, Suriyanratakorn D, Sangpueng S, Onthong N, Nettakul A, Waiyawuth W. Population genetic data of 21 STR markers in Thais of southern border provinces of Thailand. Forensic Sci. Int. Genet. Suppl. Ser. 2017;1(6) https://dio.org/10.1016/j.fsigss e523-525. .2017.09.205. [Google Scholar]
  • 5.Martínez-Cortés G., Zuñiga-Chiquette F., Celorio-Sánchez A.S., García E.R., Antelo- Figueroa A.B., Dalpozzo-Valenzuela V., Valenzuela-Coronado A., Rangel-Villalobos H. Population data for 21 autosomal STR loci (GlobalFiler kit) in two Mexican-Mestizo population from the northwest, Mexico. Int. J. Legal Med. 2019;1(3):781–783. doi: 10.1007/s00414-018-1950-1. https://dio.org/10.1007/s00 133. 414 -018-1950-1. [DOI] [PubMed] [Google Scholar]
  • 6.Al-Eitan L.N., Darwish N.N., Hakooz N.M., Dajani R.B. Assessing the forensic efficiency of the GlobalFiler STR loci among the genetically isolated Chechen subpopulation in Jordan. Gene. 2019;15(720):44078. doi: 10.1016/j.gene.2019.144078. [DOI] [PubMed] [Google Scholar]
  • 7.Khubrani Y.M., Wetton J.H., Jobling M.A. Analysis of 21 autosomal STRs in Saudi Arabia reveals population structure and the influence of consanguinity. Forensic Sci. Int. Genet. 2019;1(39):97–102. doi: 10.1016/j.fsigen.2018.12.006. [DOI] [PubMed] [Google Scholar]
  • 8.Okolie V.O., Cisana S., Schanfield M.S., Adekoya K.O., Oyedeji O.A., Podini D. Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria. Int. J. Legal Med. 1. 2018;132(3):735–737. doi: 10.1007/s00414-017-1722-3. [DOI] [PubMed] [Google Scholar]
  • 9.Kovach W.L. Multivariate techniques for biostratigraphical correlations. J. Geo. Soc. 1993;150:697–705. doi: 10.1144/gsjgs.150.4.0697. [DOI] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

mmc1.xml (364B, xml)
mmc2.xlsx (28.3KB, xlsx)
mmc3.xlsx (29.6KB, xlsx)

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