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Kofi AE, Agyemang DA, Ghansah A, Awandare GA, Hakim HM, Khan HO, Nur Haslindawaty AR, Aziz MY, Chambers GK, Edinur HA. A genetic Study of the Ghanaian Population Using 15 Autosomal STR Loci. Biochem Genet 2023; 61:1850-1866. [PMID: 36869999 DOI: 10.1007/s10528-023-10347-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/09/2023] [Indexed: 03/05/2023]
Abstract
Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.
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Affiliation(s)
- Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
- Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service, 00233, Accra, Ghana.
| | - David Adjem Agyemang
- Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service, 00233, Accra, Ghana
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, 00233, Accra, Ghana
| | - Gordon A Awandare
- School of Biological Sciences, University of Ghana, Legon, 00233, Accra, Ghana
| | - Hashom Mohd Hakim
- School of Industrial Technologies, Universiti Sains Malaysia, 11800, Gelugor, Pulau Pinang, Malaysia
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Abd Rashid Nur Haslindawaty
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
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2
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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3
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Mutation rates of 15 X chromosomal short tandem repeat markers. Int J Legal Med 2014; 128:579-87. [DOI: 10.1007/s00414-014-1016-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/30/2014] [Indexed: 11/25/2022]
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Sun K, Zhao S, Tian H, Zhang S, Li C. Development of the 16 X-STR loci typing system and genetic analysis in a Shanghai Han population from China. Electrophoresis 2013; 34:3008-15. [DOI: 10.1002/elps.201300234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/20/2013] [Accepted: 06/26/2013] [Indexed: 11/11/2022]
Affiliation(s)
| | - Shumin Zhao
- Shanghai Key Laboratory of Forensic Medicine; Institute of Forensic Sciences; P. R. China
| | | | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine; Institute of Forensic Sciences; P. R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine; Institute of Forensic Sciences; P. R. China
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Poetsch M, Wassenaar D, von Wurmb-Schwark N. Allele frequencies for 11 X chromosomal short tandem repeats in a population from Turkey. Int J Legal Med 2013; 127:913-4. [PMID: 23820971 DOI: 10.1007/s00414-013-0886-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
X chromosomal STRs are nowadays an important part of forensic genetic analysis, especially in complex kinship cases. In this study, allele frequencies and forensic efficiency parameters of the 11 X chromosomal STRs DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377 and DXS7423 in an admixed population from Turkey are presented.
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Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122 Essen, Germany.
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Liu QL, Wang JZ, Quan L, Zhao H, Wu YD, Huang XL, Lu DJ. Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China. PLoS One 2013; 8:e65570. [PMID: 23805185 PMCID: PMC3689794 DOI: 10.1371/journal.pone.0065570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/26/2013] [Indexed: 12/05/2022] Open
Abstract
Background Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. Methodology and Findings Twenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n = 1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5–20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%. Conclusions These results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.
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Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jing-Zhou Wang
- Inner Mongolia Public Security Departments, the Criminal Investigation Division, Inner Mongolia, P.R. China
| | - Li Quan
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ye-Da Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiao-Ling Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - De-Jian Lu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, P.R China
- * E-mail:
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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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Genetic analysis of the 11 X-STR loci in Uigur population from China. Forensic Sci Int Genet 2012; 6:e139-40. [DOI: 10.1016/j.fsigen.2012.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 02/01/2012] [Accepted: 02/21/2012] [Indexed: 11/19/2022]
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9
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Liu QL, Lu DJ, Quan L, Chen YF, Shen M, Zhao H. Development of multiplex PCR system with 15 X-STR loci and genetic analysis in three nationality populations from China. Electrophoresis 2012; 33:1299-305. [DOI: 10.1002/elps.201100558] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou; P. R. China
| | - De-Jian Lu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou; P. R. China
| | - Li Quan
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou; P. R. China
| | - Ye-Fei Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou; P. R. China
| | - Min Shen
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences; Ministry of Justice; Shanghai; P. R. China
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Liu QL, Zhao H, Chen JD, Wang XG, Lu DJ, Quan L. Development and population study of the 12 X-STR loci multiplexes PCR systems. Int J Legal Med 2012; 126:665-70. [PMID: 22349757 DOI: 10.1007/s00414-012-0676-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/01/2012] [Indexed: 10/28/2022]
Abstract
To develop a multiplex polymerase chain reaction (PCR) system with 12 X-chromosomal short-tandem repeat (X-STR) loci and to investigate their polymorphism and linkage and/or independence, the 12 loci (DXS6807, DXS8378, DXS9902, DXS6800, DXS6803, DXS6799, DXS6804, GATA172D05, DXS6854, HPRTB, DXS8377, and DXS7423) were simultaneously analyzed in 1,005 unrelated individuals (574 males and 431 females) from Guangdong Han individuals and Kazakh populations living in China. The allele frequencies and mutation rates were investigated. Allele frequency distribution among different populations was compared. Haplotypes of linkage disequilibrium markers (DXS6807-DXS8378-DXS9902) and linked markers (DXS6804-GATA172D05 and DXS8377-DXS7423) were also reported. A total of 117 alleles, ranging from five to 20 for each locus, were observed in our selected populations. Eight cases with mutation of the selected loci were detected in 9,480 meioses. Pairwise comparisons of allele frequencies distribution showed statistically significant differences at most loci among different populations. Haplotype diversity of linked markers was 0.9404-0.9694. The results indicated that this multiplex system is very useful for forensic analysis and may be complementarities for X-12 kits or X-8 kits in forensic case.
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Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
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11
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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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12
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Genetic polymorphisms of 12 X-STR for forensic purposes in Shanghai Han population from China. Mol Biol Rep 2011; 39:5705-7. [DOI: 10.1007/s11033-011-1379-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
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13
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Genetic analysis of the 11 X-STR loci in Uigur and Northern Han populations from China. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Penna LS, Silva FG, Salim PH, Ewald G, Jobim M, Magalhães JADA, Jobim LF. Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample. Int J Legal Med 2011; 126:327-30. [PMID: 22002550 DOI: 10.1007/s00414-011-0629-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 09/26/2011] [Indexed: 10/17/2022]
Abstract
We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni's correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PD(F)) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F (ST) between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.
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Affiliation(s)
- Larissa Siqueira Penna
- Postgraduate Program in Medicine, Medical Sciences, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast. Int J Legal Med 2011; 125:749-52. [DOI: 10.1007/s00414-011-0591-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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16
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Li C, Ma T, Zhao S, Zhang S, Xu J, Zhao Z, Jin L, Li S. Development of 11 X-STR loci typing system and genetic analysis in Tibetan and Northern Han populations from China. Int J Legal Med 2011; 125:753-6. [DOI: 10.1007/s00414-011-0592-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/16/2011] [Indexed: 12/01/2022]
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17
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Liu QL, Lu DJ, Li XG, Zhao H, Zhang JM, Lai YK, Chen YF. Development of the nine X-STR loci typing system and genetic analysis in three nationality populations from China. Int J Legal Med 2010; 125:51-8. [DOI: 10.1007/s00414-010-0520-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 09/30/2010] [Indexed: 10/18/2022]
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The new Powerplex® ESX17 and ESI17 kits in paternity and maternity analyses involving people from Africa—including allele frequencies for three African populations. Int J Legal Med 2010; 125:149-54. [DOI: 10.1007/s00414-010-0502-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022]
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Ferreira da Silva IH, Barbosa AG, Azevedo DA, Sánchez-Diz P, Gusmão L, Tavares CC, Carvalho EF, Ferreira da Silva LA. An X-chromosome pentaplex in two linkage groups: Haplotype data in Alagoas and Rio de Janeiro populations from Brazil. Forensic Sci Int Genet 2010; 4:e95-100. [DOI: 10.1016/j.fsigen.2009.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 08/06/2009] [Indexed: 12/01/2022]
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20
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Allele frequencies of 11 X-chromosomal loci of two population samples from Africa. Int J Legal Med 2010; 125:307-14. [DOI: 10.1007/s00414-010-0451-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 03/17/2010] [Indexed: 11/26/2022]
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21
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Bekada A, Benhamamouch S, Boudjema A, Fodil M, Menegon S, Torre C, Robino C. Analysis of 21 X-chromosomal STRs in an Algerian population sample. Int J Legal Med 2009; 124:287-94. [DOI: 10.1007/s00414-009-0397-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 11/18/2009] [Indexed: 11/29/2022]
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22
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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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