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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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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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Nguidi M, Flores R, Ribeiro J, Garzón A, Calvopiña M, Zapata S, Cabrera A, Yepez I, Gomes V, Gusmão L, Burgos G. The paternal heritage of self-declared Ecuadorian indigenous people. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zeye MMJ, Li J, Ouedraogo SY, Zha L, Simpore J, Jifeng C. Population data and genetic structure analysis based on 29 Y-STR loci among the ethnolinguistic groups in Burkina Faso. Int J Legal Med 2021; 135:1767-1769. [PMID: 33677620 DOI: 10.1007/s00414-021-02544-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
Burkina Faso (BF) is a landlocked Sahelian country located in the middle of West Africa. Sixty-three local languages are spoken in BF. Despite this high diversity, the BF population remains poorly investigated, and updated forensic parameters with a large number of Y chromosome short tandem repeats (Y-STRs) are still missing. Herein, 447 DNA samples were typed for a cocktail of 29 Y-STR loci. None of these 447 individuals in total shared a common haplotype. The overall Y-STR haplotypes were successfully uploaded online on the Y-STR Haplotype Reference Database (YHRD) with the accession numbers YA004690 and YA004691. The main haplotype diversity was 0.9999999965, which is much higher than that obtained with 12 Y-STRs in a previous study. Haploid Match Probability for the whole dataset was 0.002237. The phylogenetic analysis of 24 ethnic groups of BF shows that the ethnic group named BISSA is closer to Gur speakers than Mande speakers, where they belong. In addition, genetic structure analysis of 49 African subpopulations sheds light on the fact that geographic proximity turns out to be one of the best predictors of genetic affinity between populations.
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Affiliation(s)
- Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.,Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Directorate General of the National Police of Burkina Faso, Directorate of Technical and Scientific Police, Ouagadougou 01, 01 BP: 22, Burkina Faso
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Serge Yannick Ouedraogo
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Department of Biochemistry and molecular biology, School of Life sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.
| | - Cai Jifeng
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, Abdullah MT, Chambers GK, Edinur HA. Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia. Int J Legal Med 2020; 134:1335-1337. [PMID: 31897667 DOI: 10.1007/s00414-019-02237-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia.
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia.
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia
| | - Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, 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.
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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