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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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Cheffi K, El Khair A, Dahbi N, Talbi J, Hilali A, El Ossmani H. Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations. Mol Genet Genomics 2023; 298:931-941. [PMID: 37162566 DOI: 10.1007/s00438-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.
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Affiliation(s)
- Khadija Cheffi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco.
| | - Abderrazak El Khair
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Noura Dahbi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, Rabat, Morocco
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Dahbi N, Cheffi K, El Khair A, Habbibeddine L, Talbi J, Hilali A, El Ossmani H. Genetic characterization of the Berber-speaking population of Souss (Morocco) based on autosomal STRs. Mol Genet Genomic Med 2023:e2156. [PMID: 36852474 DOI: 10.1002/mgg3.2156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND The Souss, located in southern Morocco, is one of the oldest areas of human settlement in North Africa. Despite this historical relevance, the Souss has not received sufficient attention in terms of population genetic studies. METHODS In this study, we utilized the AmpFlSTR Identifiler PCR amplification system to establish the allelic frequencies and statistical parameters of 15 autosomal STRs (Short Tandem Repeats) in 150 healthy unrelated Berber-speaking individuals from the Souss. We explored the genetic relationships between Souss and other reference populations based on our dataset as well as previously published population data. RESULTS A total of 210 alleles were detected with corresponding allele frequencies ranging from 0.003 to 0.367. The most polymorphic locus was D18S51 with 23 alleles which was also the most discriminating locus as expected. The phylogenetic analysis clustered the Souss closer to the Azrou and southern Moroccan populations. The population comparison showed affinity between the Souss and most North African populations, as well as with Middle Easterners and Europeans. CONCLUSION Historical events and geographical proximity have contributed to the affinity between the Souss and surrounding North African, Southern European, and Middle Eastern populations. Overall, this study highlights the reliability of the 15 STRs for identifying individuals and assessing paternity in the Souss population.
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Affiliation(s)
- Noura Dahbi
- Laboratory of Health Sciences and Technologies, Higher Institute of Health Sciences, Hassan First University of Settat, Settat, Morocco
| | - Khadija Cheffi
- Laboratory of Health Sciences and Technologies, Higher Institute of Health Sciences, Hassan First University of Settat, Settat, Morocco
| | - Abderrazak El Khair
- Laboratory of Health Sciences and Technologies, Higher Institute of Health Sciences, Hassan First University of Settat, Settat, Morocco
| | | | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Laboratory of Health Sciences and Technologies, Higher Institute of Health Sciences, Hassan First University of Settat, Settat, Morocco
| | - Hicham El Ossmani
- Laboratory of Health Sciences and Technologies, Higher Institute of Health Sciences, Hassan First University of Settat, Settat, Morocco.,Royal Gendarmerie Criminalistics Institute, Rabat, Morocco
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Muacevic A, Adler JR. The Impact of Leukemia on the Detection of Short Tandem Repeat (STR) Markers. Cureus 2022; 14:e30954. [PMID: 36465210 PMCID: PMC9711926 DOI: 10.7759/cureus.30954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Short tandem repeats (STRs) have been used for various identity typing methods worldwide. They have high discrimination power in human identification in forensics, paternity testing, missed personal identification, genetic diseases, and gene regulatory functions. They have also been used to detect and monitor the stability of diseases, including various types of cancer. This study aimed to investigate the impact of leukemia on the detection and stability of STR markers. METHODS DNA was isolated from 30 participants (15 with chronic myeloid leukemia( CML) and 15 healthy controls) and used to amplify STR markers using specific primers. RESULTS We found that the blood of those with leukemia had more 9.3 and 9 alleles at the tyrosine hydroxylase 1 (TH01) marker than the blood of the healthy control samples. The results of this study will help researchers understand leukemia's effect on the detection and stability of STR markers in leukemic patients compared to healthy individuals. CONCLUSION Our results demonstrate that STR markers could become useful in genetic studies of leukemia cases.
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Al-Haj-Taib R, Mejri A, Børsting C, Pereira V, Elkamel S, Herrera RJ, Benammar-Elgaaied A, Fadhlaoui-Zid K. Genetic analysis of sixteen autosomal STR loci in three Tunisian populations from Makthar, Nabeul and Sousse. Ann Hum Biol 2022; 48:590-597. [DOI: 10.1080/03014460.2022.2032338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rim Al-Haj-Taib
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Abir Mejri
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Rene J. Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
- Department of Biology, College of Science, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
- Higher Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
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Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population. Sci Rep 2021; 11:15728. [PMID: 34344940 PMCID: PMC8333252 DOI: 10.1038/s41598-021-95144-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.
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Li W, Wang X, Wang X, Wang F, Du Z, Fu F, Wu W, Wang S, Mu Z, Chen C, Hu X, Ding J, Meng Y, Qiu P, Fan H. Forensic characteristics and phylogenetic analyses of one branch of Tai-Kadai language-speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia ™ Platinum System. Mol Genet Genomic Med 2020; 8:e1462. [PMID: 32862500 PMCID: PMC7549582 DOI: 10.1002/mgg3.1462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Hainan Island, located in the South China Sea and separated from the Leizhou Peninsula by Qiongzhou Strait, is the second largest island after Taiwan in China. With the expansion of Han Chinese and the gradual formation of "South Hlai and North Han", nowadays, Hainan Hlai is the second largest population after Han Chinese in Hainan Island. Ha Hlai, distributed in southwest and southern Hainan Island, is the dominant branch of Hlai and speaks Ha localism. METHODS We utilized the Huaxia™ Platinum PCR Amplification System (including 23 autosomal STRs and 2 sex-linked markers) to obtain the first STR profiling batch of 657 Ha Hlai individuals (497 males and 160 females). In order to explore the genetic relationships between the studied Ha Hlai and other reference populations with different language families, population genetic analyses, including PCA, MDS, STRUCTURE, and phylogenetic analysis, were conducted based upon the raw data and allelic frequencies of the polymorphic autosomal STR markers. RESULTS In total, 271 distinct alleles were observed at the 23 STR loci. The number of diverse alleles ranged from 7 at TPOX locus to 23 at FGA locus, and the allelic frequencies varied from 0.0008 to 0.5533. In addition, the CPE and CPD were 1-7.39 × 10-10 and 1-3.13 × 10-28 , respectively. The phylogenetic analyses indicated that Ha Hlai is a Tai-Kadai language-speaking and relatively isolated population which has a close genetic and geographical relationship with Hainan Hlai, and M95 is the dominant haplogroup in Ha Hlai (56.18%). CONCLUSION The 23 autosomal STR genetic markers were highly polymorphic as well as potentially useful for forensic applications in Hainan Ha Hlai population. The phylogenetic analyses demonstrated that small geographic scale gene flows could not be ignored and the shaping of the unique gene pool for each population was the combination effects of geographic, language, and cultural isolations.
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Affiliation(s)
- Wenhui Li
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
| | - Xianwen Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Xiehong Wang
- Criminal Technical DetachmentHaikou City Public Security BureauHaikouChina
| | - Fenfen Wang
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Zhengming Du
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Fangshu Fu
- School of Biomedical Information and EngineeringHainan Medical UniversityHaikouChina
| | - Wenlong Wu
- First Clinical Medical CollegeHainan Medical UniversityHaikouChina
| | - Shuya Wang
- School of Public HealthHainan Medical UniversityHaikouChina
| | - Ziqing Mu
- School of ManagementHainan Medical UniversityHaikouChina
| | - Chunwei Chen
- Public Security and Judicial Appraisal Center of Sanya CitySanyaChina
| | - Xiaomin Hu
- Hainan Zhujian Center for Molecular Cytogenetic Clinical TestingHaikouChina
| | - Jiuyang Ding
- School of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Yunle Meng
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Pingming Qiu
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Haoliang Fan
- School of Basic Medicine and Life ScienceHainan Medical UniversityHaikouChina
- Forensic Science Center of Hainan Medical UniversityHainan Medical UniversityHaikouChina
- School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Multi‐Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
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Abdeli A, Benhassine T. Genetic diversity of 15 autosomal STRs in a sample of Berbers from Aurès region in the Northeast of Algeria and genetic relationships with other neighbouring samples. Ann Hum Biol 2020; 47:284-293. [PMID: 32183545 DOI: 10.1080/03014460.2020.1736628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: The history of the Aurès mountains and neighbouring areas, a large region of the East of Algeria, was part of the history of the ancient independent Berber kingdoms supposed to be the ancestors of the current Berber people. The genetic background of this region has not yet been clarified.Aim: The aims of our study were to investigate the genetic characteristics of 15 autosomal short tandem repeats (STRs) in a sample from these regions, to determine the degree of heterogeneity among Algerian and North African samples and to analyse the genetic relationships with other populations.Subjects and methods: Allele frequencies, forensic parameters and Hardy-Weinberg equilibrium (HWE) of 15 autosomal STRs included in the PowerPlex® ESI 16 System were obtained from 308 individuals. Allele frequencies were used to determine the relationships with other populations.Results: All loci were highly polymorphic and no significant deviation from HWE was detected. Allele frequencies showed that the samples of Aurès region share genetic affinities with other Algerian, North African and Middle Eastern samples, with the exception of samples from Iran and Matmata.Conclusions: These markers revealed a genetic homogeneity between the Algerian and North African samples. The genetic affinities indicate that this sample could share a common ancestor with the Middle Eastern samples.
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Affiliation(s)
- Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria.,Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale, Alger, Algeria
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
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Messoussi M, Hajjej A, Ammar Elgaaied AB, Almawi WY, Arnaiz-Villena A, Hmida S, Fadhlaoui-Zid K. HLA Class II Allele and Haplotype Diversity in Libyans and Their Genetic Relationships with Other Populations. Immunol Invest 2019; 48:875-892. [PMID: 31161824 DOI: 10.1080/08820139.2019.1614950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background: Libya witnessed the succession of many civilizations and ethnic groups throughout history, thereby questioning the origin of present-day Libyans. Indeed, they were considered Africans given the geographical position of the country, Arabs at the cultural level, and Berbers because of the notable presence of Berber tribes. Genetic anthropology studies investigating the origin of Libyans were rarely reported, and thus little was known about the population structure of current Libyans, particularly at autosomic markers level. Methods: We examined HLA class II (DRB1, DQB1) gene profiles of 101 unrelated Libyans, and compared them with Arab-speaking communities and with Sub-Saharan and Mediterranean populations using Neighbour-Joining dendrograms, genetic distances, correspondence, and haplotype analysis. Results: Of the 42 DRB1 alleles identified, DRB1*07:01 (14.36%), DRB1*03:01 (12.38%) were the most frequent, while DQB1*02:01 (24.17%), DQB1*02:02 (13.86%), and DQB1*03:01 (12.38%) were the most frequent of the 17 DQB1 alleles detected. DRB1*03:01-DQB1*02:01 (6.93%), DRB1*07:01-DQB1*02:02 (4.45%), and DRB1*04:03-DQB1*03:02 (3.46%) were the most frequent DRB1-DQB1 haplotypes. Conclusion: Libyans appear to be closely related to North Africans, Saudis, and Iberians, but distinct from Levantine Arabs, East Mediterraneans, and Sub-Saharan Africans. This indicates limited genetic contribution of Levantine Arabs and Sub-Saharans on the makeup of Libyan gene pool. Our study confirmed genetic heterogeneity among Arab populations, with three identified groups. The first comprises North Africans, Saudis, and Kuwaitis who were related to Iberians and West Mediterraneans, while the second consists of Levantine Arabs who were close to East Mediterraneans, and the third contained Sudanese and Comorians, with a close relatedness to Sub-Saharans.
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Affiliation(s)
- Monia Messoussi
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia
| | - Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center , Tunis , Tunisia
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia
| | - Wassim Y Almawi
- School of Medicine, Nazarbayev University , Astana , Kazakhstan.,Department of Biological Sciences, Faculty of Sciences, El-Manar University , Tunis , Tunisia
| | - Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center , Madrid , Spain
| | - Slama Hmida
- Department of Immunogenetics, National Blood Transfusion Center , Tunis , Tunisia
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia.,Department of Biology, College of Science, Taibah University , Al Madinah Al Monawarah , Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba , Beja , Tunisia
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Elzalabany S, Taha T, Fawzi S, Shaker O. A novel allele frequency trajectories template to discriminate genetic similarity among populations. Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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AbdEl-Hafez AF, El-Alfy SH, Swelim HH, Hassan NHA. Genetic Variation at 15 Autosomal STR Loci Among Seven Egyptian Populations. Biochem Genet 2018; 57:170-191. [DOI: 10.1007/s10528-018-9879-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/20/2018] [Indexed: 11/25/2022]
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Elkamel S, Cherni L, Alvarez L, Marques SL, Prata MJ, Boussetta S, Benammar-Elgaaied A, Khodjet-El-Khil H. The Orientalisation of North Africa: New hints from the study of autosomal STRs in an Arab population. Ann Hum Biol 2016; 44:180-190. [DOI: 10.1080/03014460.2016.1205135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
- High Institute of Biotechnology, University of Monastir, Monastir, Tunisia
| | - Luis Alvarez
- Instituto de Investigação e Inovação em Saúde/Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Sofia L. Marques
- Instituto de Investigação e Inovação em Saúde/Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Maria J. Prata
- Instituto de Investigação e Inovação em Saúde/Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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Amir N, Sahnoune M, Chikhi L, Atmani D. STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups. Gene 2015; 574:140-8. [PMID: 26253162 DOI: 10.1016/j.gene.2015.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 07/29/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
Abstract
Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is a reminder of the links that connect all African regions.
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Affiliation(s)
- Nadir Amir
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Algeria
| | - Mohamed Sahnoune
- Laboratoire d'Ecologie et Environnement, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Algeria
| | - Lounes Chikhi
- CNRS, Université Paul Sabatier, ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); 118, Route de Narbonne, F-31062 Toulouse, France; Université Toulouse 3 Paul Sabatier, CNRS; UMR5174 EDB, F-31062 Toulouse, France; Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n°6, 2780-56 Oeiras, Portugal
| | - Djebbar Atmani
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Algeria.
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Zhao Z, Zhang J, Wang H, Liu ZP, Liu M, Zhang Y, Sun L, Zhang H. Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China. Meta Gene 2015; 5:150-6. [PMID: 26273562 PMCID: PMC4532769 DOI: 10.1016/j.mgene.2015.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/16/2015] [Accepted: 07/12/2015] [Indexed: 11/15/2022] Open
Abstract
STR, short tandem repeats, are well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and average mutation rates had a positive correlation with paternal age, maternal age and the time of pregnancy respectively. Additionally, the average mutation rate of coastal areas was higher than that of inland areas. 15 autosomal STR loci were analyzed in a large scale population in Mainland China. With increases of repeat units the event of loss is more than that of gain. The paternal mutation rate is higher than the maternal mutation rate. There is a positive correlation between mutation rates and age and pregnancy time. The average mutation rates of coastal areas are higher than that of inland areas.
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Affiliation(s)
- Zhuo Zhao
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Jie Zhang
- Beijing Entry-Exit Inspection Quarantine Bureau, No. 6 Tian Shui Yuan Street Chaoyang District Beijing, 100026 Beijing, China
| | - Hua Wang
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Zhi-Peng Liu
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Ming Liu
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Yuan Zhang
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Li Sun
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
| | - Hui Zhang
- Technical Center for Safety of Industrial Products, Tianjin Entry-Exit Inspection Quarantine Bureau, No. 2 Dong Wu Road Airport Economics Area Tianjin, 300308 Tianjin, China
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15
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Ayadi I, Carracedo Á, Rebai A. Paternal lineages in Libya inferred from Y-chromosome haplogroups. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:242-51. [DOI: 10.1002/ajpa.22705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Soumaya Triki-Fendri
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
| | - Imen Ayadi
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela; Galicia Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University; Jeddah Saudi Arabia
| | - Ahmed Rebai
- Research Group on Molecular and Cellular Screening Processes, Laboratory of Microorganisms and Biomolecules, Centre of Biotechnology of Sfax; Tunisia
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16
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Bentayebi K, Abada F, Ihzmad H, Amzazi S. Genetic ancestry of a Moroccan population as inferred from autosomal STRs. Meta Gene 2014; 2:427-38. [PMID: 25606427 PMCID: PMC4287812 DOI: 10.1016/j.mgene.2014.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/19/2014] [Indexed: 10/25/2022] Open
Abstract
Detecting population substructure and ancestry is a critical issue for both association studies of health behaviors and forensic genetics. Determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Within this context, fifteen autosomal short tandem repeat (STR), were used to examine population genetic structure and hypotheses of the origin of the modern Moroccan population from individuals belonging to three different ethnical groups from Morocco (Arab, Berber and Sahrawi), by comparing their autosomal STR variation with that of neighboring and non-neighboring populations in North Africa, Europe and Middle East as well as proposed ancestral populations in Morocco (Berber). We report on the results that the gradient of North African ancestry accounts for previous observations of low levels of sharing with Near East and a substantially increased gene flow especially from Morocco and Spain.
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Affiliation(s)
- K. Bentayebi
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
| | - F. Abada
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
| | - H. Ihzmad
- Laboratoire d'épidémiologie, Institut National d'Hygienne, Rabat, Morocco
| | - S. Amzazi
- Laboratoire de Biochimie Immunologie, Faculté des Sciences, Université Mohammed V, Morocco
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17
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Hossain T, Hasan MM, Mazumder AK, Momtaz P, Sharmin T, Sufian A, Das SA, Akhteruzzaman S. Population genetic data on 15 autosomal STR loci in Bangladeshi population. Forensic Sci Int Genet 2014; 13:e4-5. [DOI: 10.1016/j.fsigen.2014.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/24/2014] [Accepted: 04/28/2014] [Indexed: 11/16/2022]
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18
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Halima AB, Bahri R, Esteban E, Aribia MHB, Moral P, Chaabani H. Ethnic composition and genetic differentiation of the Libyan population: insights onAlupolymorphisms. Ann Hum Biol 2013; 41:229-37. [DOI: 10.3109/03014460.2013.850112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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