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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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Abdeli A, Benhassine T. Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation. Ann Hum Biol 2019; 46:160-168. [PMID: 30939942 DOI: 10.1080/03014460.2019.1602166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.
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Affiliation(s)
- Amine Abdeli
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria.,b Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale , Algiers , Algeria
| | - Traki Benhassine
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria
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Usefulness of COMT gene polymorphisms in North African populations. Gene 2019; 696:186-196. [DOI: 10.1016/j.gene.2019.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/08/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
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Messoussi M, Prieto-Fernández E, Baeta M, Núñez C, Gaaied ABAE, de Pancorbo MM, Fadhlaoui-Zid K. Genetic variation of 17 X-chromosome STR loci in Tunisian population of Nabeul. Int J Legal Med 2018; 133:85-88. [PMID: 29569161 DOI: 10.1007/s00414-018-1827-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
In the present study, the genetic variations of 17 X-STR markers (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) were analyzed in 139 unrelated individuals in Nabeul, aiming to perform an X-STR database for anthropological and forensic purposes. Our results indicate that DXS6809 was the most polymorphic locus, whereas DXS6807 was the least informative marker. In addition, the obtained values for the statistical parameters of forensic interest, i.e., the power of discrimination in males (PDM) and females (PDF), as well as the mean exclusion chance in duos (MECD) and trios (MECT) have demonstrated that this panel of 17 X-STRs is highly informative and useful for forensic application and anthropological research. Additionally, pairwise genetic distances based on FST were calculated between Nabeul population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations and their historical relationship was detected.
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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
| | - Endika Prieto-Fernández
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Carolina Núñez
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Amel Ben Ammar-El Gaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia.
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Hollard C, Keyser C, Delabarde T, Gonzalez A, Vilela Lamego C, Zvénigorosky V, Ludes B. Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case. Int J Legal Med 2016; 131:351-358. [DOI: 10.1007/s00414-016-1425-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022]
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Makki-Rmida F, Kammoun A, Mahfoudh N, Ayadi A, Gibriel AA, Mallek B, Maalej L, Hammami Z, Maatoug S, Makni H, Masmoudi S. Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance. Electrophoresis 2015; 36:2908-13. [PMID: 26331800 DOI: 10.1002/elps.201500204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/16/2015] [Accepted: 08/19/2015] [Indexed: 11/11/2022]
Abstract
Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications.
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Affiliation(s)
- Faten Makki-Rmida
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie.,Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
| | - Arwa Kammoun
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie
| | - Nadia Mahfoudh
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie
| | - Adnene Ayadi
- Service Médicine Légale, CHU Habib Bourguiba, Tunisie
| | - Abdullah Ahmed Gibriel
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, British University in Egypt, Cairo, Egypt
| | - Bakhta Mallek
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie
| | - Leila Maalej
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie
| | | | - Samir Maatoug
- Service Médicine Légale, CHU Habib Bourguiba, Tunisie
| | - Hafedh Makni
- Service Laboratoire, Unité Empreinte Génétique, CHU Hedi Chaker, Sfax, Tunisie
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
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Robledo R, Mameli A, Scudiero C, Vona G, Corrias L, Bachis V, Culigioni C, Calò C. Non-random distribution of 17 Y-chromosome STR loci in different areas of Sardinia. Forensic Sci Int Genet 2015; 16:26-28. [DOI: 10.1016/j.fsigen.2014.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/27/2014] [Accepted: 11/25/2014] [Indexed: 11/29/2022]
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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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Fadhlaoui-Zid K, Garcia-Bertrand R, Alfonso-Sánchez MA, Zemni R, Benammar-Elgaaied A, Herrera RJ. Sousse: extreme genetic heterogeneity in North Africa. J Hum Genet 2014; 60:41-9. [PMID: 25471516 DOI: 10.1038/jhg.2014.99] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 11/09/2022]
Abstract
The male genetic landscape of the territory currently known as Tunisia is hampered by the scarcity of data, especially from cosmopolitan areas such as the coastal city of Sousse. In order to alleviate this lacuna, 220 males from Sousse were examined, for the first time, for more than 50 Y-chromosome single-nucleotide polymorphisms (Y-SNPs) markers and compared with 3099 individuals from key geographically targeted locations in North Africa, Europe and the Near East. The paternal lineages observed belong to a common set of Y haplogroups previously described in North Africa. In addition to the prominent autochthonous North African E-M81 haplogroup which is exclusively represented by its subclade E-M183 (44.55% of Y-chromosomes), a number of Near Eastern Neolithic lineages including E-M78, J-M267 and J-M172 account for 39% of the Y-chromosomes detected. Principal component analysis based on haplogroup frequencies, multidimensional scaling based on Rst genetic distances and analyses of molecular variance using both Y-chromosome short tandem repeat haplotypes and Y-SNP haplogroup data revealed that the Tunisian and North African groups, as a whole, are intra- and inter-specific diverse with Sousse being highly heterogeneous.
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Affiliation(s)
- Karima Fadhlaoui-Zid
- 1] Biology Department, Colorado College, Colorado Springs, CO, USA [2] Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | | | - Miguel A Alfonso-Sánchez
- Departamento de Genética y Antropología Fı sica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Bilbao, Bizkaia, Spain
| | - Ramzi Zemni
- Laboratory of Immunogenetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Rene J Herrera
- Biology Department, Colorado College, Colorado Springs, CO, USA
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Are polymorphisms of the immunoregulatory factor CD40LG implicated in acute transfusion reactions? Sci Rep 2014; 4:7239. [PMID: 25430087 PMCID: PMC5384113 DOI: 10.1038/srep07239] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 11/07/2014] [Indexed: 12/11/2022] Open
Abstract
The CD40 ligand (CD40L/CD154), a member of TNF superfamily, is notably expressed on activated CD4+ T-cells and stimulated platelets. CD40L is linked to a variety of pathologies and to acute transfusion reactions (ATR). Mutations in this gene (CD40LG) lead to X-linked hyper-IgM syndrome. Some CD40LG polymorphisms are associated with variable protein expression. The rationale behind this study is that CD40L protein has been observed to be involved in ATR. We wondered whether genetic polymorphisms are implicated. We investigated genetic diversity in the CD40LG using DHPLC and capillary electrophoresis for screening and genotyping (n = 485 French and Tunisian blood donors). We identified significant difference in the CD40LG linkage pattern between the two populations. Variant minor alleles were significantly over-represented in Tunisian donors (P<0.0001 to 0.0270). We found higher heterogeneity in the Tunisian, including three novel low frequency variants. As there was not a particular pattern of CD40LG in single apheresis donors whose platelet components induced an ATR, we discuss how this information may be useful for future disease association studies on CD40LG.
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Zhu BF, Zhang YD, Liu WJ, Meng HT, Yuan GL, Lv Z, Dong N, Li Q, Yang CH, Zhang YH, Hou YL, Qian L, Fan SL, Xu P. Genetic diversity and haplotype structure of 24 Y-chromosomal STR in Chinese Hui ethnic group and its genetic relationships with other populations. Electrophoresis 2014; 35:1993-2000. [PMID: 24789806 DOI: 10.1002/elps.201300574] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/10/2022]
Abstract
In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 115 unrelated Hui male individuals from Haiyuan county or Tongxin county, Ningxia Hui Autonomous Region, China, to evaluate the forensic application of the 24 STR loci and to analyze interpopulation differentiations by making comparisons between the Hui group data and previously published data of other 13 populations. A total of 115 different haplotypes were observed on these 24 Y-STR loci. The gene diversities ranged from 0.4049 (DYS437) to 0.9729 (DYS385a, b). The overall haplotype diversity was 1 at AGCU 24 Y-STR loci level, while the values were reduced to 0.999237, 0.996949, and 0.996644 at the Y-filer 17 loci, 11 Y-STR loci of extended haplotype and 9 Y-STR loci of minimal haplotype levels, respectively; whereas, haplotype diversity for additional 7 loci (not included in Y-filer 17 loci) was 0.995271. The pairwise FST , multidimensional scaling plot and neighbor-joining tree indicated the Hui group had the closest genetic relationship with Sala in the paternal lineage in the present study. In summary, the results in our study indicated the 24 Y-STRs had a high level of polymorphism in Hui group and hence could be a powerful tool for forensic application and population genetic study.
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Affiliation(s)
- Bo-Feng Zhu
- Shanghai Key Laboratory of Forensic Sciences, Institute of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China; Xi'an Jiaotong University Health Science Center, Xi'an, P. R. China
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