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Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Sci Rep 2024; 14:9979. [PMID: 38693301 PMCID: PMC11063056 DOI: 10.1038/s41598-024-60568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.
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Affiliation(s)
- Laura Vilà-Valls
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté Des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Adda Neggaz L, Deba T, Bekada A, Meroufel Sebaa DN, Mediene Benchekor S, Benhamamouch S. Allelic frequency variation of ACKR1 in three Algerian populations: Zenata, Reguibat, and Oran. Transfus Clin Biol 2024; 31:7-12. [PMID: 37865156 DOI: 10.1016/j.tracli.2023.10.003] [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: 07/01/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
INTRODUCTION The discovery of the Duffy antigen is of great significance, given its essential role in immune response and various physiological processes. Genetic mutations in the Duffy gene not only affect antigen expression but also result in different antigen types. This underscores the importance of genetic characterization for clinical studies and exploring genetic diversity within the population. This study primarily aims to genetically characterize the Duffy blood group within three Algerian populations: the Zenata, Reguibat, and Oran populations. METHODS The genetic polymorphism of the Duffy erythrocyte group was examined, focusing on five allelic versions of the ACKR1 locus: FY*01, FY*02, FY*X, and silent alleles FY*01 N.01 and FY*02 N.01. A total of 223 Algerian individuals, including 90 from the Oran population, 66 from the Zenata population, and 67 from the Reguibat population, were analyzed using the polymerase chain reaction with sequence-specific primer (PCR-SSP) method. The results revealed the presence of the silent alleles (FY*01 N.01 and FY*02 N.01) in all three populations, with a total frequency of 78.03% in the Zenata population. Additionally, the FY*X allele was exclusively detected in the Reguibat population, with a frequency of 0.75% CONCLUSION: This study provides valuable insights into the allele and genotypic frequencies of the Duffy system in the Zenata, Reguibat and Oranpopulations, contributing to our understanding of the genetic history and origins of the Algerian population. Further research incorporating additional genetic markers and establishing a comprehensive database would enhance our knowledge in this area.
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Affiliation(s)
- Leila Adda Neggaz
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria.
| | - Tahria Deba
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria; Faculté de Médecine, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria; Centre de transfusion sanguine, Centre Hospitalier et Universitaire d'Oran, Boulevard Docteur Benzerdjeb, Plateau, Oran, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
| | - Djabaria Naima Meroufel Sebaa
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria
| | - Sounnia Mediene Benchekor
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria; Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
| | - Soraya Benhamamouch
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [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: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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Aizpurua-Iraola J, Abdeli A, Benhassine T, Calafell F, Comas D. Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements. Sci Rep 2023; 13:10395. [PMID: 37369751 DOI: 10.1038/s41598-023-37549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Despite being enclosed between the Mediterranean Sea and the Sahara Desert, North Africa has been the scenario of multiple human migrations that have shaped the genetic structure of its present-day populations. Despite its richness, North Africa remains underrepresented in genomic studies. To overcome this, we have sequenced and analyzed 264 mitogenomes from the Algerian Chaoui-speaking Imazighen (a.k.a. Berbers) living in the Aurès region. The maternal genetic composition of the Aurès is similar to Arab populations in the region, dominated by West Eurasian lineages with a moderate presence of M1/U6 North African and L sub-Saharan lineages. When focusing on the time and geographic origin of the North African specific clades within the non-autochthonous haplogroups, different geographical neighboring regions contributed to the North African maternal gene pool during time periods that could be attributed to previously suggested admixture events in the region, since Paleolithic times to recent historical movements such as the Arabization. We have also observed the role of North Africa as a source of geneflow mainly in Southern European regions since Neolithic times. Finally, the present work constitutes an effort to increase the representation of North African populations in genetic databases, which is key to understand their history.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratorie de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.
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Barbarić L, Horjan-Zanki I. Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route. Int J Legal Med 2023; 137:181-193. [PMID: 35449468 DOI: 10.1007/s00414-022-02829-7] [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: 07/30/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023]
Abstract
Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.
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Affiliation(s)
- Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia.
| | - Ivana Horjan-Zanki
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia
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6
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Bouzidi A, Charoute H, Charif M, Amalou G, Kandil M, Barakat A, Lenaers G. Clinical and genetic spectrums of 413 North African families with inherited retinal dystrophies and optic neuropathies. Orphanet J Rare Dis 2022; 17:197. [PMID: 35551639 PMCID: PMC9097391 DOI: 10.1186/s13023-022-02340-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Background Inherited retinal dystrophies (IRD) and optic neuropathies (ION) are the two major causes world-wide of early visual impairment, frequently leading to legal blindness. These two groups of pathologies are highly heterogeneous and require combined clinical and molecular diagnoses to be securely identified. Exact epidemiological studies are lacking in North Africa, and genetic studies of IRD and ION individuals are often limited to case reports or to some families that migrated to the rest of the world. In order to improve the knowledge of their clinical and genetic spectrums in North Africa, we reviewed published data, to illustrate the most prevalent pathologies, genes and mutations encountered in this geographical region, extending from Morocco to Egypt, comprising 200 million inhabitants. Main body We compiled data from 413 families with IRD or ION together with their available molecular diagnosis. The proportion of IRD represents 82.8% of index cases, while ION accounted for 17.8%. Non-syndromic IRD were more frequent than syndromic ones, with photoreceptor alterations being the main cause of non-syndromic IRD, represented by retinitis pigmentosa, Leber congenital amaurosis, and cone-rod dystrophies, while ciliopathies constitute the major part of syndromic-IRD, in which the Usher and Bardet Biedl syndromes occupy 41.2% and 31.1%, respectively. We identified 71 ION families, 84.5% with a syndromic presentation, while surprisingly, non-syndromic ION are scarcely reported, with only 11 families with autosomal recessive optic atrophies related to OPA7 and OPA10 variants, or with the mitochondrial related Leber ION. Overall, consanguinity is a major cause of these diseases within North African countries, as 76.1% of IRD and 78.8% of ION investigated families were consanguineous, explaining the high rate of autosomal recessive inheritance pattern compared to the dominant one. In addition, we identified many founder mutations in small endogamous communities. Short conclusion As both IRD and ION diseases constitute a real public health burden, their under-diagnosis in North Africa due to the absence of physicians trained to the identification of inherited ophthalmologic presentations, together with the scarcity of tools for the molecular diagnosis represent major political, economic and health challenges for the future, to first establish accurate clinical diagnoses and then treat patients with the emergent therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02340-7.
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Affiliation(s)
- Aymane Bouzidi
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Hicham Charoute
- Research Unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Majida Charif
- Genetics, and Immuno-Cell Therapy Team, Mohamed First University, Oujda, Morocco
| | - Ghita Amalou
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Abdelhamid Barakat
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Guy Lenaers
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France. .,Service de Neurologie, CHU d'Angers, Angers, France.
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7
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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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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Bensouilah FZ, Chellat-Rezgoune D, Garcia-Gonzalez MA, Carrera N, Abadi N, Dahdouh A, Satta D. Association of single nucleotide polymorphisms with renal cell carcinoma in Algerian population. AFRICAN JOURNAL OF UROLOGY 2020. [DOI: 10.1186/s12301-020-00055-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Renal cell carcinoma (RCC) is a common malignant tumor of the urinary system. The etiology of RCC is a complex interaction between environmental and multigenetic factors. Genome-wide association studies have identified new susceptibility risk loci for RCC. We examined associations of genetic variants of genes that are involved in metabolism, DNA repair and oncogenes with renal cancer risk. A total of 14 single nucleotide polymorphisms (SNPs) in 11 genes (VEGF, VHL, ATM, FAF1, LRRIQ4, RHOBTB2, OBFC1, DPF3, ALDH9A1 and EPAS1) were examined.
Methods
The current case–control study included 87 RCC patients and 114 controls matched for age, gender and ethnic origin. The 14 tag-SNPs were genotyped by Sequenom MassARRAY® iPLEX using blood genomic DNA.
Results
Genotype CG and allele G of ATM rs1800057 were significantly associated with RCC susceptibility (p = 0.043; OR = 8.47; CI = 1.00–71.76). Meanwhile, we found that genotype AA of rs67311347 polymorphism could increase the risk of RCC (p = 0.03; OR = 2.95; IC = 1.10–7.89). While, genotype TT and T allele of ALDH9A1 rs3845536 were observed to approach significance for a protective role against RCC (p = 0.007; OR = 0.26; CI = 0.09–0.70).
Conclusion
Our results indicate that ATM rs1800057 may have an effect on the risk of RCC, and suggest that ALDH9A1 was a protective factor against RCC in Algerian population.
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Crooks L, Cooper-Knock J, Heath PR, Bouhouche A, Elfahime M, Azzouz M, Bakri Y, Adnaoui M, Ibrahimi A, Amzazi S, Tazi-Ahnini R. Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing. BMC Genet 2020; 21:111. [PMID: 32957965 PMCID: PMC7507649 DOI: 10.1186/s12863-020-00917-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 09/08/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. RESULTS We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. CONCLUSIONS We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome.
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Affiliation(s)
- Lucy Crooks
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Howard Street, Sheffield,, S1 1WB, UK
| | - Johnathan Cooper-Knock
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Paul R Heath
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Ahmed Bouhouche
- Neurology and Neurogenetics, Genomic of Human Pathlogies Center, Medical School and Pharmacy, Mohammed-V University, Rabat, Morocco
| | | | - Mimoun Azzouz
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Youssef Bakri
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Mohammed Adnaoui
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Lab (MedBiotech), Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Tazi-Ahnini
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco.
- Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, S10 2RX, UK.
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Association of TERT, OGG1, and CHRNA5 Polymorphisms and the Predisposition to Lung Cancer in Eastern Algeria. Pulm Med 2020; 2020:7649038. [PMID: 32257438 PMCID: PMC7109590 DOI: 10.1155/2020/7649038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/01/2020] [Accepted: 03/03/2020] [Indexed: 01/22/2023] Open
Abstract
Lung cancer remains the most common cancer in the world. The genetic polymorphisms (rs2853669 in TERT, rs1052133 in OGG1, and rs16969968 in CHRNA5 genes) were shown to be strongly associated with the risk of lung cancer. Our study's aim is to elucidate whether these polymorphisms predispose Eastern Algerian population to non-small-cell lung cancer (NSCLC). To date, no study has considered this association in the Algerian population. This study included 211 healthy individuals and 144 NSCLC cases. Genotyping was performed using TaqMan probes and Sanger sequencing, and the data were analyzed using multivariate logistic regression adjusted for covariates. The minor allele frequencies (MAFs) of TERT rs2853669, CHRNA5 rs16969968, and OGG1 rs1052133 polymorphisms in controls were C: 20%, A: 31%, and G: 29%, respectively. Of the three polymorphisms, none shows a significant association, but stratified analysis rs16969968 showed that persons carrying the AA genotype are significantly associated with adenocarcinoma risk (pAdj = 0.03, ORAdj = 2.55). Smokers with an AA allele have a larger risk of lung cancer than smokers with GG or GA genotype (pAdj = 0.03, ORAdj = 3.91), which is not the case of nonsmokers. Our study suggests that CHRNA5 rs16969968 polymorphism is associated with a significant increase of lung adenocarcinoma risk and with a nicotinic addiction.
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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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Oras E, Anderson J, Tõrv M, Vahur S, Rammo R, Remmer S, Mölder M, Malve M, Saag L, Saage R, Teearu-Ojakäär A, Peets P, Tambets K, Metspalu M, Lees DC, Barclay MVL, Hall MJR, Ikram S, Piombino-Mascali D. Multidisciplinary investigation of two Egyptian child mummies curated at the University of Tartu Art Museum, Estonia (Late/Graeco-Roman Periods). PLoS One 2020; 15:e0227446. [PMID: 31945091 PMCID: PMC6964855 DOI: 10.1371/journal.pone.0227446] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/18/2019] [Indexed: 11/19/2022] Open
Abstract
Two ancient Egyptian child mummies at the University of Tartu Art Museum (Estonia) were, according to museum records, brought to Estonia by the young Baltic-German scholar Otto Friedrich von Richter, who had travelled in Egypt during the early 19th century. Although some studies of the mummies were conducted, a thorough investigation has never been made. Thus, an interdisciplinary team of experts studied the remains using the most recent analytical methods in order to provide an exhaustive analysis of the remains. The bodies were submitted for osteological and archaeothanatological study, radiological investigation, AMS radiocarbon dating, chemical and textile analyses, 3D modelling, entomological as well as aDNA investigation. Here we synthesize the results of one of the most extensive multidisciplinary analyses of ancient Egyptian child mummies, adding significantly to our knowledge of such examples of ancient funerary practices.
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Affiliation(s)
- Ester Oras
- Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
- Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia
- * E-mail:
| | | | - Mari Tõrv
- Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia
| | - Signe Vahur
- Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Riina Rammo
- Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia
| | - Sünne Remmer
- Estonian Forensic Science Institute, Tallinn, Estonia
| | - Maarja Mölder
- Estonian Forensic Science Institute, Tallinn, Estonia
| | - Martin Malve
- Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia
| | - Lehti Saag
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ragnar Saage
- Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia
| | - Anu Teearu-Ojakäär
- Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Pilleriin Peets
- Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | | | | | - Salima Ikram
- Department of Sociology, Egyptology and Anthropology, American University in Cairo, New Cairo, Egypt
- Department of Ancient Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Dario Piombino-Mascali
- Department of Anatomy, Histology and Anthropology, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
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Serra-Vidal G, Lucas-Sanchez M, Fadhlaoui-Zid K, Bekada A, Zalloua P, Comas D. Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa. Curr Biol 2019; 29:3953-3959.e4. [DOI: 10.1016/j.cub.2019.09.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/02/2019] [Accepted: 09/19/2019] [Indexed: 01/16/2023]
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15
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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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16
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Badache H, Boussetta S, Elgaaeid AB, Cherni L, El-khil HK. Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers. Ann Hum Biol 2019; 46:150-159. [DOI: 10.1080/03014460.2019.1588994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hocine Badache
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Amel Benammar Elgaaeid
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
| | - Houssein Khodjet El-khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
- Department of Biomedical Sciences, College of Health Sciences Qatar University, Doha, Qatar
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17
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Novillo A, Gaibar M, Romero-Lorca A, Chaabani H, Amir N, Moral P, Esteban ME, Fernández-Santander A. UDP-glucuronosyltransferase genetic variation in North African populations: a comparison with African and European data. Ann Hum Biol 2019; 45:516-523. [PMID: 30616396 DOI: 10.1080/03014460.2018.1559354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genetic variation in glucuronosyltransferases (UGT) is crucial in drug metabolism and risk of some diseases. AIM To examine genetic variation in UGT in North African populations. SUBJECTS AND METHODS Allele frequencies of SNPs UGT1A424Thr, UGT1A448Val, UGT2B1585Tyr, UGT2B15523Thr and UGT2B17 CNV deletion from Morocco, Algeria, Tunisia and Libya were compared to European and Sub-Saharan populations. RESULTS North Africans are the group with the highest genetic heterogeneity given by internal differences in the occurrence of UGT2B17 deletion, UGT1A448Val and UGT1A4 haplotypes. UGT2B15 SNPs differentiate Sub-Saharans from the rest of the populations. CONCLUSION North African populations show a high frequency of carriers of UGT2B15523Thr, a variant linked to an increased risk of prostate cancer. High Atlas Moroccans and Algerians show low frequency of UGT2B17del, a variant associated with high concentrations of testosterone and oestradiol.
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Affiliation(s)
- Apolonia Novillo
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - María Gaibar
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Alicia Romero-Lorca
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Hassen Chaabani
- b Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Nadir Amir
- c Laboratoire de Biochimie Appliquée, 5 Faculté des Sciences de la Nature et de la Vie , Université de Bejaia , Bejaia , Algeria
| | - Pedro Moral
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
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18
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Mehemmai C, Cherbal F, Hamdi Y, Guedioura A, Benbrahim W, Bakour R, Abdelhak S. BRCA1 and BRCA2 Germline Mutation Analysis in Hereditary Breast/Ovarian Cancer Families from the Aures Region (Eastern Algeria): First Report. Pathol Oncol Res 2019; 26:715-726. [PMID: 30715675 DOI: 10.1007/s12253-019-00586-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022]
Abstract
Breast cancer is currently the leading cause of cancer morbidity and mortality among Algerian women. In this study, we aimed to investigate the mutation spectrum of BRCA1 and BRCA2 genes in hereditary breast/ovarian cancer (HBOC) families from the Aures region (eastern Algeria). High risk breast/ovarian cancer families were selected from overall 1162 consecutive patients collected from cancer registry of anticancer center of Batna. Breast cancers were diagnosed between 2011 and 2015. Recurrent mutations on BRCA1 and BRCA2 previously found in Algerian patients were screened using PCR-direct sequencing in 113 HBOC families. In addition, for the first time in Algeria, HBOC patients were analyzed by NGS using a cancer panel of 30 hereditary cancer genes or BRCA1/2 genetic test. Six distinct deleterious mutations in BRCA1 and BRCA2 and a new VUS in PALB2 were detected in ten patients. Two distinct BRCA2 pathogenic variants c.1813dupA and c.8485C > T detected in two young female triple negative breast cancer (TNBC) patients, respectively, with a family history of male breast cancer, are reported here for the first time in Algerian population. Interestingly, we also detected a BRCA exon 15 deletion in two unrelated young female TNBC patients with strong family history of breast/ovarian cancer. Our study showed differences in the distribution of the mutation spectrum of BRCA genes between the Aures region and the north central region of Algeria. Our results will contribute in the implementation of genetic counseling and testing for patients and families at risk of hereditary breast and ovarian cancer.
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Affiliation(s)
- Chiraz Mehemmai
- Unit of Genetics, Laboratory of Molecular and Cellular Biology, Faculty of Biological Sciences, USTHB, POB 32 El Alia, Bab Ezzouar, 16111, Algiers, Algeria.,Faculty of Sciences of Tunis, University Campus 2092 - El Manar, Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics (LRTI, IPT 05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Farid Cherbal
- Unit of Genetics, Laboratory of Molecular and Cellular Biology, Faculty of Biological Sciences, USTHB, POB 32 El Alia, Bab Ezzouar, 16111, Algiers, Algeria.
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics (LRTI, IPT 05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | | | | | - Rabah Bakour
- Unit of Genetics, Laboratory of Molecular and Cellular Biology, Faculty of Biological Sciences, USTHB, POB 32 El Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics (LRTI, IPT 05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa. Forensic Sci Int Genet 2019; 38:185-194. [DOI: 10.1016/j.fsigen.2018.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
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20
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Elsayed LEO, Mohammed IN, Hamed AAA, Elseed MA, Salih MAM, Yahia A, Siddig RA, Amin M, Koko M, Elbashir MI, Ibrahim ME, Brice A, Ahmed AE, Stevanin G. Case report of a novel homozygous splice site mutation in PLA2G6 gene causing infantile neuroaxonal dystrophy in a Sudanese family. BMC MEDICAL GENETICS 2018; 19:72. [PMID: 29739362 PMCID: PMC5941609 DOI: 10.1186/s12881-018-0592-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022]
Abstract
Background Infantile neuroaxonal dystrophy (INAD) is a rare hereditary neurological disorder caused by mutations in PLA2G6. The disease commonly affects children below 3 years of age and presents with delay in motor skills, optic atrophy and progressive spastic tetraparesis. Studies of INAD in Africa are extremely rare, and genetic studies from Sub Saharan Africa are almost non-existent. Case presentation Two Sudanese siblings presented, at ages 18 and 24 months, with regression in both motor milestones and speech development and hyper-reflexia. Brain MRI showed bilateral and symmetrical T2/FLAIR hyperintense signal changes in periventricular areas and basal ganglia and mild cerebellar atrophy. Whole exome sequencing with confirmatory Sanger sequencing were performed for the two patients and healthy family members. A novel variant (NM_003560.2 c.1427 + 2 T > C) acting on a splice donor site and predicted to lead to skipping of exon 10 was found in PLA2G6. It was found in a homozygous state in the two patients and homozygous reference or heterozygous in five healthy family members. Conclusion This variant has one very strong (loss of function mutation) and three supporting evidences for its pathogenicity (segregation with the disease, multiple computational evidence and specific patients’ phenotype). Therefore this variant can be currently annotated as “pathogenic”. This is the first study to report mutations in PLA2G6 gene in patients from Sudan.
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Affiliation(s)
- Liena E O Elsayed
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan.
| | - Inaam N Mohammed
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Ahlam A A Hamed
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Maha A Elseed
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Mustafa A M Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan
| | - Rayan A Siddig
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Mutaz Amin
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Mahmoud Koko
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tuebingen, Germany
| | - Mustafa I Elbashir
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan
| | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Alexis Brice
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, 75013, Paris, France.,Department of genetics, APHP Pitié-Salpêtrière Hospital, 75013, Paris, France
| | - Ammar E Ahmed
- Faculty of Medicine, University of Khartoum, Qasr Street, 11111, Khartoum, Sudan.
| | - Giovanni Stevanin
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, 75013, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL research university, 75014, Paris, France.,Department of genetics, APHP Pitié-Salpêtrière Hospital, 75013, Paris, France
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21
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Dahmani CA, Benzaoui A, Amroun H, Mecabih F, Sediki FZ, Zemani-Fodil F, Fodil M, Boughrara W, Mecheti B, Attal N, Mehtar N, Petit-Teixeira E, Boudjema A. Association of the HLA-B27 antigen and the CTLA4 gene CT60/rs3087243 polymorphism with ankylosing spondylitis in Algerian population: A case-control study. Int J Immunogenet 2018; 45:109-117. [PMID: 29675891 DOI: 10.1111/iji.12369] [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: 06/12/2017] [Revised: 01/30/2018] [Accepted: 03/22/2018] [Indexed: 12/14/2022]
Abstract
Ankylosing spondylitis (AS) is a complex inflammatory disease that represents a major health problem both in Algeria and worldwide. Several lines of evidence support that genetic risk factors play a role in AS etiology and the CTLA4 gene has attracted a considerable attention. In this study, we were interested in evaluating the HLA-B27 frequency and in exploring the CTLA4 gene in a sample of the North African population. The dataset of the current study is composed of 81 patients with AS and 123 healthy controls. All samples were genotyped by TaqMan® allelic discrimination assay. The genetic risk of the HLA-B27 specificity and the CTLA4/CT60 polymorphism were assessed by odds ratios (OR) with 95% confidence intervals (CI). High spondylitis risk was detected for HLA-B27 allele (OR= 14.62, p = 10-6 ) in addition to a significant association of the CT60*G allele (OR= 1.89, p = .002). After gender and age stratifications, the association of the CT60*G allele was still significant in females sample (OR= 2.10, p = .001) and when age up to 30 years (OR = 2.21, p = .008). Interestingly, the CT60*G allele revealed an increased spondylitis risk in the B27 negative group (OR= 2.81, p = .006). The present work showed in West Algerian population that the HLA-B27 antigen and the variation in the CTLA4 3'UTR region played an important role in the ankylosing spondylitis susceptibility. The heterogeneity of this disease is deduced by genetic difference found between B27+ and B27- groups.
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Affiliation(s)
- C A Dahmani
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - A Benzaoui
- Service de Rhumatologie, Centre Hospitalo-Universitaire (CHU) d'Oran, Oran, Algeria
| | - H Amroun
- Laboratoire d'Immunogénétique et de Transplantation, Département d'Immunologie, Institut Pasteur d'Algérie à, Alger, Algeria
| | - F Mecabih
- Laboratoire d'Immunogénétique et de Transplantation, Département d'Immunologie, Institut Pasteur d'Algérie à, Alger, Algeria
| | - F Z Sediki
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - F Zemani-Fodil
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - M Fodil
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - W Boughrara
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - B Mecheti
- Laboratoire d'Immunogénétique et de Transplantation, Département d'Immunologie, Institut Pasteur d'Algérie à, Alger, Algeria
| | - N Attal
- Laboratoire d'Immunogénétique et de Transplantation, Département d'Immunologie, Institut Pasteur d'Algérie à, Alger, Algeria
| | - N Mehtar
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - E Petit-Teixeira
- Laboratoire Européen de la Polyarthrite Rhumatoide, Université d'Evry-Val D'Essonne, Evry, France
| | - A Boudjema
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB), Oran, Algeria
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Lounici Boudiaf A, Bouziane D, Smara M, Meddour Y, Haffaf EM, Oudjit B, Chaib Mamouzi S, Aouichat Bouguerra S. Could ZnT8 antibodies replace ICA, GAD, IA2 and insulin antibodies in the diagnosis of type 1 diabetes? Curr Res Transl Med 2018; 66:1-7. [PMID: 29487039 DOI: 10.1016/j.retram.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND The zinc transporter 8 (ZnT8) is an islet β-cell secretory granule membrane protein coded by the SLC30A8 gene, identified as a novel autoantigen in human type 1 diabetes (T1D). As no data of ZnT8ab in Algerian patients have been reported, we aim to evaluate the prevalence of ZnT8ab in young Algerians with T1D and determine whether ZnT8ab could be a better diagnostic tool to replace the other conventional autoantibodies detected in patients with type 1 diabetes. For this purpose, we evaluated the prevalence of islets cells antibodies (ICA), glutamic acid decarboxylase (GAD), islet antigen type 2 (IA2), insulin (IA) autoantibodies (ab) and for the first time in Algeria, the zinc transporter 8 (ZnT8) in young Algerian patients with type 1 diabetes. PATIENTS AND METHODS In our cross-sectional study, 160 patients between 1 and 35 years old, diagnosed with type 1 diabetes were enrolled. ICAab was analyzed by indirect immunofluorescence (IIF), GADab, IA2ab, IAab and ZnT8ab were analyzed by ELISA, fasting blood glucose was performed by enzymatic method (glucose-oxidase) and HbA1c by turbid metric method. RESULTS Our cohort was composed with 74 males and 86 females (OR=1.16); the mean of age was 14.09 [1-35] years old and the median diabetes duration was 4.10 [1-18] years. Our cohort had a mean of HbA1c of 9.22 [5.40-15]%, the mean of birth weight was 3360.52 [2200-4800]g; the mean of BMI was 19.30 [16.04-22.46]kg/m2. Out of 160 patients, 44 (27.5%) were under mother breastfeeding and 116/160 (72.5%) were under artificial feeding. One antibody, at least, was found in 94.38% and the ZnT8ab was significantly more positive in females (70.3%) than in males (10.7%) (***P=8.033×10-15). The concentration of ZnT8ab was higher in females than in males (females=122.25UI/mL versus males=51.38UI/mL; *P=0.03); ICAab, GADab and ZnT8ab were more present in patients with consanguineous parents (***P=0.0002, *P=0.019 and *P=0.03; respectively) CONCLUSION: Our study on ZnT8ab in T1D is the first in the Maghreb region and we observed a prevalence of 46.25%. The positivity of ZnT8ab enabled us to classify in T1DA 50% of diabetics with obvious T1D phenotype and negative routine autoantibodies, thus ZnT8ab is a good tool for differential diagnosis of type 1 diabetes. According to our results, a simultaneous analysis for ZnT8 and IA2 autoantibodies can be a better and efficient diagnosis of type 1A diabetes from the beginning of the disease.
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Affiliation(s)
- A Lounici Boudiaf
- Laboratory of Cellular and Molecular Physiopathology, Institute of Natural Sciences, University of Technological Sciences, Houari Boumediene, Algiers, Algeria.
| | - D Bouziane
- Pediatric department, Ain Taya Teaching Hospital, Algiers, Algeria
| | - M Smara
- Laboratory of Immunology, Faculty of Medicine, University of Algiers 1, Algiers Military Hospital, Mohamed Seghir Nekkache, Algiers, Algeria
| | - Y Meddour
- Laboratory of Immunology, Faculty of Medicine, University of Algiers 1, Algiers Military Hospital, Mohamed Seghir Nekkache, Algiers, Algeria
| | - E M Haffaf
- Nuclear Medicine Department, Faculty of Medicine, University of Algiers 1, Algiers Military Hospital, Mohamed Seghir Nekkache, Algiers, Algeria
| | - B Oudjit
- Pediatric department, Faculty of Medicine, University of Algiers 1, Algiers Military Hospital, Mohamed Seghir Nekkache, Algiers, Algeria
| | - S Chaib Mamouzi
- Laboratory of Immunology, Faculty of Medicine, University of Algiers 1, Algiers Military Hospital, Mohamed Seghir Nekkache, Algiers, Algeria
| | - S Aouichat Bouguerra
- Laboratory of Cellular and Molecular Physiopathology, Institute of Natural Sciences, University of Technological Sciences, Houari Boumediene, Algiers, Algeria
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Rahmoun N, El Mecherfi KE, Bouchetara A, Lardjem Hetraf S, Dahmani Amira C, Adda Neggaz L, Boudjema A, Zemani-Fodil F, Kheroua O. Association of REL Polymorphism with Cow's Milk Proteins Allergy in Pediatric Algerian Population. Fetal Pediatr Pathol 2018; 37:74-83. [PMID: 29336650 DOI: 10.1080/15513815.2017.1405468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Cow's milk proteins allergy (CMPA) pathogenesis involves complex immunological mechanisms with the participation of several cells and molecules involved in food allergy. The association of polymorphisms in the interleukin 4, Forkhead box P3 and the avian reticuloendotheliosis genes was investigated in an infant population with CMPA of Western Algeria. MATERIALS AND METHODS We obtained DNA and clinical data from milk allergic subjects during active phase and from a group of non-atopic control subjects. RESULTS Our findings showed that the allele G of the cRel gene intronic polymorphism at +7883 positions was significantly higher among cow's milk proteins allergic patients compared to control subjects. CONCLUSION The results of this study suggest a possible association of CMPA with cRel G+7883T polymorphism.
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Affiliation(s)
- Nesrine Rahmoun
- a Laboratoire de Génétique Moléculaire et Cellulaire , Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Kamel Eddine El Mecherfi
- b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,c Laboratoire de Physiologie de la Nutrition et Sécurité Alimentaire, Universitéd'Oran 1 Ahmed Benbella , Oran , Algérie
| | - Assia Bouchetara
- d Departement des maladies infectieuses, EHS Boukhroufa Abdelkader, Canastel , Oran , Algérie
| | - Sara Lardjem Hetraf
- a Laboratoire de Génétique Moléculaire et Cellulaire , Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Chahinez Dahmani Amira
- a Laboratoire de Génétique Moléculaire et Cellulaire , Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Leila Adda Neggaz
- b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Abdallah Boudjema
- a Laboratoire de Génétique Moléculaire et Cellulaire , Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Faouzia Zemani-Fodil
- a Laboratoire de Génétique Moléculaire et Cellulaire , Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie.,b Département de génétique moléculaire appliquée , Faculté des Sciences et de la vie, Université des Sciences et de a Technologie d'Oran-Mohamed Boudiaf -USTOMB- , Oran , Algérie
| | - Omar Kheroua
- c Laboratoire de Physiologie de la Nutrition et Sécurité Alimentaire, Universitéd'Oran 1 Ahmed Benbella , Oran , Algérie
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Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
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Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
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25
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Adda Neggaz L, Meroufel DN, Deba T, Bekada A, Hammadi M, Mediene Benchekor S, Rosa A, Benhamamouch S. Digital dermatoglyphic study in three west Algerian populations: Reguibates, Zenata, Oran. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2017. [DOI: 10.1080/00085030.2017.1379267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Leïla Adda Neggaz
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria
| | - Djabaria Naima Meroufel
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria
| | - Tahria Deba
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria
- Faculté de Médecine, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
- Centre de transfusion sanguine, Centre Hospitalier et Universitaire d'Oran, Boulevard Docteur Benzerdjeb, Plateau, Oran, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
| | - Mohamed Hammadi
- Faculté de Médecine, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
- Centre de transfusion sanguine, Centre Hospitalier et Universitaire d'Oran, Boulevard Docteur Benzerdjeb, Plateau, Oran, Algeria
| | - Sounnia Mediene Benchekor
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de Technologie d'Oran Mohamed Boudiaf, BP 1505 El M'Naouer 31000, Oran, Algeria
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
| | - Araceli Rosa
- Edifici Ramon Margalef, Facultat de Biologia, Universitat de Barcelona, Avinguda, Diagonal 643, 08028 Barcelona, Spain
| | - Soraya Benhamamouch
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 Ahmed Benbella, BP 1524 El M'Naouer 31000, Oran, Algeria
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Lactase persistence in Tunisia as a result of admixture with other Mediterranean populations. GENES AND NUTRITION 2017; 12:20. [PMID: 28855970 PMCID: PMC5571577 DOI: 10.1186/s12263-017-0573-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/14/2017] [Indexed: 01/06/2023]
Abstract
Background The ability to digest lactose after weaning, namely, lactase persistence (LP), is encoded by polymorphisms in the MCM6 gene and varies widely in frequency among different human populations. Although, evolution of LP-related genetic variants was investigated in many groups of Sub-Saharan African, Middle Eastern, and European ancestry, only few studies have focused on populations from North Africa and no data are especially available from the Tunisian one. For this reason, there is an urgent need to investigate the frequency patterns at these loci in Tunisia since this adaptive trait is implicated in health. Methods Forty SNPs covering the LCT/MCM6 genes and including the two functional variants − 13,910 C > T and − 22,018 G > A were genotyped in 117 Tunisian individuals using the Sequenom Mass Array technology. The observed nucleotide and haplotype patterns of variation were then compared with those of several African, European, and Mediterranean human groups for which comparable data were publicly available. Admixture analysis on a 5 Mb genomic region surrounding the LCT/MCM6 loci was also performed by extracting genotypes from a previously generated genome-wide dataset in order to deepen the reconstruction of the evolutionary history of these loci. Results We found that lactase non-persistence (LNP)-related alleles and haplotypes were predominantly present in the examined population. A clear differentiation between Tunisian, African, and North European/North Italian samples was found, while the Tunisian population showed more genetic affinity to Central and South Italian groups. Conclusions Our study provided a first report of LP-associated alleles and haplotypes in the Tunisian population. We highlighted a gradient followed by LP diffusion from Europe to North Africa. Based on the rich historic background of Tunisia, we suggest that this adaptive trait was introduced in that geographic region by a relatively recent gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12263-017-0573-3) contains supplementary material, which is available to authorized users.
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27
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Arauna LR, Mendoza-Revilla J, Mas-Sandoval A, Izaabel H, Bekada A, Benhamamouch S, Fadhlaoui-Zid K, Zalloua P, Hellenthal G, Comas D. Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa. Mol Biol Evol 2017; 34:318-329. [PMID: 27744413 PMCID: PMC5644363 DOI: 10.1093/molbev/msw218] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates. We analyze genome-wide autosomal data in five Berber and six Arab groups, and compare them to Middle Easterns, sub-Saharans, and Europeans. Haplotype-based methods show a lack of correlation between geographical and genetic populations, and a high degree of genetic heterogeneity, without strong differences between Berbers and Arabs. Berbers enclose genetically diverse groups, from isolated endogamous groups with high autochthonous component frequencies, large homozygosity runs and low effective population sizes, to admixed groups with high frequencies of sub-Saharan and Middle Eastern components. Admixture time estimates show a complex pattern of recent historical migrations, with a peak around the 7th century C.E. coincident with the Arabization of the region; sub-Saharan migrations since the 1st century B.C. in agreement with Roman slave trade; and a strong migration in the 17th century C.E., coincident with a huge impact of the trans-Atlantic and trans-Saharan trade of sub-Saharan slaves in the Modern Era. The genetic complexity found should be taken into account when selecting reference groups in population genetics and biomedical studies.
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Affiliation(s)
- Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier Mendoza-Revilla
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Genetics Institute, University College London, London, United Kingdom
| | - Alex Mas-Sandoval
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Hassan Izaabel
- Laboratoire de Biologie Cellulaire et Génétique Moléculaire (LBCGM), Université IBNZOHR, Agadir, Morocco
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Soraya Benhamamouch
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Karima Fadhlaoui-Zid
- Laboratoire de Génetique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Campus Universitaire El Manar II, Université El Manar, Tunis, Tunisia
| | - Pierre Zalloua
- The Lebanese American University, Chouran, Beirut, Lebanon
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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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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Cherni L, Pakstis AJ, Boussetta S, Elkamel S, Frigi S, Khodjet-El-Khil H, Barton A, Haigh E, Speed WC, Ben Ammar Elgaaied A, Kidd JR, Kidd KK. Genetic variation in Tunisia in the context of human diversity worldwide. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:62-71. [PMID: 27192181 PMCID: PMC5084816 DOI: 10.1002/ajpa.23008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/22/2016] [Indexed: 11/09/2022]
Abstract
OBJECTIVES North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. MATERIALS AND METHODS Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. RESULTS Average heterozygosity of the North African populations is high relative to our global samples, consistent with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found. DISCUSSION Known historical migrations and invasions did not displace or homogenize the genetic variation in the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future studies across North Africa have the potential to increase our understanding of the historical demographic factors influencing the region. Am J Phys Anthropol 161:62-71, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sabeh Frigi
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Alison Barton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
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