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Romdhane L, Kefi S, Mezzi N, Abassi N, Jmel H, Romdhane S, Shan J, Chouchane L, Abdelhak S. Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity. Sci Rep 2024; 14:4654. [PMID: 38409353 PMCID: PMC10897484 DOI: 10.1038/s41598-024-54749-8] [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: 08/09/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the "Canary" algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.
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Affiliation(s)
- Lilia Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
- Department of Biology, Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, Tunisia.
| | - Sameh Kefi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nessrine Mezzi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najla Abassi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Jmel
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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Romdhane L, Mezzi N, Dallali H, Messaoud O, Shan J, Fakhro KA, Kefi R, Chouchane L, Abdelhak S. A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa. NPJ Genom Med 2021; 6:3. [PMID: 33420067 PMCID: PMC7794582 DOI: 10.1038/s41525-020-00166-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022] Open
Abstract
Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.
- Department of Biology, Faculty of Science of Bizerte, Jarzouna, Tunisia.
| | - Nessrine Mezzi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rym Kefi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
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Fu R, Mokhtar SS, Phipps ME, Hoh BP, Xu S. A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia. Eur J Hum Genet 2018; 26:886-897. [PMID: 29476164 DOI: 10.1038/s41431-018-0120-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/20/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.
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Affiliation(s)
- Ruiqing Fu
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Maude Elvira Phipps
- School of Medicine, Monash University Sunway Campus, Petaling Jaya, Malaysia
| | - Boon-Peng Hoh
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Boon-Peng H, Mat Jusoh JA, Marshall CR, Majid F, Danuri N, Basir F, Thiruvahindrapuram B, Scherer SW, Yusoff K. Rare Copy Number Variants Identified Suggest the Regulating Pathways in Hypertension-Related Left Ventricular Hypertrophy. PLoS One 2016; 11:e0148755. [PMID: 26930585 PMCID: PMC4773219 DOI: 10.1371/journal.pone.0148755] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/20/2015] [Indexed: 01/19/2023] Open
Abstract
Left ventricular hypertrophy (LVH) is an independent risk factor for cardiovascular morbidity and mortality, and a powerful predictor of adverse cardiovascular outcomes in the hypertensive patients. It has complex multifactorial and polygenic basis for its pathogenesis. We hypothesized that rare copy number variants (CNVs) contribute to the LVH pathogenesis in hypertensive patients. Copy number variants (CNV) were identified in 258 hypertensive patients, 95 of whom had LVH, after genotyping with a high resolution SNP array. Following stringent filtering criteria, we identified 208 rare, or private CNVs that were only present in our patients with hypertension related LVH. Preliminary findings from Gene Ontology and pathway analysis of this study confirmed the involvement of the genes known to be functionally involved in cardiac development and phenotypes, in line with previously reported transcriptomic studies. Network enrichment analyses suggested that the gene-set was, directly or indirectly, involved in the transcription factors regulating the "foetal cardiac gene programme" which triggered the hypertrophic cascade, confirming previous reports. These findings suggest that multiple, individually rare copy number variants altering genes may contribute to the pathogenesis of hypertension-related LVH. In summary, we have provided further supporting evidence that rare CNV could potentially impact this common and complex disease susceptibility with lower heritability.
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Affiliation(s)
- Hoh Boon-Peng
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
- UCSI University, Jalan Menara Gading, UCSI Heights, 56000 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Julia Ashazila Mat Jusoh
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Fadhlina Majid
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
| | - Norlaila Danuri
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
| | - Fashieha Basir
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
| | | | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Khalid Yusoff
- UCSI University, Jalan Menara Gading, UCSI Heights, 56000 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
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Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, Wu S, Yang Y, Li S, Kang L, Guan Y, Hoh BP, Chung YJ, Jin L, Su B, Xu S. A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence. Am J Hum Genet 2015; 97:54-66. [PMID: 26073780 DOI: 10.1016/j.ajhg.2015.05.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/07/2015] [Indexed: 10/23/2022] Open
Abstract
Tibetan high-altitude adaptation (HAA) has been studied extensively, and many candidate genes have been reported. Subsequent efforts targeting HAA functional variants, however, have not been that successful (e.g., no functional variant has been suggested for the top candidate HAA gene, EPAS1). With WinXPCNVer, a method developed in this study, we detected in microarray data a Tibetan-enriched deletion (TED) carried by 90% of Tibetans; 50% were homozygous for the deletion, whereas only 3% carried the TED and 0% carried the homozygous deletion in 2,792 worldwide samples (p < 10(-15)). We employed long PCR and Sanger sequencing technologies to determine the exact copy number and breakpoints of the TED in 70 additional Tibetan and 182 diverse samples. The TED had identical boundaries (chr2: 46,694,276-46,697,683; hg19) and was 80 kb downstream of EPAS1. Notably, the TED was in strong linkage disequilibrium (LD; r(2) = 0.8) with EPAS1 variants associated with reduced blood concentrations of hemoglobin. It was also in complete LD with the 5-SNP motif, which was suspected to be introgressed from Denisovans, but the deletion itself was absent from the Denisovan sequence. Correspondingly, we detected that footprints of positive selection for the TED occurred 12,803 (95% confidence interval = 12,075-14,725) years ago. We further whole-genome deep sequenced (>60×) seven Tibetans and verified the TED but failed to identify any other copy-number variations with comparable patterns, giving this TED top priority for further study. We speculate that the specific patterns of the TED resulted from its own functionality in HAA of Tibetans or LD with a functional variant of EPAS1.
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Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet 2015; 134:375-92. [PMID: 25634076 DOI: 10.1007/s00439-014-1525-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/25/2014] [Indexed: 10/24/2022]
Abstract
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
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