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Ren Z, Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Le C, Wang J, Huang J. Genetic analysis of the mitochondrial DNA control region in Tai-Kadai-speaking Dong population in southwest China. Ann Hum Biol 2022; 49:354-360. [PMID: 36190920 DOI: 10.1080/03014460.2022.2131334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Dong people in Southwest China are officially recognised as an ethnic group, but there has been a lack of population genetic research on this group, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Dong population, and to provide help for the construction of a forensic mitochondrial DNA analysis reference database in East Asia. SUBJECTS AND METHODS The sequences of the mitochondrial DNA control region were analysed in 200 individuals of Dong in Guizhou. The haplotype frequencies, haplogroup distribution and paired Fst values of Guizhou Dong and 51 other populations in the world were calculated and explained to explore the genetic polymorphism and population relationships. RESULTS A total of 180 haplotypes were detected, with frequencies of 0.005-0.02. All haplotypes were assigned to 97 different haplogroups. The haplotype diversity and random matching probability were 0.998643 and 0.00635, respectively. The paired Fst values and correlation p values of 52 populations showed that the Guizhou Dong had the closest genetic relationship with the Henan Han and the Guizhou Miao in China, and were closest to the Punjab population in Pakistan and the Kashmiri population when compared with the world populations. CONCLUSIONS Our study was based on the matrilineal genetic structure of Guizhou Dong to study mitochondrial DNA, which was helpful to promote the establishment of the forensic DNA reference database in East Asia and provide reference for anthropological research.
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Affiliation(s)
- Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
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2
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Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Wang Jie, Huang J, Ren Z. The mitochondrial DNA control region sequences from the Chinese Sui population of southwestern China. Ann Hum Biol 2021; 48:635-640. [PMID: 34663140 DOI: 10.1080/03014460.2021.1994649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Sui people are officially recognised people living in southwest China, but there has been a lack of genetic research, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Sui population, with the aim of helping to promote the establishment of a forensic DNA analysis reference database in East Asia. SUBJECTS AND METHODS We analysed 201 Sui individuals and observed the sequences of the mitochondrial DNA control region. We calculated and explained the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Sui and 47 other populations in the world, in order to explore genetic polymorphisms and population relationships. RESULTS 161 haplotypes were found in the Sui population, with frequencies of 0.0049-0.0199. All samples were assigned to 80 different haplogroups. The haplotype diversity and random matching probability were 0.999938 and 0.024729, respectively. The pairwise Fst values and correlation p-values of 48 populations showed that the Sui population was most closely related to the Miao population in Guizhou and the Han population in Henan, and closer to the Punjab population and Pukhtunkhwa population in Pakistan, and was significantly different from the other 43 groups. Compared with the other 43 groups, it is relatively isolated. CONCLUSION Our results show that the study of mitochondrial DNA based on the analysis of matrilineal genetic structure of the Sui population can help to promote the establishment of a forensic DNA reference database in East Asia and provide reference for future anthropological research.
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Affiliation(s)
- Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Wang Jie
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
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3
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Eaaswarkhanth M, Pathak AK, Ongaro L, Montinaro F, Hebbar P, Alsmadi O, Metspalu M, Al-Mulla F, Thanaraj TA. Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population. Eur J Hum Genet 2021; 30:307-319. [PMID: 33753911 PMCID: PMC8904638 DOI: 10.1038/s41431-021-00861-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.
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Affiliation(s)
| | - Ajai K Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Tartu, Estonia
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Bari, Italy
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Osama Alsmadi
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait.,Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait.
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4
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Haidar M, Abbas FA, Alsaleh H, Haddrill PR. Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population. Sci Rep 2021; 11:1865. [PMID: 33479300 PMCID: PMC7820400 DOI: 10.1038/s41598-021-81425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
This study evaluates the forensic utility of 23 autosomal short tandem repeat markers in 400 samples from the Kuwaiti population, of which four markers (D10S1248, D22S1045, D2S441 and SE33) are reported for the first time for Kuwait. All the markers were shown to exhibit no deviation from Hardy–Weinberg equilibrium, nor any linkage disequilibrium between and within loci, indicating that these loci are inherited independently, and their allele frequencies can be used to estimate match probabilities in the Kuwaiti population. The low combined match probability of 7.37 × 10–30 and the high paternity indices generated by these loci demonstrate the usefulness of the PowerPlex Fusion 6C kit for human identification in this population, as well as to strengthen the power of paternity testing. Off-ladder alleles were seen at several loci, and these were identified by examining their underlying nucleotide sequences. Principal component analysis (PCA) and STRUCTURE showed no genetic structure within the Kuwaiti population. However, PCA revealed a correlation between geographic and genetic distance. Finally, phylogenetic trees demonstrated a close relationship between Kuwaitis and Middle Easterners at a global level, and a recent common ancestry for Kuwait with its northern neighbours of Iraq and Iran, at a regional level.
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Affiliation(s)
- Mahdi Haidar
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK. .,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait.
| | - Fatimah A Abbas
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK.,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK.,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK
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5
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Eaaswarkhanth M, Melhem M, Sharma P, Nizam R, Al Madhoun A, Chaubey G, Alsmadi O, AlOzairi E, Al-Mulla F. Mitochondrial DNA D-loop sequencing reveals obesity variants in an Arab population. APPLICATION OF CLINICAL GENETICS 2019; 12:63-70. [PMID: 31213875 PMCID: PMC6541754 DOI: 10.2147/tacg.s198593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/13/2019] [Indexed: 01/11/2023]
Abstract
Background: The association of mitochondrial DNA (mtDNA) variations with obesity has been investigated in diverse populations across the world. However, such obesity-associated mtDNA examinations are rarely conducted in Arab populations. Materials and methods: We re-sequenced mtDNA displacement loop (D-loop) region of 395 Arab individuals of Kuwait. We categorized the individuals based on their BMI scores as obese (n=232; BMI ≥30 kg/m2), overweight (n=110; BMI ≥25 kg/m2 and <30 kg/m2), and lean (n=53; BMI <25 kg/m2). We performed all the statistical tests by combining obese and overweight individuals in one group. Association analyses were conducted applying Fisher's exact test and logistic regression model. Results: We identified that the mtDNA variations m.73A>G, and m.523delAC were positively correlated with obesity, while m.310T>C, and m.16318A>T were negatively associated. All these variants, except m.16318A>T, remain statistically significant after adjusting for age and gender. We found that the variant m.73A>G increases the likelihood of being obese by 6-fold, whereas haplogroup H decreases the probability of being obese in Arab individuals of Kuwait. Haplotype analysis revealed that a haplotype, A263G-C309CT-T310C, defining the H2a clade of H haplogroup, reduces the probability of being obese. Conclusion: Our study reports, for the first time, the obesity-related mtDNA variants in Arabs of Kuwait. Based on the mtDNA D-loop region variations, we detected particular variants and haplogroup that are related with increased and decreased probability of being obese in the Kuwait Arab population.
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Affiliation(s)
| | - Motasem Melhem
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Prem Sharma
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Rasheeba Nizam
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Ashraf Al Madhoun
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Osama Alsmadi
- Department of Cell Therapy & Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Ebaa AlOzairi
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman, 15462, Kuwait
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6
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Ren Z, Chen H, Yang X, Zhang C. Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I. J Genet 2017; 96:119-125. [PMID: 28360396 DOI: 10.1007/s12041-017-0753-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.
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Affiliation(s)
- Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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7
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 2015; 28:203-12. [PMID: 26293354 DOI: 10.1002/ajhb.22773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2015] [Accepted: 07/25/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape. METHOD A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe. RESULTS The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan. CONCLUSION Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.
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Affiliation(s)
- Soumaya Triki-Fendri
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Suad Alfadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
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Taqi Z, Alenizi M, Alenizi H, Ismael S, Dukhyil AAB, Nazir M, Sanqoor S, Al Harbi E, Al-Jaber J, Theyab J, Moura-Neto RS, Budowle B. Population genetics of 23 Y-STR markers in Kuwaiti population. Forensic Sci Int Genet 2015; 16:203-204. [DOI: 10.1016/j.fsigen.2015.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/08/2015] [Accepted: 01/16/2015] [Indexed: 12/09/2022]
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9
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Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. BMC Genomics 2015; 16:92. [PMID: 25765185 PMCID: PMC4336699 DOI: 10.1186/s12864-015-1233-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
Background The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; “tent-dwelling” Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage. Results We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 ‘loss-of-function’ and 2,314 ’deleterious’ coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant’s family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays. Conclusions We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1233-x) contains supplementary material, which is available to authorized users.
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10
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Kundu S, Ghosh SK. Trend of different molecular markers in the last decades for studying human migrations. Gene 2014; 556:81-90. [PMID: 25510397 DOI: 10.1016/j.gene.2014.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022]
Abstract
Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.
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Affiliation(s)
- Sharbadeb Kundu
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India.
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11
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Yang X, Al-Bustan S, Feng Q, Guo W, Ma Z, Marafie M, Jacob S, Al-Mulla F, Xu S. The influence of admixture and consanguinity on population genetic diversity in Middle East. J Hum Genet 2014; 59:615-22. [PMID: 25253659 DOI: 10.1038/jhg.2014.81] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/10/2023]
Abstract
The Middle East (ME) is an important crossroad where modern humans migrated 'out of Africa' and spread into Europe and Asia. After the initial peopling and long-term isolation leading to well-differentiated populations, the ME also had a crucial role in subsequent human migrations among Africa, Europe and Asia; thus, recent population admixture has been common in the ME. On the other hand, consanguinity, a well-known practice in the ME, often reduces genetic diversity and works in opposition to admixture. Here, we explored the degree to which admixture and consanguinity jointly affected genetic diversity in ME populations. Genome-wide single-nucleotide polymorphism data were generated in two representative ME populations (Arabian and Iranian), with comparisons made with populations worldwide. Our results revealed an overall higher genetic diversity in both ME populations relative to other non-African populations. We identified a much larger number of long runs of homozygosity in ME populations than in any other populations, which was most likely attributed to high levels of consanguineous marriages that significantly decreased both individual and population heterozygosity. Additionally, we were able to distinguish African, European and Asian ancestries in ME populations and quantify the impact of admixture and consanguinity with statistical approaches. Interestingly, genomic regions with significantly excessive ancestry from individual source populations are functionally enriched in olfactory pathways, which were suspected to be under natural selection. Our findings suggest that genetic admixture, consanguinity and natural selection have collectively shaped the genetic diversity of ME populations, which has important implications in both evolutionary studies and medical practices.
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Affiliation(s)
- Xiong Yang
- 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 (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Qidi Feng
- 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 (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Guo
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zhiming Ma
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Makia Marafie
- Kuwait Medical Genetic Center, Maternity Hospital, Sulaibikhat, Kuwait
| | - Sindhu Jacob
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - 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 (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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12
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Alsmadi O, John SE, Thareja G, Hebbar P, Antony D, Behbehani K, Thanaraj TA. Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. PLoS One 2014; 9:e99069. [PMID: 24896259 PMCID: PMC4045902 DOI: 10.1371/journal.pone.0099069] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 05/10/2014] [Indexed: 01/19/2023] Open
Abstract
Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are 'novel'. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10-16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3' UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian tribe subgroup. The full-length genome sequences and the identified variants are available at ftp://dgr.dasmaninstitute.org and http://dgr.dasmaninstitute.org/DGR/gb.html.
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Affiliation(s)
- Osama Alsmadi
- Dasman Diabetes Institute, Dasman, Kuwait
- * E-mail: (TAT); (OA)
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Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John SE, Hebbar P, Behbehani K, Thanaraj TA. Genetic substructure of Kuwaiti population reveals migration history. PLoS One 2013; 8:e74913. [PMID: 24066156 PMCID: PMC3774671 DOI: 10.1371/journal.pone.0074913] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 08/07/2013] [Indexed: 12/21/2022] Open
Abstract
The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes) is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats) was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP) data to understand admixtures in each group reveals the following: the first group (Kuwait P) is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S) is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B) includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait's population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH) with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait's geographical location at the nexus of Africa, Europe, and Asia.
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