1
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Malyarchuk B, Denisova G, Litvinov A. Heterogeneity of the Southeast Belarusian mitochondrial gene pool. J Hum Genet 2025; 70:313-320. [PMID: 40195478 DOI: 10.1038/s10038-025-01337-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Revised: 03/11/2025] [Accepted: 03/28/2025] [Indexed: 04/09/2025]
Abstract
The study of mitochondrial DNA (mtDNA) variability at the level of whole mitogenomes has significant implications for the fields of human evolution and population genetics. In this paper, we present the results of a study of the complete mtDNA variability in Belarusians from the southeastern part of the Republic of Belarus. It was found that Southeast Belarusians are characterized by a high diversity of mitochondrial genomes. The analysis of genetic distances between European populations showed significant differences between the studied Belarusian sample from the bulk of East European populations, including Slavic ethnic groups. The results of the phylogeographic analysis indicated the presence of the West Asian component (12.6%) in the Belarusian mitochondrial gene pool, which can account for the observed genetic differences between Belarusians and other Eastern Slavs (Russians and Ukrainians). The East Asian component of the mitochondrial gene pool of the studied group of Belarusians is represented by haplogroup C5c1a (2.3%). The results of the phylogeographic analysis indicated that this mtDNA subclade is predominantly present in the gene pools of Slavic peoples, including Poles, Belarusians, Ukrainians, and Russians. The evolutionary age of haplogroup C5c1a is ~4000 years and, consequently, the appearance of C5c1-haplotypes in the eastern regions of Europe may be linked to the migrations of the Caspian steppe populations to the west during the Bronze Age.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
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2
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Tian Y, Koncz I, Defant S, Giostra C, Vyas DN, Sołtysiak A, Pejrani Baricco L, Fetner R, Posth C, Brandt G, Bedini E, Modi A, Lari M, Vai S, Francalacci P, Fernandes R, Steinhof A, Pohl W, Caramelli D, Krause J, Izdebski A, Geary PJ, Veeramah KR. The role of emerging elites in the formation and development of communities after the fall of the Roman Empire. Proc Natl Acad Sci U S A 2024; 121:e2317868121. [PMID: 39159385 PMCID: PMC11388374 DOI: 10.1073/pnas.2317868121] [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: 10/17/2023] [Accepted: 06/26/2024] [Indexed: 08/21/2024] Open
Abstract
Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups.
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Affiliation(s)
- Yijie Tian
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - István Koncz
- Department of Humanities, Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary
| | - Sarah Defant
- Department of History and Cultural Studies, Institute of Prehistoric Archaeology, Freie Universität Berlin, Berlin 14195, Germany
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Department of Philosophy and Humanities, Institute of Greek and Latin Languages and Literatures, Freie Universität Berlin, Berlin 14195, Germany
| | - Caterina Giostra
- Department of History, Archaeology and Art History, Catholic University Milan, Milan 20103, Italy
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Arkadiusz Sołtysiak
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
| | - Luisella Pejrani Baricco
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Torino, Torino TO 10122, Italy
| | - Rafał Fetner
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
| | - Cosimo Posth
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen 72074, Germany
| | - Guido Brandt
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Elena Bedini
- Department of History, Archaeology and Art History, Catholic University Milan, Milan 20103, Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari 09126, Italy
| | - Ricardo Fernandes
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, Warszawa 00-927, Poland
- Arne Faculty of Arts, Masaryk University, Brno-střed 602 00, Czech Republic
- Climate Change and History Research Initiative, Princeton University, Princeton, NJ 08542
| | - Axel Steinhof
- Max Planck Institute for Biogeochemistry, Jena 07745, Germany
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences; Institute for Austrian Historical Research, University of Vienna, Vienna 1020, Austria
| | - David Caramelli
- Department of Biology, University of Florence, Firenze 12-50122, Italy
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Adam Izdebski
- Max Planck Institute of Geoanthropology, Jena 07743, Germany
- Institute of History, Jagiellonian University in Krakow, Kraków 31-007, Poland
| | - Patrick J Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, NJ 08540
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
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3
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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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4
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Ji Y, Guo N, Lu C, Zhang M, Wang S, Yang L, Li Q, Lv M, Yang Y, Gao Y. Association between mtDNA haplogroups and skeletal fluorosis in Han population residing in drinking water endemic fluorosis area of northern China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:2397-2406. [PMID: 37660259 DOI: 10.1080/09603123.2023.2253161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
To investigate the association between mtDNA genetic information and the risk of SF, individuals were conducted in the drinking water endemic fluorosis area in northern China, sequenced the whole genome of mtDNA, identified the SNPs and SNVs, analyzed the haplogroups, and diagnosed SF, and then, the effect of mtDNA genetic information on the risk of SF was evaluated. We find that, D5 haplogroup and its specific SNPs reduced the risk, while the D4 haplogroup and its specific SNPs increased the risk of SF. The number of SNVs in coding regions of mitochondrial respiratory chain (MRC) is different between the controls and cases. This suggests that D5 haplogroup may play a protective role in the risk of SF, while the opposite is observed for the D4 haplogroup, this may relate to their specific SNPs. And SNVs that encode the MRC complex may also be associated with the risk of SF.
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Affiliation(s)
- Yi Ji
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ning Guo
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chunqing Lu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Meichen Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Sa Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Liu Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qiao Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Man Lv
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yanmei Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yanhui Gao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
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5
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Rider DF, Wolf ACE, Murray J, de Flamingh A, dos Santos ALC, Lanoë F, Zedeño MN, DeGiorgio M, Lindo J, Malhi RS. Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times. SCIENCE ADVANCES 2024; 10:eadl6595. [PMID: 38569022 PMCID: PMC10990285 DOI: 10.1126/sciadv.adl6595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
Mutually beneficial partnerships between genomics researchers and North American Indigenous Nations are rare yet becoming more common. Here, we present one such partnership that provides insight into the peopling of the Americas and furnishes another line of evidence that can be used to further treaty and Indigenous rights. We show that the genomics of sampled individuals from the Blackfoot Confederacy belong to a previously undescribed ancient lineage that diverged from other genomic lineages in the Americas in Late Pleistocene times. Using multiple complementary forms of knowledge, we provide a scenario for Blackfoot population history that fits with oral tradition and provides a plausible model for the evolutionary process of the peopling of the Americas.
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Affiliation(s)
| | | | - John Murray
- Blackfeet Tribal Historic Preservation Office, Browning, MT 59417, USA
| | - Alida de Flamingh
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - François Lanoë
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Maria N. Zedeño
- Bureau of Applied Research in Anthropology, School of Anthropology, The University of Arizona, Tucson, AZ 85721, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Ripan S. Malhi
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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6
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Yan Y, Du P, Zhang J, Li R, Bao H, Fang Q, Gao Y, Meng H, Xu Y, Shi H, Yan H, Chang X, Ren X, Wang L, Ru K, Allen E, Li J, Wen S, Zhang N. Mitogenome analysis reveals predominantly ancient Yellow River origin of population inhabiting Datong agro-pastoral ecotone along Great Wall. Mol Genet Genomics 2023; 298:1321-1330. [PMID: 37498358 DOI: 10.1007/s00438-023-02056-8] [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: 11/02/2022] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
The Datong Basin was an important arena for population movement and admixture between the Yellow River Valley and Eastern Steppe. In historical materials, the region was often the setting for a tug-of-war between Han farmers and non-Han nomads. The genetic makeup and population history of this Datong population has, however, remained uncertain. In this study, we analysed 289 mitogenomes from Datong individuals. Our primary findings were: (1) population summary statistics analysis revealed a high level of genetic diversity and strong signals of population expansion in the Datong population; (2) inter-population comparisons (PCA and Fst heatmap) exhibited a close clustering between the Datong population and Northern Han, especially northern frontier groups, such as the Inner Mongolia Han, Heilongjiang Han, Liaoning Han and Tianjin Han; (3) phylogeographic analysis of complete mitogenomes revealed the presence of different components in the maternal gene pools of Datong population-the northern East Asian component was dominant (66.44%), whereas the southern East Asians were the second largest component with 31.49%. We also observed a much reduced west Eurasian (2.07%) component; (4) direct comparisons with ancient groups showed closer relationship between Datong and Yellow River farmers than Eastern Steppe nomads. Despite, therefore, centuries of Eastern Steppe nomadic control over the Datong area, Yellow River farmers had a much more significant impact on the Datong population.
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Affiliation(s)
- Yuqing Yan
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Panxin Du
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Jihong Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Ruilan Li
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Haoquan Bao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Qingli Fang
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Ye Gao
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Haochen Shi
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Hailong Yan
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Li Wang
- Datong Xin Jian Kang Hospital Group Company, Datong, 037006, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China
| | - Jiehui Li
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Shaoqing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- Institute of Archaeological Science, Fudan University, Shanghai, 200433, China.
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai, 200433, China.
- Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai, 200433, China.
| | - Nianping Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Infammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China.
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7
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Vyas DN, Koncz I, Modi A, Mende BG, Tian Y, Francalacci P, Lari M, Vai S, Straub P, Gallina Z, Szeniczey T, Hajdu T, Pejrani Baricco L, Giostra C, Radzevičiūtė R, Hofmanová Z, Évinger S, Bernert Z, Pohl W, Caramelli D, Vida T, Geary PJ, Veeramah KR. Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia. Curr Biol 2023; 33:3951-3961.e11. [PMID: 37633281 DOI: 10.1016/j.cub.2023.07.063] [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: 04/06/2023] [Revised: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.1,2 To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries3,4,5 at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site6 and analyzed them alongside data from over 550 penecontemporaneous individuals.7,8,9,10,11,12,13,14,15,16,17,18,19 The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial customs and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artifacts and genetic ancestry among 5th century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.
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Affiliation(s)
- Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - István Koncz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Múzeum krt. 4/B, 1088 Budapest, Hungary
| | - Alessandra Modi
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Tóth Kálmán utca 4, 1097 Budapest, Hungary
| | - Yijie Tian
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Via T. Fiorelli 1, 09126 Cagliari, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | | | | | - Tamás Szeniczey
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Luisella Pejrani Baricco
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Torino, piazza San Giovanni 2, 10122 Torino, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell'Arte, Università Cattolica del Sacro Cuore, Largo A. Gemelli, 1, 20123 Milano, Italy
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Arna Nováka 1/1, Brno 60200, Czech Republic
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Zsolt Bernert
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences, Dr-Ignaz-Seipel-Platz 2, 1020 Vienna, Austria; Institute for Austrian Historical Research, University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - David Caramelli
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy.
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Múzeum krt. 4/B, 1088 Budapest, Hungary.
| | - Patrick J Geary
- School of Historical Studies, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA.
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA.
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8
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [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] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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9
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Dai SS, Sulaiman X, Isakova J, Xu WF, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wang MS, Shen QK, Yang XY, Yao YG, Aldashev AA, Saidov A, Chen W, Cheng LF, Peng MS, Zhang YP. The genetic echo of the Tarim mummies in modern Central Asians. Mol Biol Evol 2022; 39:6675590. [PMID: 36006373 PMCID: PMC9469894 DOI: 10.1093/molbev/msac179] [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] [Indexed: 11/24/2022] Open
Abstract
The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian–related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.
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Affiliation(s)
- Shan Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Wei Fang Xu
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen 518034, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi 830011, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wei Kang Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Ming Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Quan Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xing Yan Yang
- Key Laboratory of Chemistry in Ethnic Medicinal Resource, Yunnan Minzu University, Kunming 650504, China.,School of Chemistry and Environment, Yunnan Minzu University, Kunming 650504, China
| | - Yong Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Almaz A Aldashev
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Abdusattor Saidov
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650224, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650224, China
| | - Lu Feng Cheng
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Min Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ya Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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10
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Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5344418. [PMID: 35342764 PMCID: PMC8956381 DOI: 10.1155/2022/5344418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 11/17/2022]
Abstract
Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.
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11
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Wang Y, Huang X, Peng F, Han H, Gu Y, Liu X, Feng Z. Association of variants m.T16172C and m.T16519C in whole mtDNA sequences with high altitude pulmonary edema in Han Chinese lowlanders. BMC Pulm Med 2022; 22:72. [PMID: 35216582 PMCID: PMC8881820 DOI: 10.1186/s12890-021-01791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 12/08/2021] [Indexed: 12/05/2022] Open
Abstract
Background High altitude pulmonary edema (HAPE) is a hypoxia-induced non-cardiogenic pulmonary edema that typically occurred in un-acclimatized lowlanders, which inevitably leads to life-threatening consequences. Apart from multiple factors involved, the genetic factors also play an important role in the pathogenesis of HAPE. So far, researchers have put more energy into the nuclear genome and HAPE, and ignored the relationship between the mitochondrion DNA (mtDNA) variants and HAPE susceptibility. Methods We recruited a total of 366 individuals including 181 HAPE patients and 185 non-HAPE populations through two times. The first time, 49 HAPE patients and 58 non-HAPE individuals were performed through whole mtDNA sequences to search the mutations and haplogroups. The second time, 132 HAPE patients and 127 non-HAPE subjects were collected to apply verifying these mutations and haplogroups of mtDNA with the routine PCR method. Results We analyzed and summarized the clinical characteristics and sequence data for the 49 HAPE patients and 58 non-HAPE individuals. We found that a series of routine blood indexes including systolic arterial blood pressure (SBP), heart rate (HR), white blood cell (WBC), and C-reactive protein (CRP) in the HAPE group presented higher and displayed significant differences compared with those in the non-HAPE group. Although the average numbers of variants in different region and group samples were not statistically significant (P > 0.05), the mutation densities of different regions in the internal group showed significant differences. Then we found two mutations (T16172C and T16519C) associated with the HAPE susceptibility, the T16172C mutation increased the risk of HAPE, and the T16519C mutation decreased the HAPE rating. Furthermore, the two mutations were demonstrated with 132 HAPE patients and 127 non-HAPE individuals. Unfortunately, all the haplogroups were not associated with the HAPE haplogroups. Conclusions We provided evidence of differences in mtDNA polymorphism frequencies between HAPE and non-HAPE Han Chinese. Genotypes of mtDNA 16172C and 16519C were correlated with HAPE susceptibility, indicating the role of the mitochondrial genome in the pathogenesis of HAPE. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01791-1.
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Affiliation(s)
- Yan Wang
- Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, No. 28 Fu Xin Road, Hai Dian District, Beijing, 100853, China. .,BaYi Children's Hospital, The Seventh Medical Center of PLA General Hospital, No.5 Nan Men Cang, Dong Cheng District, Beijing, 100700, China.
| | - Xuewen Huang
- The Mountain Sickness Prevention Research Center of the General Hospital of Tibet Military Command, Tibet, China
| | - Fujun Peng
- School of Basic Medical Sciences, Weifang Medical University, Weifang, Shandong, China
| | - Huiling Han
- BaYi Children's Hospital, The Seventh Medical Center of PLA General Hospital, No.5 Nan Men Cang, Dong Cheng District, Beijing, 100700, China
| | - Yanan Gu
- BaYi Children's Hospital, The Seventh Medical Center of PLA General Hospital, No.5 Nan Men Cang, Dong Cheng District, Beijing, 100700, China
| | - Xin Liu
- BaYi Children's Hospital, The Seventh Medical Center of PLA General Hospital, No.5 Nan Men Cang, Dong Cheng District, Beijing, 100700, China
| | - Zhichun Feng
- BaYi Children's Hospital, The Seventh Medical Center of PLA General Hospital, No.5 Nan Men Cang, Dong Cheng District, Beijing, 100700, China.
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12
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García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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13
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Ni J, Liu Z, Yuan Y, Li W, Hu Y, Liu P, Hou X, Zhu X, Tang X, Liang M, Zheng S, Hou X, Du J, Tang J, Jiang H, Shen L, Tang B, Wang J. Mitochondrial genome variations are associated with amyotrophic lateral sclerosis in patients from mainland China. J Neurol 2021; 269:805-814. [PMID: 34129120 DOI: 10.1007/s00415-021-10659-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a late-onset neurodegenerative disorder. Mitochondrial dysfunction is involved in the complex pathophysiology of ALS; however, the role of mitochondrial DNA (mtDNA) variants in ALS is poorly understood. We aimed to elucidate the role of mtDNA variants in the pathogenesis of ALS. METHODS The mitochondrial haplogroups of 585 ALS patients and 371 healthy controls were determined; 38 ALS patients and 42 controls underwent long-range polymerase chain reaction combined with next-generation sequencing technology to analyze whole mitochondrial genome variants. RESULTS A higher percentage of variants accumulated in ALS patients than in controls. Analysis of coding region variations that were further stratified by mtDNA genes revealed that nonsynonymous variants were more vulnerable in ALS patients than in controls, particularly in the ND4L, ND5, and ATP8 genes. Moreover, pathogenic nonsynonymous variants tended to over-represent in ALS patients. Unsurprisingly, nonsynonymous variants were not related to the phenotype. Haplogroup analysis did not found evidence of association between haplogroups with the risk of ALS, however, patients belonging to haplogroup Y and M7c were prone to develop later onset of ALS. CONCLUSIONS This is the first study to profile mtDNA variants in ALS patients from mainland China. Our results suggest that an increase in the number of nonsynonymous variants is linked to the pathogenesis of ALS. Moreover, haplogroup Y and M7c may modulate the clinical expression of ALS. Our findings provide independent, albeit limited, evidence for the role of mtDNA in the pathogenesis of ALS.
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Affiliation(s)
- Jie Ni
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Zhen Liu
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Yanchun Yuan
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Wanzhen Li
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Yiting Hu
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Pan Liu
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Xiaorong Hou
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Xiangyu Zhu
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Xuxiong Tang
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Mingyu Liang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Siqi Zheng
- Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Xuan Hou
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Juan Du
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China
| | - Jianguang Tang
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China.,Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410008, People's Republic of China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China.,Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410008, People's Republic of China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China.,Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410008, People's Republic of China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, 87 Xiangya Rd, Changsha, Hunan, People's Republic of China. .,Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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14
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Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. Int J Mol Sci 2021; 22:ijms22115747. [PMID: 34072215 PMCID: PMC8198973 DOI: 10.3390/ijms22115747] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.
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15
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Polymorphisms and haplotype of mitochondrial DNA D-loop region are associated with polycystic ovary syndrome in a Chinese population. Mitochondrion 2020; 57:173-181. [PMID: 33385542 DOI: 10.1016/j.mito.2020.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/16/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023]
Abstract
Polymorphisms in mitochondrial DNA (mtDNA) have been linked to a range of diseases. Here we investigate the relationship between mtDNA D-loop region polymorphisms, mtDNA haplotype and polycystic ovary syndrome (PCOS), as well as the correlation of D-loop variants and clinical characteristics of PCOS, in a Chinese population. The mtDNA D-loop of whole blood samples from 421 PCOS patients and 409 controls underwent next generation sequencing. The variants G207A (PBH<0.05), 16036GGins (PBH<0.05) and 16049Gins (PBH<0.001) were associated with decreased risk of PCOS. No variants were associated with PCOS, and within the PCOS group, no statistical significance was found between D-loop polymorphisms and clinical characteristics. Patient haplotype was identified from D-loop single nucleotide polymorphisms and analysis suggested that haplotype A15 (P adjusted <0.01) was significantly associated with decreased risk of PCOS. In conclusion, mtDNA D-loop alterations and haplotype appear to confer resistance to PCOS in Chinese women.
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16
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Jaimes Díaz H, Martínez Covarrubias EI, Murcia Garzón JE, Flores Valdez M, Muñoz Ramírez ZY, Ramírez Calzada CA, Bohra R, Méndez Tenorio A. Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints. Mitochondrion 2020; 57:294-299. [PMID: 33301927 DOI: 10.1016/j.mito.2020.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
In the present study, we evaluated the ability of the Virtual Analysis Method for Phylogenomic fingerprint Estimation (VAMPhyRE) toolkit to classify human mitochondrial DNA (mtDNA) haplogroups. In total, 357 random mtDNA sequences were obtained from different haplogroups, based on the classification of PhyloTree. Additionally, we included a control group of five sequences (Pan paniscus, Pan troglodytes, Homo sapiens neanderthalensis, Yoruba15, and the revised Cambridge reference sequence). VAMPhyRE employs a virtual hybridization technique, using probes that specifically bind to their complementary sequences in the genome. We used 65,536 probes of 8 nucleotides to identify potential sites where hybridization occurs between the mtDNA and the specific probe, forming different heteroduplexes and thus, creating a unique and specific genomic fingerprint for each sequence. Genomic fingerprints were compared, and a table of distances was calculated to obtain a mitochondrial phylogenomic tree with the macrohaplogroups, L, N, M, and R, and their corresponding haplogroups, according to universal nomenclature. The results obtained suggest an accuracy of 97.25% for the distribution of the 357 mtDNA sequences in the four macrohaplogroups and their corresponding haplogroups when compared with other mtDNA classification tools that require reference sequences and do not offer an analysis based on an evolutionary approach. These data are available online at http://biomedbiotec.encb.ipn.mx/VAMPhyRE/.
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Affiliation(s)
- Hueman Jaimes Díaz
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Elvira Ivonne Martínez Covarrubias
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Jazmin E Murcia Garzón
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Mauricio Flores Valdez
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Zilia Y Muñoz Ramírez
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Crystel A Ramírez Calzada
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Rekha Bohra
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Alfonso Méndez Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica. Departamento de Bioquímica. Escuela Nacional de Ciencias Biológicas. Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
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17
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Asally R, Markham R, Manconi F. Mitochondrial DNA haplogroup H association with endometriosis and possible role in inflammation and pain. JOURNAL OF ENDOMETRIOSIS AND PELVIC PAIN DISORDERS 2020. [DOI: 10.1177/2284026520940518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Introduction: Endometriosis is an inflammatory disease characterised by the presence of endometrial-like tissue outside the uterus and affects approximately 10%–15% of women in their reproductive years. Pain is one of the predominant symptoms of the disease. Oxidative stress is involved in the pathophysiology of endometriosis and develops when there is an imbalance between the reactive oxygen species and reactive nitrogen species production, and the elimination capacity of antioxidants in the reproductive tract. High levels of reactive oxygen species can induce pain indirectly through oxidative stress-associated inflammation or directly through sensitising the nociceptive neurons that transmit the signals to the cerebral sensory cortex which are perceived as a feeling of pain. Mitochondria are the main source of reactive oxygen species, which generate through oxidative phosphorylation. Given that the mitochondria are involved in reactive oxygen species formation and energy production, which are required for the activation and proliferation of peripheral lymphocytes, it has been suggested that mitochondrial DNA variants are involved in the pathogenesis of endometriosis. This study has provided a better understanding of maternally inherited risk factors which contribute to the pain mechanisms associated with endometriosis. Results: Mitochondrial DNA haplogroup H was found to be significantly higher in women with endometriosis. This study was the first to report the association between the European mitochondrial haplogroup H and the risk of pain associated with endometriosis. Discussion: The results suggest that there are maternally inherited risk factors in women with endometriosis causing high reactive oxygen species production and oxidative stress, which facilitate pain generation in women with endometriosis.
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Affiliation(s)
- Razan Asally
- Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney, Camperdown, NSW, Australia
- Saudi Arabian Ministry of Higher Education, Riyadh, Saudi Arabia
| | - Robert Markham
- Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney, Camperdown, NSW, Australia
| | - Frank Manconi
- Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney, Camperdown, NSW, Australia
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18
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Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas. Sci Rep 2020; 10:10592. [PMID: 32601317 PMCID: PMC7324373 DOI: 10.1038/s41598-020-67519-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
High-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, Pamiri Tajiks and Sarikoli Tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies.
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19
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Li YC, Ye WJ, Jiang CG, Zeng Z, Tian JY, Yang LQ, Liu KJ, Kong QP. River Valleys Shaped the Maternal Genetic Landscape of Han Chinese. Mol Biol Evol 2020; 36:1643-1652. [PMID: 31112995 DOI: 10.1093/molbev/msz072] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A general south-north genetic divergence has been observed among Han Chinese in previous studies. However, these studies, especially those on mitochondrial DNA (mtDNA), are based either on partial mtDNA sequences or on limited samples. Given that Han Chinese comprise the world's largest population and reside around the whole China, whether the north-south divergence can be observed after all regional populations are considered remains unknown. Moreover, factors involved in shaping the genetic landscape of Han Chinese need further investigation. In this study, we dissected the matrilineal landscape of Han Chinese by studying 4,004 mtDNA haplogroup-defining variants in 21,668 Han samples from virtually all provinces in China. Our results confirmed the genetic divergence between southern and northern Han populations. However, we found a significant genetic divergence among populations from the three main river systems, that is, the Yangtze, the Yellow, and the Zhujiang (Pearl) rivers, which largely attributed to the prevalent distribution of haplogroups D4, B4, and M7 in these river valleys. Further analyses based on 4,986 mitogenomes, including 218 newly generated sequences, indicated that this divergence was already established during the early Holocene and may have resulted from population expansion facilitated by ancient agricultures along these rivers. These results imply that the maternal gene pools of the contemporary Han populations have retained the genetic imprint of early Neolithic farmers from different river basins, or that river valleys represented relative migration barriers that facilitated genetic differentiation, thus highlighting the importance of the three ancient agricultures in shaping the genetic landscape of the Han Chinese.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Wei-Jian Ye
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | | | - Zhen Zeng
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Kai-Jun Liu
- Chengdu 23 Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
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20
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Zhao D, Ding Y, Lin H, Chen X, Shen W, Gao M, Wei Q, Zhou S, Liu X, He N. Mitochondrial Haplogroups N9 and G Are Associated with Metabolic Syndrome Among Human Immunodeficiency Virus-Infected Patients in China. AIDS Res Hum Retroviruses 2019; 35:536-543. [PMID: 30950284 DOI: 10.1089/aid.2018.0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Increasing evidence shows that mitochondrial DNA (mtDNA) variations have an important effect on metabolic disorders, but such studies have not been conducted in HIV-infected patients in Asia. We investigated the distribution of mtDNA haplogroups and their correlation with metabolic disorders in HIV-infected patients. A cross-sectional survey was performed among 296 HIV patients older than the age of 40 years in a rural prefecture, Eastern China. The entire mtDNA sequence was amplified by polymerase chain reaction using four overlapping pairs of primers that have been standardly used. In this sample, mtDNA haplogroups B, D, M7, and F were the most dominant haplogroups. The overall prevalence of metabolic syndrome (MetS) was 36.1%, and was highest (77.8%) among those with haplogroup G and lowest (21.4%) among those with haplogroup M8. In multivariable analysis, haplogroups G and N9 were significantly associated with the presence of MetS [adjusted odds ratio (aOR) = 13.5, 95% confidence interval (CI): 1.9-94.7; aOR = 8.1, 95% CI: 1.8-36.1; respectively]. Moreover, patients with haplogroup G had increased odds of elevated glycated hemoglobin (HbA1c) (aOR = 10.1, 95% CI: 1.4-71.1), patients with haplogroup N9 had increased odds of elevated triglycerides (aOR = 13.5, 95% CI: 2.4-76.8). No significant association between mtDNA haplogroups and other MetS components was observed. Our data demonstrate the association between mtDNA haplogroups and MetS in HIV-infected patients. The Asian-specific mtDNA haplogroups G and N9 may confer higher risk for the development of MetS in HIV-infected patients, which requires further longitudinal investigation.
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Affiliation(s)
- Dan Zhao
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Health Technology Assessment of Ministry of Health, Fudan University, Shanghai, China
| | - Yingying Ding
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Haijiang Lin
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Xiaoxiao Chen
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Weiwei Shen
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Meiyang Gao
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Qian Wei
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Sujuan Zhou
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Xing Liu
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Na He
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Health Technology Assessment of Ministry of Health, Fudan University, Shanghai, China
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21
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Bai H, Guo X, Narisu N, Lan T, Wu Q, Xing Y, Zhang Y, Bond SR, Pei Z, Zhang Y, Zhang D, Jirimutu J, Zhang D, Yang X, Morigenbatu M, Zhang L, Ding B, Guan B, Cao J, Lu H, Liu Y, Li W, Dang N, Jiang M, Wang S, Xu H, Wang D, Liu C, Luo X, Gao Y, Li X, Wu Z, Yang L, Meng F, Ning X, Hashenqimuge H, Wu K, Wang B, Suyalatu S, Liu Y, Ye C, Wu H, Leppälä K, Li L, Fang L, Chen Y, Xu W, Li T, Liu X, Xu X, Gignoux CR, Yang H, Brody LC, Wang J, Kristiansen K, Burenbatu B, Zhou H, Yin Y. Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia. Nat Genet 2018; 50:1696-1704. [PMID: 30397334 DOI: 10.1038/s41588-018-0250-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/03/2018] [Indexed: 12/30/2022]
Abstract
The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.
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Affiliation(s)
- Haihua Bai
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China.,Inner Mongolia Engineering Research Center of Personalized Medicine, Tongliao, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tianming Lan
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qizhu Wu
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yanping Xing
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Stephen R Bond
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhili Pei
- College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yanru Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Dandan Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jirimutu Jirimutu
- College of Mathematics, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Dong Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xukui Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Morigenbatu Morigenbatu
- College of Mongolian Studies, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Li Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bingyi Ding
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Baozhu Guan
- Inner Mongolia International Mongolian Hospital, Hohhot, China
| | - Junwei Cao
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yiyi Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wangsheng Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ningxin Dang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mingyang Jiang
- College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Shenyuan Wang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Huixin Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Dingzhu Wang
- College of Mongolian Studies, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Chunxia Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Luo
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ying Gao
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Xueqiong Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zongze Wu
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Liqing Yang
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China
| | - Fanhua Meng
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolian Ning
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | | | - Kaifeng Wu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Suyalatu Suyalatu
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yingchun Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Huiguang Wu
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lu Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Lin Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yujie Chen
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Wenhao Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Science and Technology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, China
| | - Tao Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Lawrence C Brody
- Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Burenbatu Burenbatu
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China.
| | - Huanmin Zhou
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China.
| | - Ye Yin
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,BGI Genomics, BGI-Shenzhen, Shenzhen, China. .,School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
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22
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Piotrowska-Nowak A, Kosior-Jarecka E, Schab A, Wrobel-Dudzinska D, Bartnik E, Zarnowski T, Tonska K. Investigation of whole mitochondrial genome variation in normal tension glaucoma. Exp Eye Res 2018; 178:186-197. [PMID: 30312593 DOI: 10.1016/j.exer.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023]
Abstract
Glaucoma is one of the leading causes of visual impairment and blindness worldwide. However, the cause of retinal ganglion cell loss and damage of the optic nerve in its pathogenesis is largely unknown. The high energy demands of these cells may reflect their strong dependence on mitochondrial function and thus sensitivity to mitochondrial defects. To address this issue, we studied whole mitochondrial genome variation in normal tension glaucoma patients and control individuals from the Polish population using next generation sequencing. Our findings indicate that few features of mitochondrial DNA variation are different for glaucoma patients and control subjects. New insights into normal tension glaucoma development are discussed. We provide also a comprehensive approach for mitochondrial DNA analysis and variant evaluation.
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Affiliation(s)
- Agnieszka Piotrowska-Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Aleksandra Schab
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Dominika Wrobel-Dudzinska
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland; Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Tomasz Zarnowski
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Katarzyna Tonska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
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23
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De Angelis F, Scorrano G, Martínez-Labarga C, Scano G, Macciardi F, Rickards O. Mitochondrial variability in the Mediterranean area: a complex stage for human migrations. Ann Hum Biol 2018; 45:5-19. [PMID: 29382277 DOI: 10.1080/03014460.2017.1416172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. OBJECTIVE This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. METHODS Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. RESULTS The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. CONCLUSION Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
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Affiliation(s)
- Flavio De Angelis
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Gabriele Scorrano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Cristina Martínez-Labarga
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Giuseppina Scano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Fabio Macciardi
- b Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior , University of California , Irvine , CA , USA
| | - Olga Rickards
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
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24
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ElHefnawi M, Jeon S, Bhak Y, ElFiky A, Horaiz A, Jun J, Kim H, Bhak J. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes. Gene 2018; 668:129-134. [DOI: 10.1016/j.gene.2018.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/13/2018] [Indexed: 12/27/2022]
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25
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Smieszek S, Mitchell SL, Farber-Eger EH, Veatch OJ, Wheeler NR, Goodloe RJ, Wells QS, Murdock DG, Crawford DC. Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification. PeerJ 2018; 6:e5149. [PMID: 29967758 PMCID: PMC6022720 DOI: 10.7717/peerj.5149] [Citation(s) in RCA: 9] [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: 11/20/2017] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.
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Affiliation(s)
- Sandra Smieszek
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Sabrina L. Mitchell
- Vanderbilt Eye Institute and Department of Ophthalmology & Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric H. Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivia J. Veatch
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas R. Wheeler
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robert J. Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Quinn S. Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Deborah G. Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dana C. Crawford
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
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26
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Mitochondrial DNA variants modulate genetic susceptibility to Parkinson's disease in Han Chinese. Neurobiol Dis 2018; 114:17-23. [DOI: 10.1016/j.nbd.2018.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/18/2018] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
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Li J, Zhang Y, Zhao Y, Chen Y, Ochir A, Sarenbilige, Zhu H, Zhou H. The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:895-905. [PMID: 29681138 DOI: 10.1002/ajpa.23491] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 03/07/2018] [Accepted: 04/05/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA-M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino-Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran. MATERIALS AND METHODS The mtDNA hypervariable sequence I (HVS-I) and Y-chromosome SNPs were analyzed, and capture of the paternal non-recombining region of the Y chromosome (NRY) and whole-genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual. RESULTS The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y-chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. (). DISCUSSION We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu-Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic- and Manchu-speaking populations.
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Affiliation(s)
- Jiawei Li
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.,College of Life Science, Jilin University, Changchun 130012, People's Republic of China
| | - Ye Zhang
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Yongbin Zhao
- Life Science College, Jilin Normal University, Siping 136000, People's Republic of China
| | - Yongzhi Chen
- Director, Inner Mongolian Museum, Hohhot 010011, People's Republic of China
| | - A Ochir
- Coordinator, International Institute for Study of Nomadic Civilization, 210620A, Ulaanbaatar 11, Mongolia
| | - Sarenbilige
- Editorial department, Cultural Relics and Archaeological Institute of Inner Mongolia, Hohhot 010010, People's Republic of China
| | - Hong Zhu
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Hui Zhou
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.,College of Life Science, Jilin University, Changchun 130012, People's Republic of China
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Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives. Genes (Basel) 2018; 9:genes9030124. [PMID: 29495418 PMCID: PMC5867845 DOI: 10.3390/genes9030124] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Distinguishing between maternal relatives through mitochondrial (mt) DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS) approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2–10% of the sequencing reads. A total of 17 pairs exhibited differentiating heteroplasmy (44%), with the majority of sites (76%, 16 of 21) occurring in the coding region, further illustrating the value of conducting sequence analysis on the entire mtgenome. A number of the sites of differentiating heteroplasmy resulted in non-synonymous changes in protein sequence (5 of 21), and to changes in transfer or ribosomal RNA sequences (5 of 21), highlighting the potentially deleterious nature of these heteroplasmic states. Shared heteroplasmy was observed in 12 of the 39 mother-child pairs (31%), with no duplicate sites of either differentiating or shared heteroplasmy observed; a single nucleotide position (16093) was duplicated between the data sets. Finally, rates of heteroplasmy in blood and buccal cells were compared, as it is known that rates can vary across tissue types, with similar observations in the current study. Our data support the view that differentiating heteroplasmy across the mtgenome can be used to frequently distinguish maternal relatives, and could be of interest to both the medical genetics and forensic communities.
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29
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Genetic variation in populations from central Argentina based on mitochondrial and Y chromosome DNA evidence. J Hum Genet 2018; 63:493-507. [DOI: 10.1038/s10038-017-0406-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022]
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30
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Li X, Zhou TC, Wu CH, Tao LL, Bi R, Chen LJ, Deng DY, Liu C, Otecko NO, Tang Y, Lai X, Zhang L, Wei J. Correlations between mitochondrial DNA haplogroup D5 and chronic hepatitis B virus infection in Yunnan, China. Sci Rep 2018; 8:869. [PMID: 29343698 PMCID: PMC5772044 DOI: 10.1038/s41598-018-19184-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial abnormality is frequently reported in individuals with hepatitis B virus (HBV) infection, but the associated hosts’ mitochondrial genetic factors remain obscure. We hypothesized that mitochondria may affect host susceptibility to HBV infection. In this study, we aimed to detect the association between chronic HBV infection and mitochondrial DNA in Chinese from Yunnan, Southwest China. A total of 272 individuals with chronic HBV infection (CHB), 310 who had never been infected by HBV (healthy controls, HC) and 278 with a trace of HBV infection (spontaneously recovered, SR) were analysed for mtDNA sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between HBV infected patients, HCs and SRs. Haplogroup D5 presented a higher frequency in CHBs than in HCs (P = 0.017, OR = 2.87, 95% confidence interval [CI] = (1.21–6.81)) and SRs (P = 0.049, OR = 2.90, 95% CI = 1.01–8.35). The network of haplogroup D5 revealed a distinct distribution pattern between CHBs and non-CHBs. A trend of higher viral load among CHBs with haplogroup D5 was observed. Our results indicate the risk potential of mtDNA haplogroup D5 in chronic HBV infection in Yunnan, China.
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Affiliation(s)
- Xiao Li
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Tai-Cheng Zhou
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang-Hui Wu
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Li-Lin Tao
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China
| | - Li-Jun Chen
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - De-Yao Deng
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang Liu
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yang Tang
- The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, 650000, China
| | - Xin Lai
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Liang Zhang
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
| | - Jia Wei
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
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31
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Peng MS, Xu W, Song JJ, Chen X, Sulaiman X, Cai L, Liu HQ, Wu SF, Gao Y, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wu M, Li GM, Yang XY, Rakha A, Yao YG, Upur H, Zhang YP. Mitochondrial genomes uncover the maternal history of the Pamir populations. Eur J Hum Genet 2017; 26:124-136. [PMID: 29187735 DOI: 10.1038/s41431-017-0028-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/08/2017] [Accepted: 10/06/2017] [Indexed: 12/22/2022] Open
Abstract
The Pamirs, among the world's highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East-West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Weifang Xu
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.,Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, China
| | - Jiao-Jiao Song
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Liuhong Cai
- The Second People's Hospital of Kashi, Kashi, 844000, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Miao Wu
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xing-Yan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Allah Rakha
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,Department of Forensic Sciences, University of Health Sciences, Lahore, 54600, Pakistan
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Halmurat Upur
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
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32
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Rakha A, Fatima, Peng MS, Adan A, Bi R, Yasmin M, Yao YG. mtDNA sequence diversity of Hazara ethnic group from Pakistan. Forensic Sci Int Genet 2017; 30:e1-e5. [DOI: 10.1016/j.fsigen.2017.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/02/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
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33
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Chen C, Ba Y, Li D, Du X, Lia X, Yang H, An J, Xing J, Yang H, Dong G, Guo X. Genetic variations of mitochondrial genome modify risk and prognosis of hepatocellular carcinoma patients. Clin Res Hepatol Gastroenterol 2017; 41:378-385. [PMID: 28215537 DOI: 10.1016/j.clinre.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 11/21/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Previous studies have indicated that mitochondrial genetic variations were associated with the risk of many cancers. However, there are few reports on the association between single nucleotide polymorphisms (SNPs) or haplogroups of mitochondrial DNA (mtDNA) and the risk or prognosis of hepatocellular carcinoma (HCC). METHODS In order to investigate the predictive and prognostic role of mtDNA SNPs and haplogroups in HCC, the mitochondrial genome of 188 HCC patients and 344 healthy controls were sequenced by next generation sequencing technology. Then, logistic regression analysis was used to determine the effect of mtDNA SNP or haplogroup on risk and prognosis of HCC patients. RESULTS The haplogroup M7 had an odds ratio (OR) of 0.47 (95% CI=0.24-0.91; P=0.026) to develop HCC. The frequency of 152T/C, 199T/C, 4048G/A, 9824T/C, 15784T/C, 16185C/T and 16399A/G was significantly different between HCC patients and the controls. In addition, multivariate analysis with COX hazards model showed that the patients with haplogroup M8 had lower survival rate than the patients with haplogroup D4 (HR=2.62, 95% CI=1.03-6.68; P=0.044). Three SNPs 15784T/C, 16185C/T and 16399A/G were also identified to have a statistically significant association with postoperative survival in HCC. CONCLUSIONS To date, these results provide the first evidence that mtDNA SNPs and haplogroups may be potential risk factors for susceptibility and survival of HCC patients.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, 169, Changle West Road, 710032 Xi'an, China
| | - Yanna Ba
- Department of Clinical Immunology, Xijing Hospital, The Fourth Military Medical University, 710032 Xi'an, China
| | - Deyang Li
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, 169, Changle West Road, 710032 Xi'an, China
| | - Xiaohong Du
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, 169, Changle West Road, 710032 Xi'an, China
| | - Xin Lia
- Department of Pain Treatment, 403 Clinical Department, 210 Hospital of PLA, 116021 Liaoning, China
| | - Hai Yang
- Dean's Office, Department of Training, The Fourth Military Medical University, 710032 Xi'an, China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, 710032 Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, 169, Changle West Road, 710032 Xi'an, China
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, 19107 Philadelphia, PA, USA
| | - Guanglong Dong
- Department of General Surgery, The General Hospital of PLA, 28, Fuxing Road, 100853 Beijing, China.
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, The Fourth Military Medical University, 169, Changle West Road, 710032 Xi'an, China.
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Xu FL, Ding M, Yao J, Shi ZS, Wu X, Zhang JJ, Pang H, Xing JX, Xuan JF, Wang BJ. Association between mitochondrial DNA variations and schizophrenia in the northern Chinese Han population. PLoS One 2017; 12:e0182769. [PMID: 28846698 PMCID: PMC5573569 DOI: 10.1371/journal.pone.0182769] [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: 01/11/2017] [Accepted: 07/24/2017] [Indexed: 12/20/2022] Open
Abstract
To determine whether mitochondrial DNA (mtDNA) variations are associated with schizophrenia, 313 patients with schizophrenia and 326 unaffected participants of the northern Chinese Han population were included in a prospective study. Single-nucleotide polymorphisms (SNPs) including C5178A, A10398G, G13708A, and C13928G were analyzed by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP). Hypervariable regions I and II (HVSI and HVSII) were analyzed by sequencing. The results showed that the 4 SNPs and 11 haplotypes, composed of the 4 SNPs, did not differ significantly between patient and control groups. No significant association between haplogroups and the risk of schizophrenia was ascertained after Bonferroni correction. Drawing a conclusion, there was no evidence of an association between mtDNA (the 4 SNPs and the control region) and schizophrenia in the northern Chinese Han population.
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Affiliation(s)
- Feng-ling Xu
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Mei Ding
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Zhang-sen Shi
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Xue Wu
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jing-jing Zhang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Hao Pang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jia-xin Xing
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jin-feng Xuan
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Bao-jie Wang
- School of Forensic Medicine, China Medical University, Shenyang, China
- * E-mail:
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35
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Ishiya K, Ueda S. MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing. PeerJ 2017; 5:e3406. [PMID: 28584729 PMCID: PMC5452969 DOI: 10.7717/peerj.3406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
Recent rapid advances in high-throughput, next-generation sequencing (NGS) technologies have promoted mitochondrial genome studies in the fields of human evolution, medical genetics, and forensic casework. However, scientists unfamiliar with computer programming often find it difficult to handle the massive volumes of data that are generated by NGS. To address this limitation, we developed MitoSuite, a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome. MitoSuite generates a visual report on NGS data with simple mouse operations. Moreover, it analyzes high-coverage sequencing data but runs on a stand-alone computer, without the need for file upload. Therefore, MitoSuite offers outstanding usability for handling massive NGS data, and is ideal for evolutionary, clinical, and forensic studies on the human mitochondrial genome variations. It is freely available for download from the website https://mitosuite.com.
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Affiliation(s)
- Koji Ishiya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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36
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Weiler N, Baca K, Ballard D, Balsa F, Bogus M, Børsting C, Brisighelli F, Červenáková J, Chaitanya L, Coble M, Decroyer V, Desmyter S, van der Gaag K, Gettings K, Haas C, Heinrich J, João Porto M, Kal A, Kayser M, Kúdelová A, Morling N, Mosquera-Miguel A, Noel F, Parson W, Pereira V, Phillips C, Schneider P, Syndercombe Court D, Turanska M, Vidaki A, Woliński P, Zatkalíková L, Sijen T. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing. Forensic Sci Int Genet 2017; 26:77-84. [DOI: 10.1016/j.fsigen.2016.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/04/2016] [Accepted: 10/23/2016] [Indexed: 01/27/2023]
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37
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Mehta R, Jeiran K, Koenig AB, Otgonsuren M, Goodman Z, Baranova A, Younossi Z. The role of mitochondrial genomics in patients with non-alcoholic steatohepatitis (NASH). BMC MEDICAL GENETICS 2016; 17:63. [PMID: 27596100 PMCID: PMC5011877 DOI: 10.1186/s12881-016-0324-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/20/2016] [Indexed: 02/06/2023]
Abstract
Background Visceral obesity and metabolic syndrome are commonly associated with non-alcoholic fatty liver disease (NAFLD). The progression of steatosis to NASH depends on a number of metabolic and patient-related factors. The mechanisms of genetic predisposition towards the development of NASH and related fibrosis remain unclear. In this study, our aim was to utilize mitotyping and identify mitochondrial haplotypes that may be associated with NAFLD. Methods We examined mitochondrial haplotypes along with patatin-like phospholipase domain containing 3 (PNPLA3) rs738409 genotype to determine their association with NAFLD phenotypes. Whole blood samples were obtained from 341 patients (BMI > 35) undergoing weight reduction surgery after written consent. Liver biopsies were centrally reviewed by a single pathologist based on predetermined pathologic protocol (41.9 % Non-NASH NAFLD, 30.4 % NASH, 27.5 % controls). A 1,122 bp of the mitochondrial control loop was sequenced for each sample and classified into haplogroups. Results The presence of haplogroup L exhibits protection against the development of NASH and pericellular fibrosis. The alleles of PNPLA3 locus showed differential distribution in cohorts with NAFLD, NASH and pericellular fibrosis. Heterozygosity at this locus is independently associated with higher risk of having NASH and pericellular fibrosis. Conclusion Mitochondrial genetics play an important role in NASH probably by modulation of oxidative stress and the efficiency of oxidative phosphorylation. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0324-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rohini Mehta
- Betty and Guy Beatty Center for Integrated Research, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Kianoush Jeiran
- Center for the Study of Chronic Metabolic and Rare Diseases, George Mason University, Fairfax, VA, 22033, USA
| | - Aaron B Koenig
- Betty and Guy Beatty Center for Integrated Research, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Munkzhul Otgonsuren
- Betty and Guy Beatty Center for Integrated Research, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Zachary Goodman
- Betty and Guy Beatty Center for Integrated Research, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Ancha Baranova
- Center for the Study of Chronic Metabolic and Rare Diseases, George Mason University, Fairfax, VA, 22033, USA
| | - Zobair Younossi
- Betty and Guy Beatty Center for Integrated Research, Inova Fairfax Medical Campus, Falls Church, VA, USA. .,Betty and Guy Beatty Center for Integrated Research, Claude Moore Center for Research and Education, 3300 Gallows Road, Falls Church, VA, 22033, USA.
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Zhang Y, Li J, Zhao Y, Wu X, Li H, Yao L, Zhu H, Zhou H. Genetic diversity of two Neolithic populations provides evidence of farming expansions in North China. J Hum Genet 2016; 62:199-204. [PMID: 27581844 DOI: 10.1038/jhg.2016.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/23/2016] [Accepted: 07/26/2016] [Indexed: 11/09/2022]
Abstract
The West Liao River Valley and the Yellow River Valley are recognized Neolithic farming centers in North China. The population dynamics between these two centers have significantly contributed to the present-day genetic patterns and the agricultural advances of North China. To understand the Neolithic farming expansions between the West Liao River Valley and the Yellow River Valley, we analyzed mitochondrial DNA (mtDNA) and the Y chromosome of 48 individuals from two archeological sites, Jiangjialiang (>3000 BC) and Sanguan (~1500 BC). These two sites are situated between the two farming centers and experienced a subsistence shift from hunting to farming. We did not find a significant difference in the mtDNA, but their genetic variations in the Y chromosome were different. Individuals from the Jiangjialiang belonged to two Y haplogroups, N1 (not N1a or N1c) and N1c. The individuals from the Sanguan are Y haplogroup O3. Two stages of migration are supported. Populations from the West Liao River Valley spread south at about 3000 BC, and a second northward expansion from the Yellow River Valley occurred later (3000-1500 BC).
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Affiliation(s)
- Ye Zhang
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China
| | - Jiawei Li
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China
| | - Yongbin Zhao
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China.,Laboratory of Ancient DNA, College of Life Science, Jilin Normal University, Siping, China
| | - Xiyan Wu
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China
| | - Hongjie Li
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China.,Laboratory of Anthropology, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
| | - Lu Yao
- Department of Anthropology, Committee on Evolutionary Biology, University of Chicago, Chicago, USA
| | - Hong Zhu
- Laboratory of Anthropology, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
| | - Hui Zhou
- Laboratory of Ancient DNA, School of Life Science, Jilin University, Changchun, China.,Laboratory of Anthropology, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
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Li H, Bi R, Fan Y, Wu Y, Tang Y, Li Z, He Y, Zhou J, Tang J, Chen X, Yao YG. mtDNA Heteroplasmy in Monozygotic Twins Discordant for Schizophrenia. Mol Neurobiol 2016; 54:4343-4352. [DOI: 10.1007/s12035-016-9996-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/14/2016] [Indexed: 12/30/2022]
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40
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Sun GJ, He F, Yao HM, Han ZY, Lu WJ, Chen XJ, Wang ZB, Qiu CG. Assessment of mitochondrial DNA mutations in Chinese family with essential hypertension. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:1740-1741. [PMID: 25242182 DOI: 10.3109/19401736.2014.961148] [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] [Indexed: 06/03/2023]
Abstract
Mitochondrial DNA (MtDNA) mutations played an important role in the development of essential hypertension. Mitochondrial tRNA point mutations, caused the failure in tRNA metabolism, responsible for the pathogenesis of this complex disease. In this study, we evaluated the possible role of the 4329C >G mutation in the clinical expression of hypertension in a Chinese family. Analysis of the complete mtDNA sequence variants showed that other mutations may play synergic roles in the phenotypic manifestation of hypertension. In addition, other potential pitfalls were also discussed in this context.
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Affiliation(s)
- Guo-Ju Sun
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Fei He
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Hai-Mu Yao
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Zhan-Ying Han
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Wen-Jie Lu
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Xiao-Jie Chen
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Zheng-Bin Wang
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Chun-Guang Qiu
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
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41
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Wang CC, Huang Y, Yu X, Chen C, Jin L, Li H. Agriculture driving male expansion in Neolithic Time. SCIENCE CHINA-LIFE SCIENCES 2016; 59:643-6. [PMID: 27132019 DOI: 10.1007/s11427-016-5057-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/03/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Chuan-Chao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yunzhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xue'er Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chun Chen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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42
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Exploring the maternal history of the Tai people. J Hum Genet 2016; 61:721-9. [PMID: 27098877 DOI: 10.1038/jhg.2016.36] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 01/04/2023]
Abstract
In the past decades, the Tai people are increasingly being focused by genetic studies. However, a systematic genetic study of the whole Tai people is still lacking, thus making the population structure as well as the demographic history of this group uninvestigated from genetic perspective. Here we extensively analyzed the variants of hypervariable segments I and II (HVS-I and HVS-II) of mitochondrial DNA (mtDNA) of 719 Tai samples from 19 populations, covering virtually all of the current Tai people's residences. We observed a general close genetic affinity of the Tai people, reflecting a common origin of this group. Taken into account the phylogeographic analyses of their shared components, including haplogroups F1a, M7b and B5a, our study supported a southern Yunnan origin of the Tai people, consistent with the historical records. In line with their diverse cultures and languages, substantial genetic divergences can be observed among different Tai populations that could be attributable to assimilation of maternal components from neighboring populations. Our study further implied the advent of rice agriculture in Mainland Southeast Asia at ∼5 kya (kilo years ago) had greatly promoted the population expansion of the Tai people.
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43
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Mitochondrial genome variations and functional characterization in Han Chinese families with schizophrenia. Schizophr Res 2016; 171:200-6. [PMID: 26822593 DOI: 10.1016/j.schres.2016.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 12/09/2015] [Accepted: 01/04/2016] [Indexed: 11/23/2022]
Abstract
The relationship between mitochondrial DNA (mtDNA) variants and schizophrenia has been strongly debated. To test whether mtDNA variants are involved in schizophrenia in Han Chinese patients, we sequenced the entire mitochondrial genomes of probands from 11 families with a family history and maternal inheritance pattern of schizophrenia. Besides the haplogroup-specific variants, we found 11 nonsynonymous private variants, one rRNA variant, and one tRNA variant in 5 of 11 probands. Among the nonsynonymous private variants, mutations m.15395 A>G and m.8536 A>G were predicted to be deleterious after web-based searches and in silico program affiliated analysis. Functional characterization further supported the potential pathogenicity of the two variants m.15395 A>G and m.8536 A>G to cause mitochondrial dysfunction at the cellular level. Our results showed that mtDNA variants were actively involved in schizophrenia in some families with maternal inheritance of this disease.
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44
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Bagnall RD, Crompton DE, Petrovski S, Lam L, Cutmore C, Garry SI, Sadleir LG, Dibbens LM, Cairns A, Kivity S, Afawi Z, Regan BM, Duflou J, Berkovic SF, Scheffer IE, Semsarian C. Exome-based analysis of cardiac arrhythmia, respiratory control, and epilepsy genes in sudden unexpected death in epilepsy. Ann Neurol 2016; 79:522-34. [PMID: 26704558 DOI: 10.1002/ana.24596] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 12/14/2015] [Accepted: 12/20/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The leading cause of epilepsy-related premature mortality is sudden unexpected death in epilepsy (SUDEP). The cause of SUDEP remains unknown. To search for genetic risk factors in SUDEP cases, we performed an exome-based analysis of rare variants. METHODS Demographic and clinical information of 61 SUDEP cases were collected. Exome sequencing and rare variant collapsing analysis with 2,936 control exomes were performed to test for genes enriched with damaging variants. Additionally, cardiac arrhythmia, respiratory control, and epilepsy genes were screened for variants with frequency of <0.1% and predicted to be pathogenic with multiple in silico tools. RESULTS The 61 SUDEP cases were categorized as definite SUDEP (n = 54), probable SUDEP (n = 5), and definite SUDEP plus (n = 2). We identified de novo mutations, previously reported pathogenic mutations, or candidate pathogenic variants in 28 of 61 (46%) cases. Four SUDEP cases (7%) had mutations in common genes responsible for the cardiac arrhythmia disease, long QT syndrome (LQTS). Nine cases (15%) had candidate pathogenic variants in dominant cardiac arrhythmia genes. Fifteen cases (25%) had mutations or candidate pathogenic variants in dominant epilepsy genes. No gene reached genome-wide significance with rare variant collapsing analysis; however, DEPDC5 (p = 0.00015) and KCNH2 (p = 0.0037) were among the top 30 genes, genome-wide. INTERPRETATION A sizeable proportion of SUDEP cases have clinically relevant mutations in cardiac arrhythmia and epilepsy genes. In cases with an LQTS gene mutation, SUDEP may occur as a result of a predictable and preventable cause. Understanding the genetic basis of SUDEP may inform cascade testing of at-risk family members.
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Affiliation(s)
- Richard D Bagnall
- Agnes Ginges Center for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Douglas E Crompton
- Neurology Department, Northern Health, Melbourne, Australia.,Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Slavé Petrovski
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,Institute for Genomic Medicine, Columbia University, New York, NY
| | - Lien Lam
- Agnes Ginges Center for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Carina Cutmore
- Agnes Ginges Center for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Sarah I Garry
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Lynette G Sadleir
- Department of Pediatrics and Child Health, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Leanne M Dibbens
- Epilepsy Research Program, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Anita Cairns
- Neurosciences Department, Lady Cilento Children's Hospital, Brisbane, Australia
| | - Sara Kivity
- Epilepsy Unit, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
| | - Zaid Afawi
- Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Brigid M Regan
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Johan Duflou
- Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Forensic Medicine, Sydney, Australia
| | - Samuel F Berkovic
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,Department of Neurology, The Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia.,Florey Institute of Neurosciences and Mental Health, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Christopher Semsarian
- Agnes Ginges Center for Molecular Cardiology, Centenary Institute, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
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45
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Vellarikkal SK, Dhiman H, Joshi K, Hasija Y, Sivasubbu S, Scaria V. mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets. Hum Mutat 2015; 36:419-24. [PMID: 25677119 DOI: 10.1002/humu.22767] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 01/26/2015] [Indexed: 12/27/2022]
Abstract
The human mitochondrial genome has been reported to have a very high mutation rate as compared with the nuclear genome. A large number of mitochondrial mutations show significant phenotypic association and are involved in a broad spectrum of diseases. In recent years, there has been a remarkable progress in the understanding of mitochondrial genetics. The availability of next-generation sequencing (NGS) technologies have not only reduced sequencing cost by orders of magnitude but has also provided us good quality mitochondrial genome sequences with high coverage, thereby enabling decoding of a number of human mitochondrial diseases. In this study, we report a computational and experimental pipeline to decipher the human mitochondrial DNA variations and examine them for their clinical correlation. As a proof of principle, we also present a clinical study of a patient with Leigh disease and confirmed maternal inheritance of the causative allele. The pipeline is made available as a user-friendly online tool to annotate variants and find haplogroup, disease association, and heteroplasmic sites. The "mit-o-matic" computational pipeline represents a comprehensive cloud-based tool for clinical evaluation of mitochondrial genomic variations from NGS datasets. The tool is freely available at http://genome.igib.res.in/mitomatic/.
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Affiliation(s)
- Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi, India
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46
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Vyas DN, Kitchen A, Miró‐Herrans AT, Pearson LN, Al‐Meeri A, Mulligan CJ. Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:382-93. [DOI: 10.1002/ajpa.22890] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/21/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa City IA52242
| | - Aida T. Miró‐Herrans
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Laurel N. Pearson
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
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Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists. J Hum Genet 2015; 61:103-8. [PMID: 26511065 DOI: 10.1038/jhg.2015.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/17/2015] [Accepted: 09/26/2015] [Indexed: 11/08/2022]
Abstract
The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga-Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.
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48
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Mitochondrial DNA Haplogroup A Decreases the Risk of Drug Addiction but Conversely Increases the Risk of HIV-1 Infection in Chinese Addicts. Mol Neurobiol 2015; 53:3873-3881. [PMID: 26162319 DOI: 10.1007/s12035-015-9323-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/24/2015] [Indexed: 01/19/2023]
Abstract
Drug addiction is one of the most serious social problems in the world today and addicts are always at a high risk of acquiring HIV infection. Mitochondrial impairment has been reported in both drug addicts and in HIV patients undergoing treatment. In this study, we aimed to investigate whether mitochondrial DNA (mtDNA) haplogroup could affect the risk of drug addiction and HIV-1 infection in Chinese. We analyzed mtDNA sequence variations of 577 Chinese intravenous drug addicts (289 with HIV-1 infection and 288 without) and compared with 2 control populations (n = 362 and n = 850). We quantified the viral load in HIV-1-infected patients with and without haplogroup A status and investigated the potential effect of haplogroup A defining variants m.4824A > G and m.8794C > T on the cellular reactive oxygen species (ROS) levels by using an allotopic expression assay. mtDNA haplogroup A had a protective effect against drug addiction but appeared to confer an increased risk of HIV infection in addicts. HIV-1-infected addicts with haplogroup A had a trend for a higher viral load, although the mean viral load was similar between carriers of haplogroup A and those with other haplogroup. Hela cells overexpressing allele m.8794 T showed significantly decreased ROS levels as compared to cells with the allele m.8794C (P = 0.03). Our results suggested that mtDNA haplogroup A might protect against drug addiction but increase the risk of HIV-1 infection. The contradictory role of haplogroup A might be caused by an alteration in mitochondrial function due to a particular mtDNA ancestral variant.
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49
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Ranasinghe R, Tennekoon KH, Karunanayake EH, Lembring M, Allen M. A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka. Leg Med (Tokyo) 2015; 17:539-46. [PMID: 26065620 DOI: 10.1016/j.legalmed.2015.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
Diversity of the hypervariable regions (HV) I and II of the mitochondrial genome was studied in maternally unrelated Sri Lankans (N=202) from six ethnic groups (i.e.: Sinhalese, Sri Lankan Tamil, Muslim, Malay, Indian Tamil and Vedda). DNA was extracted from blood and buccal swabs and HVI and HVII regions were PCR amplified and sequenced. Resulting sequences were aligned and edited between 16024-16365 and 73-340 regions and compared with revised Cambridge reference sequences (rCRS). One hundred and thirty-five unique haplotypes and 22 shared haplotypes were observed. A total of 145 polymorphic sites and 158 polymorphisms were observed. Hypervariable region I showed a higher polymorphic variation than hypervariable region II. Nucleotide diversities were quite low and similar for all ethnicities apart from a slightly higher value for Indian Tamils and a much lower value for the Vedda population compared to the other groups. When the total population was considered South Asian (Indian) haplogroups were predominant, but there were differences in the distribution of phylo-geographical haplogroups between ethnic groups. Sinhalese, Sri Lankan Tamil and Vedda populations had a considerable presence of West Eurasian haplogroups. About 2/3rd of the Vedda population comprised of macro-haplogroup N or its subclades R and U, whereas macro-haplogroup M was predominant in all other populations. The Vedda population clustered separately from other groups and Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils. Thus this study provides useful information for forensic analysis and anthropological studies of Sri Lankans.
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Affiliation(s)
- Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Kamani H Tennekoon
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Eric H Karunanayake
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Maria Lembring
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical Centre, Box 815, 751 08 Uppsala, Sweden.
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical Centre, Box 815, 751 08 Uppsala, Sweden.
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50
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Mitochondrial DNA haplogroups and short-term neurological outcomes of ischemic stroke. Sci Rep 2015; 5:9864. [PMID: 25993529 PMCID: PMC4438613 DOI: 10.1038/srep09864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/23/2015] [Indexed: 01/17/2023] Open
Abstract
Stroke is one of the leading causes of death and long-term disability worldwide. Mitochondrial DNA (mtDNA) is a potential contributor for the sex differences of ischemic stroke heritability. Although mtDNA haplogroups were associated with stroke onset, their impacts on stroke outcomes remain unclear. This study aimed to evaluate the impacts of mtDNA haplogroups on short-term outcomes of neurological functions in patients with ischemic stroke. A total of 303 patients were included, and their clinical data and mtDNA sequences were analyzed. Based on the changes between baseline and 14-day follow-up stroke severity, our results showed that haplogroup N9 was an independent protective factor against neurological worsening in acute ischemic stroke patients. These findings supported that mtDNA variants play a role in post-stroke neurological recovery, thus providing evidences for future pharmacological intervention in mitochondrial function.
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