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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: 0] [Impact Index Per Article: 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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2
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Yonova-Doing E, Calabrese C, Gomez-Duran A, Schon K, Wei W, Karthikeyan S, Chinnery PF, Howson JMM. An atlas of mitochondrial DNA genotype-phenotype associations in the UK Biobank. Nat Genet 2021; 53:982-993. [PMID: 34002094 PMCID: PMC7611844 DOI: 10.1038/s41588-021-00868-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Mitochondrial DNA (mtDNA) variation in common diseases has been underexplored, partly due to a lack of genotype calling and quality-control procedures. Developing an at-scale workflow for mtDNA variant analyses, we show correlations between nuclear and mitochondrial genomic structures within subpopulations of Great Britain and establish a UK Biobank reference atlas of mtDNA-phenotype associations. A total of 260 mtDNA-phenotype associations were new (P < 1 × 10-5), including rs2853822 /m.8655 C>T (MT-ATP6) with type 2 diabetes, rs878966690 /m.13117 A>G (MT-ND5) with multiple sclerosis, 6 mtDNA associations with adult height, 24 mtDNA associations with 2 liver biomarkers and 16 mtDNA associations with parameters of renal function. Rare-variant gene-based tests implicated complex I genes modulating mean corpuscular volume and mean corpuscular hemoglobin. Seven traits had both rare and common mtDNA associations, where rare variants tended to have larger effects than common variants. Our work illustrates the value of studying mtDNA variants in common complex diseases and lays foundations for future large-scale mtDNA association studies.
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Affiliation(s)
- Ekaterina Yonova-Doing
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Aurora Gomez-Duran
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - Katherine Schon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Joanna M M Howson
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK.
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3
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Kursun O, Yemisci M, van den Maagdenberg AMJM, Karatas H. Migraine and neuroinflammation: the inflammasome perspective. J Headache Pain 2021; 22:55. [PMID: 34112082 PMCID: PMC8192049 DOI: 10.1186/s10194-021-01271-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Neuroinflammation has an important role in the pathophysiology of migraine, which is a complex neuro-glio-vascular disorder. The main aim of this review is to highlight findings of cortical spreading depolarization (CSD)-induced neuroinflammatory signaling in brain parenchyma from the inflammasome perspective. In addition, we discuss the limited data of the contribution of inflammasomes to other aspects of migraine pathophysiology, foremost the activation of the trigeminovascular system and thereby the generation of migraine pain. MAIN BODY Inflammasomes are signaling multiprotein complexes and key components of the innate immune system. Their activation causes the production of inflammatory cytokines that can stimulate trigeminal neurons and are thus relevant to the generation of migraine pain. The contribution of inflammasome activation to pain signaling has attracted considerable attention in recent years. Nucleotide-binding domain (NOD)-like receptor family pyrin domain containing 3 (NLRP3) is the best characterized inflammasome and there is emerging evidence of its role in a variety of inflammatory pain conditions, including migraine. In this review, we discuss, from an inflammasome point of view, cortical spreading depolarization (CSD)-induced neuroinflammatory signaling in brain parenchyma, the connection with genetic factors that make the brain vulnerable to CSD, and the relation of the inflammasome with diseases that are co-morbid with migraine, including stroke, epilepsy, and the possible links with COVID-19 infection. CONCLUSION Neuroinflammatory pathways, specifically those involving inflammasome proteins, seem promising candidates as treatment targets, and perhaps even biomarkers, in migraine.
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Affiliation(s)
| | - Muge Yemisci
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey.,Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hulya Karatas
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey.
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4
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Hagen CM, Elson JL, Hedley PL, Aidt FH, Havndrup O, Jensen MK, Kanters JK, Atherton JJ, McGaughran J, Bundgaard H, Christiansen M. Evolutionary dissection of mtDNA hg H: a susceptibility factor for hypertrophic cardiomyopathy. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:238-244. [PMID: 32602800 DOI: 10.1080/24701394.2020.1782897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroup (hg) H has been reported as a susceptibility factor for hypertrophic cardiomyopathy (HCM). This was established in genetic association studies, however, the SNP or SNP's that are associated with the increased risk have not been identified. Hg H is the most frequent European mtDNA hg with greater than 80 subhaplogroups (subhgs) each defined by specific SNPs. We tested the hypothesis that the distribution of H subhgs might differ between HCM patients and controls. The subhg H distribution in 55 HCM index cases was compared to that of two Danish mtDNA hg H control groups (n = 170 and n = 908, respectively). In the HCM group, H and 12 different H subhgs were found. All these, except subhgs H73, were also found in both control groups. The HCM group was also characterized by a higher proportion of H3 compared to H2. In the HCM group the H3/H2 proportion was 1.7, whereas it was 0.45 and 0.54 in the control groups. This tendency was replicated in an independent group of Hg H HCM index cases (n = 39) from Queensland, Australia, where the H3/H2 ratio was 1.5. In conclusion, the H subhgs distribution differs between HCM cases and controls, but the difference is subtle, and the understanding of the pathogenic significance is hampered by the lack of functional studies on the subhgs of H.
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Affiliation(s)
- Christian M Hagen
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanna L Elson
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Frederik H Aidt
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Hospital, Roskilde, Denmark
| | - Morten K Jensen
- Department of Medicine B, The Heart Center, Copenhagen, Denmark
| | - Jørgen K Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John J Atherton
- Department of Cardiology, Royal Brisbane Hospital and School of Medicine, University of Queensland, Brisbane, Australia
| | - Julie McGaughran
- Queensland Clinical Genetics Service, Royal Children's Hospital and School of Medicine, Brisbane, Australia
| | | | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Venter M, Tomas C, Pienaar IS, Strassheim V, Erasmus E, Ng WF, Howell N, Newton JL, Van der Westhuizen FH, Elson JL. MtDNA population variation in Myalgic encephalomyelitis/Chronic fatigue syndrome in two populations: a study of mildly deleterious variants. Sci Rep 2019; 9:2914. [PMID: 30814539 PMCID: PMC6393470 DOI: 10.1038/s41598-019-39060-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023] Open
Abstract
Myalgic Encephalomyelitis (ME), also known as Chronic Fatigue Syndrome (CFS) is a debilitating condition. There is growing interest in a possible etiologic or pathogenic role of mitochondrial dysfunction and mitochondrial DNA (mtDNA) variation in ME/CFS. Supporting such a link, fatigue is common and often severe in patients with mitochondrial disease. We investigate the role of mtDNA variation in ME/CFS. No proven pathogenic mtDNA mutations were found. We then investigated population variation. Two cohorts were analysed, one from the UK (n = 89 moderately affected; 29 severely affected) and the other from South Africa (n = 143 moderately affected). For both cohorts, ME/CFS patients had an excess of individuals without a mildly deleterious population variant. The differences in population variation might reflect a mechanism important to the pathophysiology of ME/CFS.
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Affiliation(s)
- Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Cara Tomas
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, BN1 9PH, United Kingdom.,Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | - Victoria Strassheim
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom.,Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | - Elardus Erasmus
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Wan-Fai Ng
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Neil Howell
- Department of Radiation Therapy, UTMB, Galveston, Texas, USA
| | - Julia L Newton
- Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa. .,Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom.
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6
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Cerezo M, Gusmão L, Černý V, Uddin N, Syndercombe-Court D, Gómez-Carballa A, Göbel T, Schneider PM, Salas A. Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography. J Genet Genomics 2015; 43:133-43. [PMID: 27020033 DOI: 10.1016/j.jgg.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/30/2015] [Accepted: 09/15/2015] [Indexed: 01/15/2023]
Abstract
Africa is the cradle of all human beings, and although it has been the focus of a number of genetic studies, there are many questions that remain unresolved. We have performed one of the largest and most comprehensive meta-analyses of mitochondrial DNA (mtDNA) lineages carried out in the African continent to date. We generated high-throughput mtDNA single nucleotide polymorphism (SNP) data (230 SNPs) from 2024 Africans, where more than 500 of them were additionally genotyped for the control region. These data were analyzed together with over 12,700 control region profiles collected from the literature, representing more than 300 population samples from Africa. Insights into the African homeland of humans are discussed. Phylogeographic patterns for the African continent are shown at a high phylogeographic resolution as well as at the population and regional levels. The deepest branch of the mtDNA tree, haplogroup L0, shows the highest sub-haplogroup diversity in Southeast and East Africa, suggesting this region as the homeland for modern humans. Several demographic estimates point to the coast as a facilitator of human migration in Africa, but the data indicate complex patterns, perhaps mirroring the effect of recent continental-scaled demographic events in re-shaping African mtDNA variability.
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain; The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-900, Brazil; IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto, Porto 4200-465, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague 118-01, Czech Republic
| | - Nabeel Uddin
- Faculty of Life Sciences and Medicine, King's College London, London SE1 9NH, UK
| | | | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain
| | - Tanja Göbel
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain.
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7
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Roos-Araujo D, Stuart S, Lea RA, Haupt LM, Griffiths LR. Epigenetics and migraine; complex mitochondrial interactions contributing to disease susceptibility. Gene 2014; 543:1-7. [PMID: 24704026 DOI: 10.1016/j.gene.2014.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 04/01/2014] [Indexed: 02/08/2023]
Abstract
Migraine is a common neurological disorder classified by the World Health Organisation (WHO) as one of the top twenty most debilitating diseases in the developed world. Current therapies are only effective for a proportion of sufferers and new therapeutic targets are desperately needed to alleviate this burden. Recently the role of epigenetics in the development of many complex diseases including migraine has become an emerging topic. By understanding the importance of acetylation, methylation and other epigenetic modifications, it then follows that this modification process is a potential target to manipulate epigenetic status with the goal of treating disease. Bisulphite sequencing and methylated DNA immunoprecipitation have been used to demonstrate the presence of methylated cytosines in the human D-loop of mitochondrial DNA (mtDNA), proving that the mitochondrial genome is methylated. For the first time, it has been shown that there is a difference in mtDNA epigenetic status between healthy controls and those with disease, especially for neurodegenerative and age related conditions. Given co-morbidities with migraine and the suggestive link between mitochondrial dysfunction and the lowered threshold for triggering a migraine attack, mitochondrial methylation may be a new avenue to pursue. Creative thinking and new approaches are needed to solve complex problems and a systems biology approach, where multiple layers of information are integrated is becoming more important in complex disease modelling.
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Affiliation(s)
- Deidré Roos-Araujo
- Genomics Research Centre, Institute for Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Shani Stuart
- Genomics Research Centre, Institute for Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Rod A Lea
- Genomics Research Centre, Institute for Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute for Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute for Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia.
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8
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Abstract
Mutations in the human mitochondrial genome are known to cause an array of diverse disorders, most of which are maternally inherited, and all of which are associated with defects in oxidative energy metabolism. It is now emerging that somatic mutations in mitochondrial DNA (mtDNA) are also linked to other complex traits, including neurodegenerative diseases, ageing and cancer. Here we discuss insights into the roles of mtDNA mutations in a wide variety of diseases, highlighting the interesting genetic characteristics of the mitochondrial genome and challenges in studying its contribution to pathogenesis.
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9
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Cerezo M, Černý V, Carracedo Á, Salas A. New insights into the Lake Chad Basin population structure revealed by high-throughput genotyping of mitochondrial DNA coding SNPs. PLoS One 2011; 6:e18682. [PMID: 21533064 PMCID: PMC3080428 DOI: 10.1371/journal.pone.0018682] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 03/13/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Located in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert. METHODOLOGY/PRINCIPAL FINDINGS Samples from twelve ethnic groups from the Chad Basin (n = 542) have been high-throughput genotyped for 230 coding region mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (mtSNPs) using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry. This set of mtSNPs allowed for much better phylogenetic resolution than previous studies of this geographic region, enabling new insights into its population history. Notable haplogroup (hg) heterogeneity has been observed in the Chad Basin mirroring the different demographic histories of these ethnic groups. As estimated using a Bayesian framework, nomadic populations showed negative growth which was not always correlated to their estimated effective population sizes. Nomads also showed lower diversity values than sedentary groups. CONCLUSIONS/SIGNIFICANCE Compared to sedentary population, nomads showed signals of stronger genetic drift occurring in their ancestral populations. These populations, however, retained more haplotype diversity in their hypervariable segments I (HVS-I), but not their mtSNPs, suggesting a more ancestral ethnogenesis. Whereas the nomadic population showed a higher Mediterranean influence signaled mainly by sub-lineages of M1, R0, U6, and U5, the other populations showed a more consistent sub-Saharan pattern. Although lifestyle may have an influence on diversity patterns and hg composition, analysis of molecular variance has not identified these differences. The present study indicates that analysis of mtSNPs at high resolution could be a fast and extensive approach for screening variation in population studies where labor-intensive techniques such as entire genome sequencing remain unfeasible.
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, The Czech Republic
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain
- * E-mail:
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10
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Juo SHH, Lu MY, Bai RK, Liao YC, Trieu RB, Yu ML, Wong LJC. A common mitochondrial polymorphism 10398A>G is associated metabolic syndrome in a Chinese population. Mitochondrion 2010; 10:294-9. [PMID: 20067846 DOI: 10.1016/j.mito.2010.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 12/24/2009] [Accepted: 01/05/2010] [Indexed: 01/01/2023]
Abstract
We conducted a two-step case-control study to investigate the association between mtDNA variants and metabolic syndrome (MS) in Chinese. We initially screened 79 mitochondrial single nucleotide polymorphisms (mtSNPs) in 141 cases and 506 controls, and five mtSNPs had a p<0.05. We replicated results for the most significant mtSNP 10398A>G in additional 396 case and 424 controls (p=0.047, OR=1.26). The G allele frequency in the screening and follow up data was 66% and 55.2% in the cases, and 52.3% and 50.2% in the controls, respectively. Our results suggest the G allele of 10398A>G increases a risk for MS.
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Affiliation(s)
- Suh-Hang H Juo
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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11
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Byrne EM, McRae AF, Duffy DL, Zhao ZZ, Martin NG, Wright MJ, Montgomery GW, Visscher PM. Association Study of Common Mitochondrial Variants and Cognitive Ability. Behav Genet 2009; 39:504-12. [DOI: 10.1007/s10519-009-9276-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 04/22/2009] [Indexed: 10/20/2022]
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12
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McRae AF, Byrne EM, Zhao ZZ, Montgomery GW, Visscher PM. Power and SNP tagging in whole mitochondrial genome association studies. Genome Res 2008; 18:911-7. [PMID: 18356315 DOI: 10.1101/gr.074872.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The application of genetic association studies to detect mitochondrial variants responsible for phenotypic variation has recently been demonstrated. However, the only power estimates currently available are based on the use of mitochondrial haplogroups, which can only tag a small fraction of the common variation in the mitochondrial genome. Here, power estimates are derived for a SNP-based study design for both disease (case-control) and quantitative trait mapping studies. Power is estimated using simulations based on a collection of publicly available mitochondrial sequences of European origin. The power when testing all common mitochondrial SNPs is shown to be equivalent to that when testing only tagging SNPs, despite the relatively high ratio of tagging SNPs to total SNPs resulting from the tagging of all SNPs with a minor allele frequency greater than 1%. The sample size requirements of mitochondrial genome association studies are compared with that of nuclear whole-genome studies. Remarkably, the trade off between the number of tests being performed and the proportion of phenotypic variance explained for a fixed effect size results in approximately equal sample sizes required for both study types, although the per individual cost for the mitochondrial association study is much less. To test the representation of the sequences used in the power simulations, a sample of 3839 individuals from 1037 Australian families was genotyped for 69 tagging SNPs. The strong concordance in allele frequencies and linkage disequilibrium between the European sequences and the Australian sample indicates that the results presented here are transferable across populations of European descent.
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Affiliation(s)
- Allan F McRae
- Queensland Institute of Medical Research, Brisbane 4006, Australia.
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13
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Saxena R, de Bakker PI, Groop LC, Daly MJ, Altshuler D. Reply to Elson et al. Am J Hum Genet 2007. [DOI: 10.1086/511653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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