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Aquilano E, de la Fuente C, Rodríguez Golpe D, Motti JMB, Bravi CM. Sequencing errors in Native American mitogenomes: impact on clade definitions, haplogroup assignation, and beyond. Mitochondrion 2023; 70:54-58. [PMID: 37003527 DOI: 10.1016/j.mito.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Available evidence allows the interpretation that some cases of absence of otherwise expected variation, based on phylogenetic expectations in mitogenomes of Native American origin, are due to artificial recombination rather than to homoplasy, while other more complex scenarios involving combination of original Cambridge Reference Sequence mistakes plus incomplete or incorrect scoring of variation are also showed. Several instances of mismatched control and coding regions as well as partially duplicated HV2 are observed in Peruvians, while intra-haplogroup chimaeras of different D1 subhaplogroups are referred to in Mexican Native Americans. A revised definition for haplogroup B2h is proposed, and preventive quality control measures are suggested.
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Affiliation(s)
- Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | | | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | - Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana (LEEH), Facultad de Ciencias Sociales (FACSO), Universidad Nacional del Centro de la Provincia de Buenos Aires-CONICET, Calle 508 #881, 7631 Quequén, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina.
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2
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Guo H, Guo L, Yuan Y, Liang XY, Bi R. Co-occurrence of m.15992A>G and m.15077G>A Is Associated With a High Penetrance of Maternally Inherited Hypertension in a Chinese Pedigree. Am J Hypertens 2022; 35:96-102. [PMID: 34346491 DOI: 10.1093/ajh/hpab123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) pathogenic variants have been identified to be associated with maternally inherited essential hypertension (MIEH). However, the distinctive clinical features and molecular pathogenesis of MIEH are not fully understood. METHODS In this study, we collected a Chinese MIEH family with extraordinary higher penetrance of essential hypertension (88.89%) and early ages of onset (31-40 years old), and performed clinical and genetic characterization for this family. The complete mitochondrial genome of the proband was sequenced and analyzed. RESULTS The maternally related members in this family were presented with severe increased blood pressure, left ventricular remodeling, and metabolic abnormalities. Through sequencing the entire mtDNA of the proband and performing systematic analysis of the mtDNA variants with a phylogenic approach, we identified a potentially pathogenic tRNA variant (m.15992A>G in the MT-TP gene) that may account for the MIEH in this family. One nonsynonymous variant (m.15077G>A in the MT-CYB gene) was identified to play a synergistic role with m.15992A>G to cause a high penetrance of MIEH. CONCLUSIONS Our results, together with previous findings, have indicated that tRNA pathogenic variants in the mtDNA could act important roles in the pathogenesis of MIEH through reducing mitochondrial translation and disturbing mitochondrial function.
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Affiliation(s)
- Hao Guo
- Department of Cardiology, 1st Affiliated Hospital of Kunming Medical University, Kunming, China
- Department of Cardiology, Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan, China
| | - Li Guo
- Department of Radiology, 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yong Yuan
- Department of emergency, 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xin-yue Liang
- Department of Cardiology, 1st Affiliated Hospital of Kunming Medical University, Kunming, China
- Department of Cardiology, Graduate School of the Kunming Medical University, Kunming, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
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Spangenberg L, Graña M, Mansilla S, Martínez J, Tapié A, Greif G, Montano N, Vaglio A, Gueçaimburú R, Robello C, Castro L, Quijano C, Raggio V, Naya H. Deep sequencing discovery of causal mtDNA mutations in a patient with unspecific neurological disease. Mitochondrion 2019; 46:337-344. [DOI: 10.1016/j.mito.2018.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/30/2018] [Accepted: 09/11/2018] [Indexed: 11/15/2022]
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Huber N, Parson W, Dür A. Next generation database search algorithm for forensic mitogenome analyses. Forensic Sci Int Genet 2018; 37:204-214. [PMID: 30241075 DOI: 10.1016/j.fsigen.2018.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop.online) to produce reliable and conservative frequency estimates that are required in the forensic context. However, ambiguity remained in how laboratories have been reporting mitotypes, as often more than one single alignment of a given mtDNA sequence was feasible. In order to overcome this limitation we here describe a concept and provide software for producing stable, harmonized phylogenetic alignment of mtDNA sequences for database searches. The new software SAM 2 will be made available via EMPOP and provide the user with the already established conservative frequency estimates. In addition, SAM 2 offers the rCRS-coded haplotype of a given mtDNA sequence following the established and widely accepted phylogenetic alignment. This provides the user with feedback on how mitotypes are stored in EMPOP and how they should be reported in order to harmonize nomenclature. Finally, this approach does not only permit reliable mtDNA nomenclature in forensics but invites related disciplines to take advantage of a standardized way of reporting mtDNA variation, thus closing the ranks between different genetic fields and supporting dialogue and collaboration between mtDNA scholars from various disciplines.
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Affiliation(s)
- Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
| | - Arne Dür
- Institute of Mathematics, University of Innsbruck, Austria
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5
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Niroula A, Vihinen M. PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations. Nucleic Acids Res 2016; 44:2020-7. [PMID: 26843426 PMCID: PMC4797295 DOI: 10.1093/nar/gkw046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.
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Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
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Stewart JB, Chinnery PF. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat Rev Genet 2015; 16:530-42. [PMID: 26281784 DOI: 10.1038/nrg3966] [Citation(s) in RCA: 564] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Common genetic variants of mitochondrial DNA (mtDNA) increase the risk of developing several of the major health issues facing the western world, including neurodegenerative diseases. In this Review, we consider how these mtDNA variants arose and how they spread from their origin on one single molecule in a single cell to be present at high levels throughout a specific organ and, ultimately, to contribute to the population risk of common age-related disorders. mtDNA persists in all aerobic eukaryotes, despite a high substitution rate, clonal propagation and little evidence of recombination. Recent studies have found that de novo mtDNA mutations are suppressed in the female germ line; despite this, mtDNA heteroplasmy is remarkably common. The demonstration of a mammalian mtDNA genetic bottleneck explains how new germline variants can increase to high levels within a generation, and the ultimate fixation of less-severe mutations that escape germline selection explains how they can contribute to the risk of late-onset disorders.
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Affiliation(s)
- James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Patrick F Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 1BZ, UK
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7
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Just RS, Irwin JA, Parson W. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing. Forensic Sci Int Genet 2015; 18:131-9. [PMID: 26009256 PMCID: PMC4550493 DOI: 10.1016/j.fsigen.2015.05.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/24/2015] [Accepted: 05/05/2015] [Indexed: 12/12/2022]
Abstract
Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method.
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Affiliation(s)
- Rebecca S Just
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, Dover, DE, USA; American Registry of Pathology, Rockville, MD, USA
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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8
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Salas A, García-Magariños M, Logan I, Bandelt HJ. The saga of the many studies wrongly associating mitochondrial DNA with breast cancer. BMC Cancer 2014; 14:659. [PMID: 25199876 PMCID: PMC4180149 DOI: 10.1186/1471-2407-14-659] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/26/2014] [Indexed: 11/14/2022] Open
Abstract
Background A large body of genetic research has focused on the potential role that mitochondrial DNA (mtDNA) variants might play on the predisposition to common and complex (multi-factorial) diseases. It has been argued however that many of these studies could be inconclusive due to artifacts related to genotyping errors or inadequate design. Methods Analyses of the data published in case–control breast cancer association studies have been performed using a phylogenetic-based approach. Variation observed in these studies has been interpreted in the light of data available on public resources, which now include over >27,000 complete mitochondrial sequences and the worldwide phylogeny determined by these mitogenomes. Complementary analyses were carried out using public datasets of partial mtDNA sequences, mainly corresponding to control-region segments. Results By way of example, we show here another kind of fallacy in these medical studies, namely, the phenomenon of SNP-SNP interaction wrongly applied to haploid data in a breast cancer study. We also reassessed the mutually conflicting studies suggesting some functional role of the non-synonymous polymorphism m.10398A > G (ND3 subunit of mitochondrial complex I) in breast cancer. In some studies, control groups were employed that showed an extremely odd haplogroup frequency spectrum compared to comparable information from much larger databases. Moreover, the use of inappropriate statistics signaled spurious “significance” in several instances. Conclusions Every case–control study should come under scrutiny in regard to the plausibility of the control-group data presented and appropriateness of the statistical methods employed; and this is best done before potential publication.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultad de Medicina, Universidad de Santiago de Compostela, 15782 Galicia, Spain.
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9
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Iglesias P, Salas A, Costoya JA. The maintenance of mitochondrial genetic stability is crucial during the oncogenic process. Commun Integr Biol 2012; 5:34-8. [PMID: 22482007 DOI: 10.4161/cib.18160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The main energetic resources of the cell are the mitochondria. As such, these organelles control a number of processes related to the life and death of the cell and also have a prominent function in the maintenance of tumor cells. In the last years, several authors have proposed an active role for mitochondria in tumorigenesis, more specifically concerning somatic mutations in mitochondrial DNA (mtDNA). Here, we wanted to evaluate this hypothesis based on the conclusions obtained in a model of gliomagenesis with elevated levels of ROS (reactive oxygen species), a toxic by-product of tumor metabolism. According to our findings, none of the mtDNA variants were found relevant to the tumoral process or suggest the involvement of mitochondria in tumorigenesis beyond the metabolic requirements of the tumoral cell. We conclude that there is not enough evidence to support the claim that mitochondrial instability holds any relevant role in the tumoral process.
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10
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A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics. Forensic Sci Int Genet 2012; 6:e182-4. [PMID: 22840856 DOI: 10.1016/j.fsigen.2012.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022]
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11
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Elson JL, Sweeney MG, Procaccio V, Yarham JW, Salas A, Kong QP, van der Westhuizen FH, Pitceathly RDS, Thorburn DR, Lott MT, Wallace DC, Taylor RW, McFarland R. Toward a mtDNA locus-specific mutation database using the LOVD platform. Hum Mutat 2012; 33:1352-8. [PMID: 22581690 DOI: 10.1002/humu.22118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022]
Abstract
The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information.
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Affiliation(s)
- Joanna L Elson
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.
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12
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Li H, Liu D, Lu J, Bai Y. Physiology and pathophysiology of mitochondrial DNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:39-51. [PMID: 22399417 DOI: 10.1007/978-94-007-2869-1_2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria are the only organelles in animal cells which possess their own genomes. Mitochondrial DNA (mtDNA) alterations have been associated with various human conditions. Yet, their role in pathogenesis remains largely unclear. This review focuses on several major features of mtDNA: (1) mtDNA haplogroup, (2) mtDNA common deletion, (3) mtDNA mutations in the control region or D-loop, (4) mtDNA copy number alterations, (5) mtDNA mutations in translational machinery, (6) mtDNA mutations in protein coding genes (7) mtDNA heteroplasmy. We will also discuss their implications in various human diseases.
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Affiliation(s)
- Hongzhi Li
- Wenzhou Medical College, Wenzhou, Zhejiang, China
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Rubino F, Piredda R, Calabrese FM, Simone D, Lang M, Calabrese C, Petruzzella V, Tommaseo-Ponzetta M, Gasparre G, Attimonelli M. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res 2011; 40:D1150-9. [PMID: 22139932 PMCID: PMC3245114 DOI: 10.1093/nar/gkr1086] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
HmtDB (http://www.hmtdb.uniba.it:8080/hmdb) is a open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar software based on site-specific nucleotide and amino acid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to (i) browse the database through the use of a multi-criterion ‘query’ system; (ii) analyze their own human mitochondrial sequences via the ‘classify’ tool (for complete genomes) or by downloading the ‘fragment-classifier’ tool (for partial sequences); (iii) download multi-alignments with reference genomes as well as variability data.
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Affiliation(s)
- Francesco Rubino
- Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Università degli studi di Bari, Bari 70126, Italy
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A statistical framework for the interpretation of mtDNA mixtures: forensic and medical applications. PLoS One 2011; 6:e26723. [PMID: 22053205 PMCID: PMC3203886 DOI: 10.1371/journal.pone.0026723] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 10/02/2011] [Indexed: 11/19/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) variation is commonly analyzed in a wide range of different biomedical applications. Cases where more than one individual contribute to a stain genotyped from some biological material give rise to a mixture. Most forensic mixture cases are analyzed using autosomal markers. In rape cases, Y-chromosome markers typically add useful information. However, there are important cases where autosomal and Y-chromosome markers fail to provide useful profiles. In some instances, usually involving small amounts or degraded DNA, mtDNA may be the only useful genetic evidence available. Mitochondrial DNA mixtures also arise in studies dealing with the role of mtDNA variation in tumorigenesis. Such mixtures may be generated by the tumor, but they could also originate in vitro due to inadvertent contamination or a sample mix-up. Methods/Principal Findings We present the statistical methods needed for mixture interpretation and emphasize the modifications required for the more well-known methods based on conventional markers to generalize to mtDNA mixtures. Two scenarios are considered. Firstly, only categorical mtDNA data is assumed available, that is, the variants contributing to the mixture. Secondly, quantitative data (peak heights or areas) on the allelic variants are also accessible. In cases where quantitative information is available in addition to allele designation, it is possible to extract more precise information by using regression models. More precisely, using quantitative information may lead to a unique solution in cases where the qualitative approach points to several possibilities. Importantly, these methods also apply to clinical cases where contamination is a potential alternative explanation for the data. Conclusions/Significance We argue that clinical and forensic scientists should give greater consideration to mtDNA for mixture interpretation. The results and examples show that the analysis of mtDNA mixtures contributes substantially to forensic casework and may also clarify erroneous claims made in clinical genetics regarding tumorigenesis.
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Wang CY, Li H, Hao XD, Liu J, Wang JX, Wang WZ, Kong QP, Zhang YP. Uncovering the profile of somatic mtDNA mutations in Chinese colorectal cancer patients. PLoS One 2011; 6:e21613. [PMID: 21738732 PMCID: PMC3125228 DOI: 10.1371/journal.pone.0021613] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/03/2011] [Indexed: 12/20/2022] Open
Abstract
In the past decade, a high incidence of somatic mitochondrial DNA (mtDNA) mutations has been observed, mostly based on a fraction of the molecule, in various cancerous tissues; nevertheless, some of them were queried due to problems in data quality. Obviously, without a comprehensive understanding of mtDNA mutational profile in the cancerous tissue of a specific patient, it is unlikely to disclose the genuine relationship between somatic mtDNA mutations and tumorigenesis. To achieve this objective, the most straightforward way is to directly compare the whole mtDNA genome variation among three tissues (namely, cancerous tissue, para-cancerous tissue, and distant normal tissue) from the same patient. Considering the fact that most of the previous studies on the role of mtDNA in colorectal tumor focused merely on the D-loop or partial segment of the molecule, in the current study we have collected three tissues (cancerous, para-cancerous and normal tissues) respectively recruited from 20 patients with colorectal tumor and completely sequenced the mitochondrial genome of each tissue. Our results reveal a relatively lower incidence of somatic mutations in these patients; intriguingly, all somatic mutations are in heteroplasmic status. Surprisingly, the observed somatic mutations are not restricted to cancer tissues, for the para-cancer tissues and distant normal tissues also harbor somatic mtDNA mutations with a lower frequency than cancerous tissues but higher than that observed in the general population. Our results suggest that somatic mtDNA mutations in cancerous tissues could not be simply explained as a consequence of tumorigenesis; meanwhile, the somatic mtDNA mutations in normal tissues might reflect an altered physiological environment in cancer patients.
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Affiliation(s)
- Cheng-Ye Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Dan Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Jia Liu
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Jia-Xin Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- * E-mail: (Y-PZ); (Q-PK)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- * E-mail: (Y-PZ); (Q-PK)
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16
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Czarnecka AM, Bartnik E. The role of the mitochondrial genome in ageing and carcinogenesis. J Aging Res 2011; 2011:136435. [PMID: 21403887 PMCID: PMC3042732 DOI: 10.4061/2011/136435] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/03/2011] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA mutations and polymorphisms have been the focus of intensive investigations for well over a decade in an attempt to understand how they affect fundamental processes such as cancer and aging. Initial interest in mutations occurring in mitochondrial DNA of cancer cells diminished when most were found to be the same mutations which occurred during the evolution of human mitochondrial haplogroups. However, increasingly correlations are being found between various mitochondrial haplogroups and susceptibility to cancer or diseases in some cases and successful aging in others.
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Affiliation(s)
- Anna M. Czarnecka
- Laboratory of Molecular Oncology, Department of Oncology, Military Institute of Medicine, ul. Szaserów 128, 01-141 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, Kronenberg F. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat 2010; 32:25-32. [PMID: 20960467 DOI: 10.1002/humu.21382] [Citation(s) in RCA: 354] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 09/16/2010] [Indexed: 01/02/2023]
Abstract
An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at.
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Affiliation(s)
- Anita Kloss-Brandstätter
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Austria.
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18
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Molecular oncology focus - is carcinogenesis a 'mitochondriopathy'? J Biomed Sci 2010; 17:31. [PMID: 20416110 PMCID: PMC2876137 DOI: 10.1186/1423-0127-17-31] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 04/25/2010] [Indexed: 01/08/2023] Open
Abstract
Mitochondria are sub-cellular organelles that produce adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS). As suggested over 70 years ago by Otto Warburg and recently confirmed with molecular techniques, alterations in respiratory activity and in mitochondrial DNA (mtDNA) appear to be common features of malignant cells. Somatic mtDNA mutations have been reported in many types of cancer cells, and some reports document the prevalence of inherited mitochondrial DNA polymorphisms in cancer patients. Nevertheless, a careful reanalysis of methodological criteria and methodology applied in those reports has shown that numerous papers can't be used as relevant sources of data for systematic review, meta-analysis, or finally for establishment of clinically applicable markers. In this review technical and conceptual errors commonly occurring in the literature are summarized. In the first place we discuss, why many of the published papers cannot be used as a valid and clinically useful sources of evidence in the biomedical and healthcare contexts. The reasons for introduction of noise in data and in consequence - bias for the interpretation of the role of mitochondrial DNA in the complex process of tumorigenesis are listed. In the second part of the text practical aspects of mtDNA research and requirements necessary to fulfill in order to use mtDNA analysis in clinics are shown. Stringent methodological criteria of a case-controlled experiment in molecular medicine are indicated. In the third part we suggest, what lessons can be learned for the future and propose guidelines for mtDNA analysis in oncology. Finally we conclude that, although several conceptual and methodological difficulties hinder the research on mitochondrial patho-physiology in cancer cells, this area of molecular medicine should be considered of high importance for future clinical practice.
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Yu D, Jia X, Zhang AM, Guo X, Zhang YP, Zhang Q, Yao YG. Molecular characterization of six Chinese families with m.3460G>A and Leber hereditary optic neuropathy. Neurogenetics 2010; 11:349-56. [DOI: 10.1007/s10048-010-0236-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 02/15/2010] [Indexed: 12/19/2022]
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Weissensteiner H, Schönherr S, Specht G, Kronenberg F, Brandstätter A. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. BMC Bioinformatics 2010; 11:122. [PMID: 20214782 PMCID: PMC2841209 DOI: 10.1186/1471-2105-11-122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 03/09/2010] [Indexed: 11/30/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle), security aspects (by using database technology) and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs). It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.
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Affiliation(s)
- Hansi Weissensteiner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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21
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Explaining the imperfection of the molecular clock of hominid mitochondria. PLoS One 2009; 4:e8260. [PMID: 20041137 PMCID: PMC2794369 DOI: 10.1371/journal.pone.0008260] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 11/16/2009] [Indexed: 11/19/2022] Open
Abstract
The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.
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22
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Yao YG, Salas A, Logan I, Bandelt HJ. mtDNA data mining in GenBank needs surveying. Am J Hum Genet 2009; 85:929-33; author reply 933. [PMID: 20004768 DOI: 10.1016/j.ajhg.2009.10.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/06/2009] [Accepted: 10/24/2009] [Indexed: 11/26/2022] Open
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23
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Czarnecka AM, Klemba A, Semczuk A, Plak K, Marzec B, Krawczyk T, Kofler B, Golik P, Bartnik E. Common mitochondrial polymorphisms as risk factor for endometrial cancer. Int Arch Med 2009; 2:33. [PMID: 19863780 PMCID: PMC2775024 DOI: 10.1186/1755-7682-2-33] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 10/28/2009] [Indexed: 01/15/2023] Open
Abstract
Endometrial carcinoma is the most commonly diagnosed gynaecological cancer in developed countries. Although the molecular genetics of this disease has been in the focus of many research laboratories for the last 20 years, relevant prognostic and diagnostic markers are still missing. At the same time mitochondrial DNA mutations have been reported in many types of cancer during the last two decades. It is therefore very likely that the mitochondrial genotype is one of the cancer susceptibility factors. To investigate the presence of mtDNA somatic mutations and distribution of inherited polymorphisms in endometrial adenocarcinoma patients we analyzed the D-loop sequence of cancer samples and their corresponding normal tissues and moreover performed mitochondrial haplogroup analysis. We detected 2 somatic mutation and increased incidence of mtDNA polymorphisms, in particular 16223C (80% patients, p = 0.005), 16126C (23%, p = 0.025) and 207A (19%, p = 0.027). Subsequent statistical analysis revealed that endometrial carcinoma population haplogroup distribution differs from the Polish population and that haplogroup H (with its defining polymorphism - C7028T) is strongly underrepresented (p = 0.003), therefore might be a cancer-protective factor. Our report supports the notion that mtDNA polymorphisms establish a specific genetic background for endometrial adenocarcinoma development and that mtDNA analysis may result in the development of new molecular tool for cancer detection.
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Affiliation(s)
- Anna M Czarnecka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,School of Molecular Medicine, Medical University of Warsaw, Zwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Aleksandra Klemba
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Andrzej Semczuk
- II Clinic and Ward of Gynecology, Medical University of Lublin, Lublin, Poland
| | - Katarzyna Plak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Barbara Marzec
- Department of Human Genetics, Lublin University School of Medicine, Lublin, Poland
| | - Tomasz Krawczyk
- Clinical Pathology Laboratory, Monument Institute of Polish Mothers Health Center, Lodz, Poland
| | - Barbara Kofler
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Müllner Hauptstr 48, A-5020 Salzburg, Austria
| | - Pawel Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Bandelt HJ, Yao YG, Bravi CM, Salas A, Kivisild T. Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies. J Hum Genet 2009; 54:174-81. [PMID: 19322152 DOI: 10.1038/jhg.2009.9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive problems, caused by sample mix-up, contamination, biochemical problems, incomplete sequencing, misdocumentation and insufficient reference to previously published data. To assess data quality in case studies of mitochondrial diseases, it is recommended to compare any mtDNA sequence under consideration to their phylogenetically closest lineages available in the Web. The median network method has proven useful for visualizing potential problems with the data. We contrast some early reports of complete mtDNA sequences to more recent total mtDNA sequencing efforts in studies of various mitochondrial diseases. We conclude that the quality of complete mtDNA sequences generated in the medical field in the past few years is somewhat unsatisfactory and may even fall behind that of pioneer manual sequencing in the early nineties. Our study provides a paradigm for an a posteriori evaluation of sequence quality and for detection of potential problems with inferring a pathogenic status of a particular mutation.
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25
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Lertrit P, Poolsuwan S, Thosarat R, Sanpachudayan T, Boonyarit H, Chinpaisal C, Suktitipat B. Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 137:425-40. [PMID: 18615504 DOI: 10.1002/ajpa.20884] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.
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Affiliation(s)
- Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine, Mahidol University, Bangkok 10700, Thailand.
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26
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Populationsgenetische mitochondriale DNA-Daten. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Der populationsgenetische Aspekt der Nutzung mitochondrialer DNA in der Forensik und medizinischen Genetik bezieht sich implizit auf die gesamte Datengrundlage und die mtDNA-Phylogenie, von der in Hinblick auf die zu untersuchenden Fragestellungen gezielt Teile ausgesondert werden. Wir heben besonders jene Aspekte hervor, die in der Vergangenheit bei vielen Untersuchungen nicht adäquat berücksichtigt wurden.
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27
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Fagundes NJR, Kanitz R, Bonatto SL. A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia. PLoS One 2008; 3:e3157. [PMID: 18797501 PMCID: PMC2527677 DOI: 10.1371/journal.pone.0003157] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/08/2008] [Indexed: 11/18/2022] Open
Abstract
The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.
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Affiliation(s)
- Nelson J. R. Fagundes
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ricardo Kanitz
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L. Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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28
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Zhang AM, Jia X, Yao YG, Zhang Q. Co-occurrence of A1555G and G11778A in a Chinese family with high penetrance of Leber's hereditary optic neuropathy. Biochem Biophys Res Commun 2008; 376:221-4. [PMID: 18775412 DOI: 10.1016/j.bbrc.2008.08.128] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 08/27/2008] [Indexed: 02/09/2023]
Abstract
Co-occurrence of double pathogenic mtDNA mutations with different claimed pathological roles in one mtDNA is infrequent. It is tentative to believe that each of these pathogenic mutations would have its own deleterious effect. Here we reported one three-generation Chinese family with a high penetrance of LHON (78.6%). Analysis of the complete mitochondrial genome in the proband revealed the presence of the LHON primary mutation G11778A in the NADH dehydrogenase 4 (ND4) gene and a deafness-associated mutation A1555G in the 12S rRNA gene. The other mtDNA variants in this family suggested a haplogroup status G2b. Although A1555G has long been confirmed to be a primary mutation for aminoglycoside-induced and non-syndromic hearing loss, none of the maternally related members in this family showed hearing impairment. It thus seems that the occurrence of A1555G in this family had no pathological manifestation. However, whether A1555G has a synergistic effect with G11778A and contribute to the high penetrance of LHON remained an open question. To our knowledge, this is the first report that identified the co-existence of a deafness mutation A1555G and a primary LHON mutation G11778A in one family.
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Affiliation(s)
- A-Mei Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Jiaochang Donglu 32, Kunming, Yunnan 650223, China
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29
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Wang HW, Jia X, Ji Y, Kong QP, Zhang Q, Yao YG, Zhang YP. Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A. Mutat Res 2008; 643:48-53. [PMID: 18619472 DOI: 10.1016/j.mrfmmm.2008.06.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Revised: 06/10/2008] [Accepted: 06/14/2008] [Indexed: 05/26/2023]
Abstract
The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P<0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON.
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Affiliation(s)
- Hua-Wei Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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30
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Kong QP, Salas A, Sun C, Fuku N, Tanaka M, Zhong L, Wang CY, Yao YG, Bandelt HJ. Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS One 2008; 3:e3016. [PMID: 18714389 PMCID: PMC2515346 DOI: 10.1371/journal.pone.0003016] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 07/21/2008] [Indexed: 11/19/2022] Open
Abstract
Background Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. Methodology/Principal Findings We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. Conclusions We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach.
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Affiliation(s)
- Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
| | - Chang Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Noriyuki Fuku
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China
| | - Cheng-Ye Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Abstract
PURPOSE OF REVIEW Mitochondrial diseases are a major category of childhood illness that produce a wide variety of symptoms and multisystemic disorders. This review highlights recent clinically important developments in diagnostic evaluation and treatment of mitochondrial diseases. RECENT FINDINGS Major advances have been made in understanding the genetic bases of mitochondrial diseases. Molecular defects have recently been reported in mitochondrial DNA maintenance, RNA translation and protein import and in mitochondrial fusion and fission, opening new areas of cell disorder. Diagnostic testing is struggling to keep pace with these fundamental discoveries. The diagnostic approach to children suspected of mitochondrial disease is rapidly evolving but few patients have a molecular diagnosis. A better notion of the prognosis of affected children is emerging from studies of long-term outcome. Some therapeutic successes are reported, such as in coenzyme Q deficiency conditions. SUMMARY Mitochondrial diseases can present with signs in almost any organ. Well planned clinical evaluation is the key to successful diagnostic work-up of mitochondrial diseases. An approach is presented for further testing in specialized laboratories. Mitochondrial diseases can be caused by mutations in mitochondrial DNA or, more commonly in children, in nuclear genes. Mitochondrial DNA mutations pose special challenges for genetic counseling and prenatal diagnosis. Supportive treatment and avoidance of environmental stresses are important aspects of patient care. Specific treatment of mitochondrial diseases is in its infancy and is a major challenge for pediatric medicine.
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Álvarez-Iglesias V, Barros F, Carracedo Á, Salas A. Minisequencing mitochondrial DNA pathogenic mutations. BMC MEDICAL GENETICS 2008; 9:26. [PMID: 18402672 PMCID: PMC2377236 DOI: 10.1186/1471-2350-9-26] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 04/10/2008] [Indexed: 12/18/2022]
Abstract
BACKGROUND There are a number of well-known mutations responsible of common mitochondrial DNA (mtDNA) diseases. In order to overcome technical problems related to the analysis of complete mtDNA genomes, a variety of different techniques have been proposed that allow the screening of coding region pathogenic mutations. METHODS We here propose a minisequencing assay for the analysis of mtDNA mutations. In a single reaction, we interrogate a total of 25 pathogenic mutations distributed all around the whole mtDNA genome in a sample of patients suspected for mtDNA disease. RESULTS We have detected 11 causal homoplasmic mutations in patients suspected for Leber disease, which were further confirmed by standard automatic sequencing. Mutations m.11778G>A and m.14484T>C occur at higher frequency than expected by change in the Galician (northwest Spain) patients carrying haplogroup J lineages (Fisher's Exact test, P-value < 0.01). The assay performs well in mixture experiments of wild:mutant DNAs that emulate heteroplasmic conditions in mtDNA diseases. CONCLUSION We here developed a minisequencing genotyping method for the screening of the most common pathogenic mtDNA mutations which is simple, fast, and low-cost. The technique is robust and reproducible and can easily be implemented in standard clinical laboratories.
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Affiliation(s)
- Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Francisco Barros
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
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Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ. The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS One 2008; 3:e1764. [PMID: 18335039 PMCID: PMC2258150 DOI: 10.1371/journal.pone.0001764] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 02/09/2008] [Indexed: 11/18/2022] Open
Abstract
Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università degli Studi di Perugia, Perugia, Italy
| | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Claudio M. Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), La Plata, Argentina
| | - Michael D. Coble
- Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Rockville, Maryland, United States of America
| | - Qing-Peng Kong
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Grupo de Medicina Xenómica, Hospital Clínico Universitario, Santiago de Compostela, Galicia, Spain
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- * To whom correspondence should be addressed. E-mail:
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Pereira L, Gonçalves J, Bandelt HJ. Mutation C11994T in the mitochondrial ND4 gene is not a cause of low sperm motility in Portugal. Fertil Steril 2008; 89:738-41. [PMID: 17517394 DOI: 10.1016/j.fertnstert.2007.03.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 03/13/2007] [Accepted: 03/13/2007] [Indexed: 11/26/2022]
Abstract
It has recently been suggested that a hitherto unobserved mutation, C11994T, causes oligoasthenozoospermia in men from India but at the same time does not affect systems other than the motility of the sperm. There are good reasons to question this proposition, in view of the worldwide mtDNA database and the Indian record in particular. We have further analyzed the oligoasthenozoospermic samples from a previous systematic study of infertile Portuguese men and found no instance of C11994T.
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Affiliation(s)
- Luísa Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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Pätsi J, Kervinen M, Finel M, Hassinen IE. Leber hereditary optic neuropathy mutations in the ND6 subunit of mitochondrial complex I affect ubiquinone reduction kinetics in a bacterial model of the enzyme. Biochem J 2008; 409:129-37. [PMID: 17894548 DOI: 10.1042/bj20070866] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
LHON (Leber hereditary optic neuropathy) is a maternally inherited disease that leads to sudden loss of central vision at a young age. There are three common primary LHON mutations, occurring at positions 3460, 11778 and 14484 in the human mtDNA (mitochondrial DNA), leading to amino acid substitutions in mitochondrial complex I subunits ND1, ND4 and ND6 respectively. We have now examined the effects of ND6 mutations on the function of complex I using the homologous NuoJ subunit of Escherichia coli NDH-1 (NADH:quinone oxidoreductase) as a model system. The assembly level of the NDH-1 mutants was assessed using electron transfer from deamino-NADH to the 'shortcut' electron acceptor HAR (hexammine ruthenium), whereas ubiquinone reductase activity was determined using DB (decylubiquinone) as a substrate. Mutant growth in minimal medium with malate as the main carbon source was used for initial screening of the efficiency of energy conservation by NDH-1. The results indicated that NuoJ-M64V, the equivalent of the common LHON mutation in ND6, had a mild effect on E. coli NDH-1 activity, while nearby mutations, particularly NuoJ-Y59F, NuoJ-V65G and NuoJ-M72V, severely impaired the DB reduction rate and cell growth on malate. NuoJ-Met64 and NuoJ-Met72 position mutants lowered the affinity of NDH-1 for DB and explicit C-type inhibitors, whereas NuoJ-Y59C displayed substrate inhibition by oxidized DB. The results are compatible with the notion that the ND6 subunit delineates the binding cavity of ubiquinone substrate, but does not directly take part in the catalytic reaction. How these changes in the enzyme's catalytic properties contribute to LHON pathogenesis is discussed.
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Affiliation(s)
- Jukka Pätsi
- Department of Medical Biochemistry and Molecular Biology, University of Oulu, P.O. Box 5000, FIN-90014 Oulu, Finland
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Wang CY, Wang HW, Yao YG, Kong QP, Zhang YP. Somatic mutations of mitochondrial genome in early stage breast cancer. Int J Cancer 2007; 121:1253-6. [PMID: 17514652 DOI: 10.1002/ijc.22822] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The complete mitochondrial genomes of the primary cancerous, matched paracancerous normal and distant normal tissues from 10 early-stage breast cancer patients were analyzed in this study, with special attempt (i) to investigate whether the reported high frequency of mitochondrial DNA (mtDNA) somatic mutations in breast cancer could be repeated under a stringent data quality control, and (ii) to characterize the spectrum of mtDNA somatic mutations in Chinese breast cancer patients and evaluate their potential significance in early cancer diagnosis. Two heteroplasmic somatic transitions (T2275C and A8601G) were identified in our samples. The transition A8601G was present in the primary cancerous and paracancerous normal tissues from patient no. 3. Transition T2275C was found in the primary cancerous tissue but not in other normal tissues from patient no. 6; this transition has been reported in the colonic crypts and is located at a highly conserved site in the 16S rRNA gene. Subsequent cloning sequencing confirmed the absence of both mutations in the distant normal tissues from the 2 patients. The overall rate of somatic mutations in our patients was much lower than those of previous studies of breast cancer. Our results gave support to the recent claim that the high frequency of mtDNA somatic mutations in cancer studies is overestimated. Based on the mtDNA mutation pattern in early stage breast cancer observed in this study, we cautioned the enthusiasm and efforts to look for somatic mutations that were of diagnostic value in cancer early detection.
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Affiliation(s)
- Cheng-Ye Wang
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Ji Y, Jia X, Zhang Q, Yao YG. mtDNA haplogroup distribution in Chinese patients with Leber's hereditary optic neuropathy and G11778A mutation. Biochem Biophys Res Commun 2007; 364:238-42. [PMID: 17942074 DOI: 10.1016/j.bbrc.2007.09.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 09/25/2007] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA background has been shown to be involved in the penetrance of Leber's hereditary optic neuropathy (LHON) in western Eurasian populations. To analyze mtDNA haplogroup distribution pattern in Han Chinese patients with LHON and G11778A mutation, we analyzed the mtDNA haplogroups of 41 probands with LHON known to harbor G11778A mutation by sequencing the mtDNA control region hypervariable segments and some coding region polymorphisms. Each mtDNA was classified according to the available East Asian haplogroup system. The haplogroup distribution pattern of LHON sample was then compared to the reported Han Chinese samples. Haplogroups M7, D, B, and A were detected in 11 (26.8%), 10 (24.4%), 8 (19.5%), and 5 (12.2%) LHON families, respectively, and accounted for 82.9% of the total samples examined. For the remaining seven mtDNAs, six belonged to M8a, M10a, C, N9a, F1a, and R11, respectively, and one could only be assigned into macro-haplogroup M. The LHON sample was distinguished from other Han Chinese samples in the principal component map based on haplogroup distribution frequency. Our results show that matrilineal genetic components of Chinese LHON patients with G11778A are diverse and differ from related Han Chinese regional samples. mtDNA background might affect the expression of LHON and the G11778A mutation in Chinese population.
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Affiliation(s)
- Yanli Ji
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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Yao YG, Bandelt HJ, Young NS. External contamination in single cell mtDNA analysis. PLoS One 2007; 2:e681. [PMID: 17668059 PMCID: PMC1930155 DOI: 10.1371/journal.pone.0000681] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 06/19/2007] [Indexed: 12/31/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) variation in single hematopoietic cells, muscle fibers, oocytes, and from tiny amount of tumor tissues and degraded clinical specimens has been reported in many medical publications. External DNA contamination, notoriously difficult to avoid, threatens the integrity of such studies. Methodology/Principal Findings Employing a phylogenetic approach, we analyzed the geographic origins of mtDNA sequence anomalies observed during multiple studies of mtDNA sequence variation in a total of 7094 single hematopoietic cells. 40 events with irregular mtDNA patterns were detected: eight instances (from seven different haplotypes) could be traced to laboratory personnel; six cases were caused by sample cross-contamination. The sources of the remaining events could not be identified, and the anomalous sequence variation referred to matrilines from East Asia, Africa, or West Eurasia, respectively. These mtDNA sequence anomalies could be best explained by contamination. Conclusions Using the known world mtDNA phylogeny, we could distinguish the geographic origin of the anomalous mtDNA types, providing some useful information regarding the source of contamination. Our data suggest that routine mtDNA sequence analysis of laboratory personnel is insufficient to identify and eliminate all contaminants. A rate of 0.6% of external contamination in this study, while low, is not negligible: Unrecognized contaminants will be mistaken as evidence of remarkable somatic mutations associated with the development of cancer and other diseases. The effective contamination rate can increase by a factor of more than an order of magnitude in some studies that did not institute high standards. Our results are of particular relevance to mtDNA research in medicine, and such an approach should be adopted to maintain and improve quality control in single-cell analyses.
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Affiliation(s)
- Yong-Gang Yao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
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