1
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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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Zalloua P, Collins CJ, Gosling A, Biagini SA, Costa B, Kardailsky O, Nigro L, Khalil W, Calafell F, Matisoo-Smith E. Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza. Sci Rep 2018; 8:17567. [PMID: 30514893 PMCID: PMC6279797 DOI: 10.1038/s41598-018-35667-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022] Open
Abstract
Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.
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Affiliation(s)
- Pierre Zalloua
- School of Medicine, Lebanese American University, Byblos, Lebanon.
| | - Catherine J Collins
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Anna Gosling
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Simone Andrea Biagini
- Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Benjamí Costa
- Museu Arqueològic d'Eivissa i Formentera, Universitat de Barcelona, Illes Balears, Spain
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Lorenzo Nigro
- Facoltà di Lettere e Filosofia, Università di Roma, La Sapienza, Rome, Italy
| | - Wissam Khalil
- Department of Arts and Archaeology, Lebanese University, Beirut, Lebanon
| | - Francesc Calafell
- Department de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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3
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Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 2018; 32:88-93. [DOI: 10.1016/j.fsigen.2017.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 11/05/2017] [Indexed: 11/15/2022]
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4
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Hagen CM, Aidt FH, Havndrup O, Hedley PL, Jensen MK, Kanters JK, Pham TT, Bundgaard H, Christiansen M. Private mitochondrial DNA variants in danish patients with hypertrophic cardiomyopathy. PLoS One 2015; 10:e0124540. [PMID: 25923817 PMCID: PMC4414448 DOI: 10.1371/journal.pone.0124540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/19/2015] [Indexed: 02/02/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA) haplogroups are susceptibility factors for HCM. Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446 variants. After elimination of 312 (69.9%) non-coding and synonymous variants, a further 109 (24.4%) with a global prevalence > 0.1%, three (0.7%) haplogroup associated and 19 (2.0%) variants with a low predicted in silico likelihood of pathogenicity, three variants: MT-TC: m.5772G>A, MT-TF: m.644A>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM.
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Affiliation(s)
- Christian M. Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederik H. Aidt
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Hospital, Roskilde, Denmark
| | - Paula L. Hedley
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Morten K. Jensen
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tam T. Pham
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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5
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Salas A, Elson JL. Mitochondrial DNA as a risk factor for false positives in case-control association studies. J Genet Genomics 2015; 42:169-72. [PMID: 25953355 DOI: 10.1016/j.jgg.2015.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/12/2015] [Accepted: 03/10/2015] [Indexed: 02/04/2023]
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, Galicia 15782, Spain.
| | - Joanna L Elson
- Mitochondrial Research Group, Institute of Genetic Medicine, Centre for Life, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
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6
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Carroll CJ, Brilhante V, Suomalainen A. Next-generation sequencing for mitochondrial disorders. Br J Pharmacol 2014; 171:1837-53. [PMID: 24138576 DOI: 10.1111/bph.12469] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 10/03/2013] [Accepted: 10/13/2013] [Indexed: 12/30/2022] Open
Abstract
A great deal of our understanding of mitochondrial function has come from studies of inherited mitochondrial diseases, but still majority of the patients lack molecular diagnosis. Furthermore, effective treatments for mitochondrial disorders do not exist. Development of therapies has been complicated by the fact that the diseases are extremely heterogeneous, and collecting large enough cohorts of similarly affected individuals to assess new therapies properly has been difficult. Next-generation sequencing technologies have in the last few years been shown to be an effective method for the genetic diagnosis of inherited mitochondrial diseases. Here we review the strategies and findings from studies applying next-generation sequencing methods for the genetic diagnosis of mitochondrial disorders. Detailed knowledge of molecular causes also enables collection of homogenous cohorts of patients for therapy trials, and therefore boosts development of intervention.
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Affiliation(s)
- C J Carroll
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
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7
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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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8
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Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA). Forensic Sci Int Genet 2013; 7:601-609. [PMID: 23948335 PMCID: PMC3819997 DOI: 10.1016/j.fsigen.2013.07.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 07/01/2013] [Accepted: 07/08/2013] [Indexed: 12/02/2022]
Abstract
The assignment of haplogroups to mitochondrial DNA haplotypes contributes substantial value for quality control, not only in forensic genetics but also in population and medical genetics. The availability of Phylotree, a widely accepted phylogenetic tree of human mitochondrial DNA lineages, led to the development of several (semi-)automated software solutions for haplogrouping. However, currently existing haplogrouping tools only make use of haplogroup-defining mutations, whereas private mutations (beyond the haplogroup level) can be additionally informative allowing for enhanced haplogroup assignment. This is especially relevant in the case of (partial) control region sequences, which are mainly used in forensics. The present study makes three major contributions toward a more reliable, semi-automated estimation of mitochondrial haplogroups. First, a quality-controlled database consisting of 14,990 full mtGenomes downloaded from GenBank was compiled. Together with Phylotree, these mtGenomes serve as a reference database for haplogroup estimates. Second, the concept of fluctuation rates, i.e. a maximum likelihood estimation of the stability of mutations based on 19,171 full control region haplotypes for which raw lane data is available, is presented. Finally, an algorithm for estimating the haplogroup of an mtDNA sequence based on the combined database of full mtGenomes and Phylotree, which also incorporates the empirically determined fluctuation rates, is brought forward. On the basis of examples from the literature and EMPOP, the algorithm is not only validated, but both the strength of this approach and its utility for quality control of mitochondrial haplotypes is also demonstrated.
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9
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MitoLSDB: a comprehensive resource to study genotype to phenotype correlations in human mitochondrial DNA variations. PLoS One 2013; 8:e60066. [PMID: 23585830 PMCID: PMC3621970 DOI: 10.1371/journal.pone.0060066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/20/2013] [Indexed: 01/16/2023] Open
Abstract
Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease association studies on mtDNA (http://mitolsdb.igib.res.in). The main goal of MitoLSDB is to provide a central platform for direct submissions of novel variants that can be curated by the Mitochondrial Research Community. MitoLSDB provides access to standardized and annotated data from literature and databases encompassing information from 5231 individuals, 675 populations and 27 phenotypes. This platform is developed using the Leiden Open (source) Variation Database (LOVD) software. MitoLSDB houses information on all 37 genes in each population amounting to 132397 variants, 5147 unique variants. For each variant its genomic location as per the Revised Cambridge Reference Sequence, codon and amino acid change for variations in protein-coding regions, frequency, disease/phenotype, population, reference and remarks are also listed. MitoLSDB curators have also reported errors documented in literature which includes 94 phantom mutations, 10 NUMTs, six documentation errors and one artefactual recombination. MitoLSDB is the largest repository of mtDNA variants systematically standardized and presented using the LOVD platform. We believe that this is a good starting resource to curate mtDNA variants and will facilitate direct submissions enhancing data coverage, annotation in context of pathogenesis and quality control by ensuring non-redundancy in reporting novel disease associated variants.
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10
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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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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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Skonieczna K, Malyarchuk BA, Grzybowski T. The landscape of mitochondrial DNA variation in human colorectal cancer on the background of phylogenetic knowledge. Biochim Biophys Acta Rev Cancer 2011; 1825:153-9. [PMID: 22178219 DOI: 10.1016/j.bbcan.2011.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 01/07/2023]
Abstract
Recently, an increasing number of studies indicate that mutations in mitochondrial genome may contribute to cancer development or metastasis. Hence, it is important to determine whether the mitochondrial DNA might be a good, clinically applicable marker of cancer. This review describes hereditary as well as somatic mutations reported in mitochondrial DNA of colorectal cancer cells. We showed here that the entire mitochondrial genome mutational spectra are different in colorectal cancer and non-tumor cells. We also placed the described mutations on the phylogenetic context, which highlighted the recurrent problem of data quality. Therefore, the most important rules for adequately assessing the quality of mitochondrial DNA sequence analysis in cancer have been summarized. As follows from this review, neither the reliable spectrum of mtDNA somatic mutations nor the association between hereditary mutations and colorectal cancer risk have been resolved. This indicates that only high resolution studies on mtDNA variability, followed by a proper data interpretation employing phylogenetic knowledge may finally verify the utility of mtDNA sequence (if any) in clinical practice.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Molecular and Forensic Genetics, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
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13
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Fridman C, Cardena M, Krieger J, Pereira A. Evaluation of the relationship between mitochondrial haplogroup and development of heart failure in Brazilian sample. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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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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15
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Liu J, Wang LD, Sun YB, Li EM, Xu LY, Zhang YP, Yao YG, Kong QP. Deciphering the Signature of Selective Constraints on Cancerous Mitochondrial Genome. Mol Biol Evol 2011; 29:1255-61. [DOI: 10.1093/molbev/msr290] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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16
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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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17
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Gómez-Carballa A, Cerezo M, Balboa E, Heredia C, Castro-Feijóo L, Rica I, Barreiro J, Eirís J, Cabanas P, Martínez-Soto I, Fernández-Toral J, Castro-Gago M, Pombo M, Carracedo Á, Barros F, Salas A. Evolutionary analyses of entire genomes do not support the association of mtDNA mutations with Ras/MAPK pathway syndromes. PLoS One 2011; 6:e18348. [PMID: 21526175 PMCID: PMC3079712 DOI: 10.1371/journal.pone.0018348] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 02/25/2011] [Indexed: 01/23/2023] Open
Abstract
Background There are several known autosomal genes responsible for
Ras/MAPK pathway syndromes, including
Noonan syndrome (NS) and related disorders (such as LEOPARD,
neurofibromatosis type 1), although mutations of these genes do not explain
all cases. Due to the important role played by the mitochondrion in the
energetic metabolism of cardiac muscle, it was recently proposed that
variation in the mitochondrial DNA (mtDNA) genome could be a risk factor in
the Noonan phenotype and in hypertrophic cardiomyopathy (HCM), which is a
common clinical feature in Ras/MAPK pathway syndromes. In order to test
these hypotheses, we sequenced entire mtDNA genomes in the largest series of
patients suffering from Ras/MAPK pathway
syndromes analyzed to date (n = 45),
most of them classified as NS patients
(n = 42). Methods/Principal Findings The results indicate that the observed mtDNA lineages were mostly of European
ancestry, reproducing in a nutshell the expected haplogroup (hg) patterns of
a typical Iberian dataset (including hgs H, T, J, and U). Three new branches
of the mtDNA phylogeny (H1j1, U5b1e, and L2a5) are described for the first
time, but none of these are likely to be related to NS or
Ras/MAPK pathway syndromes when
observed under an evolutionary perspective. Patterns of variation in tRNA
and protein genes, as well as redundant, private and heteroplasmic variants,
in the mtDNA genomes of patients were as expected when compared with the
patterns inferred from a worldwide mtDNA phylogeny based on more than 8700
entire genomes. Moreover, most of the mtDNA variants found in patients had
already been reported in healthy individuals and constitute common
polymorphisms in human population groups. Conclusions/Significance As a whole, the observed mtDNA genome variation in the NS patients was
difficult to reconcile with previous findings that indicated a pathogenic
role of mtDNA variants in NS.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - María Cerezo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - Emilia Balboa
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Claudia Heredia
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Lidia Castro-Feijóo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Itxaso Rica
- Servicio de Endocrinología Infantil, Hospital de Cruces,
Barakaldo, Basque Country, Spain
| | - Jesús Barreiro
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Jesús Eirís
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Paloma Cabanas
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Isabel Martínez-Soto
- Unidad de Cardiología Infantil, Departamento de Pediatría,
Hospital Clínico Universitario de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | | | - Manuel Castro-Gago
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Manuel Pombo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Francisco Barros
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- * E-mail:
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18
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Bi R, Li WL, Chen MQ, Zhu Z, Yao YG. Rapid identification of mtDNA somatic mutations in gastric cancer tissues based on the mtDNA phylogeny. Mutat Res 2011; 709-710:15-20. [PMID: 21419139 DOI: 10.1016/j.mrfmmm.2011.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA (mtDNA) somatic mutations have been identified in nearly all kinds of cancer during the past decade. Normally one need to determine the complete mtDNA sequences from both cancerous and normal tissues of the same patient to score the somatic mutation in cancer. In this study, we intended to explore a strategy to quickly identify somatic mutations in the entire mtDNA genome based on its phylogeny. The principal assumption for this strategy is that somatic mutations, as recently accumulated in cancerous tissue, have younger age and will be located in the terminal branches of mtDNA phylogenetic tree. In contrast, the haplogroup-specific variants, which appear as germline variants and have ancient age, will be located in the basal or intermediate-node branches of the tree, depending on their relative age. When the complete mtDNA sequence of the cancerous tissue is determined and is classified relative to the available mtDNA phylogeny, we only need to screen the variants that are located in the terminal branch in the paracancerous tissue or other normal tissue from the same patient to identify somatic mutations in cancer. We validated this strategy by using paired gastric cancer tissue and paracancerous tissue or blood from 10 Chinese patients (including one with gastric stromal tumor). A total of seven somatic mutations were identified in the cancerous tissues from four patients. Our result suggests that employing mtDNA phylogenetic knowledge facilitates rapid identification of mitochondrial genome somatic mutations in cancer.
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Affiliation(s)
- Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
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19
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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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20
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Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V. Population expansion in the North African late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evol Biol 2010; 10:390. [PMID: 21176127 PMCID: PMC3016289 DOI: 10.1186/1471-2148-10-390] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/21/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene. RESULTS Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East. CONCLUSIONS A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6's European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast.
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Affiliation(s)
- Luísa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.
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21
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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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22
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Uehara DT, Rincon D, Abreu-Silva RS, de Mello Auricchio MTB, Tabith A, Kok F, Mingroni-Netto RC. Role of the Mitochondrial Mutations, m.827A>G and the Novel m.7462C>T, in the Origin of Hearing Loss. Genet Test Mol Biomarkers 2010; 14:611-6. [DOI: 10.1089/gtmb.2010.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniela Tiaki Uehara
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel Rincon
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ronaldo Serafim Abreu-Silva
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Alfredo Tabith
- Divisão de Educação e Reabilitação de Distúrbios da Comunicação, Pontifícia Universidade Católica, São Paulo, Brazil
| | - Fernando Kok
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Neurologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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23
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Klemba A, Kowalewska M, Kukwa W, Tonska K, Szybinska A, Mossakowska M, Scinska A, Golik P, Koper K, Radziszewski J, Kukwa A, Czarnecka AM, Bartnik E. Mitochondrial genotype in vulvar carcinoma - cuckoo in the nest. J Biomed Sci 2010; 17:73. [PMID: 20825678 PMCID: PMC2944255 DOI: 10.1186/1423-0127-17-73] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 09/08/2010] [Indexed: 01/09/2023] Open
Abstract
Vulvar squamous cell carcinoma (VSCC) is a rare female genital neoplasm. Although numerous molecular changes have been reported in VSCC, biomarkers of clinical relevance are still lacking. On the other hand, there is emerging evidence on the use of mtDNA as a diagnostic tool in oncology. In order to investigate mtDNA status in VSCC patients, haplogroup distribution analysis and D-loop sequencing were performed. The results were compared with available data for the general Polish population, cancer free-centenarians as well as patients with endometrial and head and neck cancer. The obtained data were also compared with the current status of mitochondrial databases. Significant differences in haplogroup distribution between VSCC cohort, general Polish population and cancer-free centenarians cohort were found. Moreover, a correlation between the VSCC patients haplogroup and HPV status was observed. Finally, a specific pattern of mtDNA polymorphisms was found in VSCC. Our results suggest that the mitochondrial genetic background may influence the risk of VSCC occurrence as well as susceptibility to HPV infection.
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Affiliation(s)
- Aleksandra Klemba
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, ul, Pawinskiego 5A, 02-106, Warsaw, Poland
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24
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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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25
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Seligmann H. The ambush hypothesis at the whole-organism level: Off frame, ‘hidden’ stops in vertebrate mitochondrial genes increase developmental stability. Comput Biol Chem 2010; 34:80-5. [DOI: 10.1016/j.compbiolchem.2010.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/02/2010] [Indexed: 01/24/2023]
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26
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McKnight AJ, Currie D, Maxwell AP. Unravelling the genetic basis of renal diseases; from single gene to multifactorial disorders. J Pathol 2010; 220:198-216. [PMID: 19882676 DOI: 10.1002/path.2639] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chronic kidney disease is common with up to 5% of the adult population reported to have an estimated glomerular filtration rate of < 60 ml/min/1.73 m(2). A large number of pathogenic mutations have been identified that are responsible for 'single gene' renal disorders, such as autosomal dominant polycystic kidney disease and X-linked Alport syndrome. These single gene disorders account for < 15% of the burden of end-stage renal disease that requires dialysis or kidney transplantation. It has proved more difficult to identify the genetic susceptibility underlying common, complex, multifactorial kidney conditions, such as diabetic nephropathy and hypertensive nephrosclerosis. This review describes success to date and explores strategies currently employed in defining the genetic basis for a number of renal disorders. The complementary use of linkage studies, candidate gene and genome-wide association analyses are described and a collation of renal genetic resources highlighted.
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Affiliation(s)
- Amy J McKnight
- Nephrology Research Group, Queen's University of Belfast, Belfast BT9 7AB, Northern Ireland, UK
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27
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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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28
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Cerezo M, Bandelt HJ, Martín-Guerrero I, Ardanaz M, Vega A, Carracedo Á, García-Orad Á, Salas A. High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 2009; 4:e7902. [PMID: 19924307 PMCID: PMC2775629 DOI: 10.1371/journal.pone.0007902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/20/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL. METHODOLOGY/PRINCIPAL FINDINGS The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis. CONCLUSIONS/SIGNIFICANCE Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- Databases, Genetic
- Granulocytes/cytology
- Haplotypes
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytes/cytology
- Models, Statistical
- Molecular Sequence Data
- Mutation
- Phylogeny
- Sequence Analysis, DNA
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | | | - Idoia Martín-Guerrero
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Maite Ardanaz
- Servicio de Hematología, Hospital Txagorritxu, Vitoria, Spain
| | - Ana Vega
- 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, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - África García-Orad
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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29
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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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30
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Ji Y, Zhang AM, Jia X, Zhang YP, Xiao X, Li S, Guo X, Bandelt HJ, Zhang Q, Yao YG. Mitochondrial DNA haplogroups M7b1'2 and M8a affect clinical expression of leber hereditary optic neuropathy in Chinese families with the m.11778G-->a mutation. Am J Hum Genet 2008; 83:760-8. [PMID: 19026397 DOI: 10.1016/j.ajhg.2008.11.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 10/27/2008] [Accepted: 11/06/2008] [Indexed: 02/01/2023] Open
Abstract
Leber hereditary optic neuropathy (LHON) is the most extensively studied mitochondrial disease, with the majority of the cases being caused by one of three primary mitochondrial DNA (mtDNA) mutations. Incomplete disease penetrance and gender bias are two features of LHON and indicate involvement of additional genetic or environmental factors in the pathogenesis of the disorder. Haplogroups J, K, and H have been shown to influence the clinical expression of LHON in subjects harboring primary mutations in European families. However, whether mtDNA haplogroups would affect the penetrance of LHON in East Asian families has not been evaluated yet. By studying the penetrance of LHON in 1859 individuals from 182 Chinese families (including one from Cambodia) with the m.11778G-->A mutation, we found that haplogroup M7b1'2 significantly increases the risk of visual loss, whereas M8a has a protective effect. Analyses of the complete mtDNA sequences from LHON families with m.11778G-->A narrow the association of disease expression to m.12811T-->C (Y159H) in the NADH dehydrogenase 5 gene (MT-ND5) in haplogroup M7b1'2 and suggest that the specific combination of amino acid changes (A20T-T53I) in the ATP synthase 6 protein (MT-ATP6) caused by m.8584G-->A and m.8684C-->T might account for the beneficial background effect of M8a. Protein secondary-structure prediction for the MT-ATP6 with the two M8a-specific amino acid changes further supported our inferences. These findings will assist in further understanding the pathogenesis of LHON and guide future genetic counseling in East Asian patients with m.11778G-->A.
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31
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Application of the phylogenetic analysis in mitochondrial disease study. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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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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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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Abstract
PURPOSE OF REVIEW Mitochondrial disorders are increasingly acknowledged as a major category in clinical neurology. In this review we highlight the most recent advances in the field, including the characterization of new disease genes, new physiopathological insights, and the role of mitochondrial dysfunction in neurodegeneration. RECENT FINDINGS Substantial progress has been made on the genetic basis and pathogenic mechanisms in disorders associated with altered mitochondrial DNA stability and expression. These defects include a wide spectrum of neurological conditions caused by genetic abnormalities of the mitochondrial replication and translation machineries, and of the metabolic pathways controlling the nucleotide supply to organelles, cells and tissues. Another relevant contribution has been given to the molecular dissection of coenzyme Q deficiency, a clinically heterogeneous, potentially treatable condition, thanks to the biochemical and genetic characterization of the first defects in coenzyme Q biosynthesis. Finally, the genetic determinants controlling the penetrance of mitochondrial disorders, as well as the role of mitochondrial dysfunction in neurodegenerative conditions such as Parkinson's and Huntington's diseases, have been investigated in both patients and animal models. SUMMARY The dual genetic contribution controlling mitochondrial biogenesis, and the intricacy and universality of the metabolic pathways operating in the mitochondrion explain the complexity of what is now known as 'mitochondrial medicine'.
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Affiliation(s)
- Massimo Zeviani
- Unit of Molecular Neurogenetics, Institute of Neurology C. Besta, Foundation IRCCS, Milan, Italy.
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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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Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T, Villems R, Zakharov I. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 2007; 81:1025-41. [PMID: 17924343 DOI: 10.1086/522933] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 07/26/2007] [Indexed: 11/03/2022] Open
Abstract
To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ~7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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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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40
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Brandstätter A, Egyed B, Zimmermann B, Duftner N, Padar Z, Parson W. Migration rates and genetic structure of two Hungarian ethnic groups in Transylvania, Romania. Ann Hum Genet 2007; 71:791-803. [PMID: 17532745 DOI: 10.1111/j.1469-1809.2007.00371.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csángó and the Székely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csángó to the Székely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csángó population, which is, in its genetic structure, clearly different from the Székely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (http://www.empop.org).
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Affiliation(s)
- A Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Austria
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41
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Irwin J, Saunier J, Strouss K, Paintner C, Diegoli T, Sturk K, Kovatsi L, Brandstätter A, Cariolou MA, Parson W, Parsons TJ. Mitochondrial control region sequences from northern Greece and Greek Cypriots. Int J Legal Med 2007; 122:87-9. [PMID: 17492459 DOI: 10.1007/s00414-007-0173-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 04/02/2007] [Indexed: 10/23/2022]
Abstract
Entire mitochondrial control region data were generated for population samples of 319 unrelated individuals from northern Greece and 91 unrelated individuals from Cyprus. The samples from northern Greece have been previously typed for 15 nuclear short tandem repeat (STR; Kovatsi et al., Forensic Sci. Int. 159:61-63, 2006).
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Affiliation(s)
- Jodi Irwin
- Armed Forces Institute of Pathology, 20850, Rockville, MD, USA,
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Abstract
With the recent increase in the available number of high-quality, full-length mitochondrial sequences, it is now possible to construct and analyze a comprehensive human mitochondrial consensus sequence. Using a data set of 827 carefully selected sequences, it is shown that modern humans contain extremely low levels of divergence from the mitochondrial consensus sequence, differing by a mere 21.6 nt sites on average. Fully 84.1% of the mitochondrial genome was found to be invariant and ‘private’ mutations accounted for 43.8% of the variable sites. Ninety eight percent of the variant sites had a primary nucleotide with an allele frequency of 0.90 or greater. Interestingly, the few truly ambiguous nucleotide sites could all be reliably assigned to either a purine or pyrimidine ancestral state. A comparison of this consensus sequence to several ancestral sequences derived from phylogenetic studies reveals a great deal of similarity, where, as expected, the most phylogenetically informative nucleotides in the ancestral studies tended to be the most variable nucleotides in the consensus. Allowing for this fact, the consensus approach provides variation data on the positions that do not contribute to phylogenetic reconstructions, and these data provide a baseline for measuring human mitochondrial variation in populations worldwide.
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Affiliation(s)
- Robert W Carter
- FMS Foundation, 7160 Stone Hill Rd., Livonia, NY 14487, USA.
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Bandelt HJ, Olivieri A, Bravi C, Yao YG, Torroni A, Salas A. 'Distorted' mitochondrial DNA sequences in schizophrenic patients. Eur J Hum Genet 2007; 15:400-2; author reply 402-4. [PMID: 17264866 DOI: 10.1038/sj.ejhg.5201781] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Cerný V, Salas A, Hájek M, Zaloudková M, Brdicka R. A bidirectional corridor in the Sahel-Sudan belt and the distinctive features of the Chad Basin populations: a history revealed by the mitochondrial DNA genome. Ann Hum Genet 2007; 71:433-52. [PMID: 17233755 DOI: 10.1111/j.1469-1809.2006.00339.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chad Basin was sparsely inhabited during the Stone Age, and its continual settlement began with the Holocene. The role played by Lake Chad in the history and migration patterns of Africa is still unclear. We studied the mitochondrial DNA (mtDNA) variability in 448 individuals from 12 ethnically and/or economically (agricultural/pastoral) different populations from Cameroon, Chad, Niger and Nigeria. The data indicate the importance of this region as a corridor connecting East and West Africa; however, this bidirectional flow of people in the Sahel-Sudan Belt did not erase features peculiar to the original Chad Basin populations. A new sub-clade, L3f2, is described, which together with L3e5 is most probably autochthonous in the Chad Basin. The phylogeography of these two sub-haplogroups seems to indicate prehistoric expansion events in the Chad Basin around 28,950 and 11,400 Y.B.P., respectively. The distribution of L3f2 is virtually restricted to the Chad Basin alone, and in particular to Chadic speaking populations, while L3e5 shows evidence for diffusion into North Africa at about 7,100 Y.B.P. The absence of L3f2 and L3e5 in African-Americans, and the limited number of L-haplotypes shared between the Chad Basin populations and African-Americans, indicate the low contribution of the Chad region to the Atlantic slave trade.
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Affiliation(s)
- V Cerný
- Department of Anthropology and Environment, Institute of Archaeology, Czech Academy of Sciences, 118 01 Prague 1, Czech Republic.
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45
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Pereira L, Gonçalves J, Franco-Duarte R, Silva J, Rocha T, Arnold C, Richards M, Macaulay V. No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males. Mol Biol Evol 2007; 24:868-74. [PMID: 17218641 DOI: 10.1093/molbev/msm004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The first complete mitochondrial DNA (mtDNA) sequences (approximately 16,569 bp) in 20 patients with asthenozoospermia and a comparison with 23 new complete mtDNA sequences in teratoasthenozoospermic individuals, confirmed no sharing of specific polymorphisms or specific mitochondrial lineages between these individuals. This is strong evidence against the accepted claim of a major role played by mtDNA in male fertility, once supported by haplogroup association studies based on the screening of hypervariable region I. The hypothesis of maternally driven selection acting in male reproductive success must thus be treated with caution.
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Affiliation(s)
- Luísa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, (IPATIMUP), Porto, Portugal.
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Endicott P, Metspalu M, Stringer C, Macaulay V, Cooper A, Sanchez JJ. Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PLoS One 2006; 1:e81. [PMID: 17218991 PMCID: PMC1766372 DOI: 10.1371/journal.pone.0000081] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 10/30/2006] [Indexed: 11/18/2022] Open
Abstract
The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups approximately 30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity.
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Affiliation(s)
- Phillip Endicott
- Department of Zoology, University of Oxford Oxford, United Kingdom.
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Kang D, Hamasaki N. Mitochondrial disease: maintenance of mitochondrial genome and molecular diagnostics. Adv Clin Chem 2006; 42:217-54. [PMID: 17131628 DOI: 10.1016/s0065-2423(06)42006-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) is essential for the aerobic ATP synthesis system that is responsible for about 80% of normal cellular energy demands. In addition to rare genetic disorders causing neuromyopathy, alterations of mtDNA have been found also in so-called common diseases such as heart failure, diabetes, and cancer. Although some of these alterations are inherited, some are considered to be generated and/or accumulated in somatic cells with age. One reason for the somatic mutations is that mtDNA is more vulnerable than is nuclear DNA. For example, mitochondrial respiratory chain produces a large amount of reactive oxygen species as inevitable byproducts of oxidative phosphorylation. However, the molecular mechanisms for maintenance of mitochondrial genome are much less elucidated than those for nuclear genome. In spite of its increasing importance, the molecular diagnosis of mitochondrial DNA-related diseases is well done only in very limited expert laboratories. In this chapter, we focus on maintenance of mtDNA in somatic cells, its clinical importance, and recent developments of molecular tests.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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Raule N, Sevini F, Santoro A, Altilia S, Franceschi C. Association studies on human mitochondrial DNA: methodological aspects and results in the most common age-related diseases. Mitochondrion 2006; 7:29-38. [PMID: 17306632 DOI: 10.1016/j.mito.2006.11.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 09/21/2006] [Indexed: 11/15/2022]
Abstract
Mitochondrial DNA (mtDNA) follows direct maternal inheritance and, as such, can be used in phylogenetic studies to determine a human lineage tree. The presence of common polymorphisms allows a classification of mtDNA in haplogroups and sub-haplogroups, according to the branch they belong to. Thanks to the rapidly growing number of mtDNA sequences available, this classification is being corrected and redefined to be more accurate. In parallel with this process, several studies are trying to identify an association between common mtDNA polymorphisms and common complex traits, as hypothesized by the common disease-common variant theory. Here we review the associations already reported with the main age-related complex diseases and we identify the critical points (sample size, size of the recruiting area, careful matching between cases and controls regarding geographical origin and ethnicity, data quality checking) to be taken in account in planning such studies. On the whole, this research area is opening a new perspective as an important component of "mitochondrial medicine", capable of identifying new molecular targets for the diagnosis, prevention and treatment of common complex diseases.
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Affiliation(s)
- Nicola Raule
- Centro Interdipartimentale L. Galvani, via S. Giacomo 12, 40126 Bologna, Italy.
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49
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Alvarez-Iglesias V, Jaime JC, Carracedo A, Salas A. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Sci Int Genet 2006; 1:44-55. [PMID: 19083727 DOI: 10.1016/j.fsigen.2006.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/15/2006] [Accepted: 09/17/2006] [Indexed: 11/30/2022]
Abstract
We have developed a single PCR multiplex SNaPshot reaction that consists of 32 coding region SNPs that allows (i) increasing the discrimination power of the mitochondrial DNA (mtDNA) typing in forensic casework, and (ii) haplogroup assignments of mtDNA profiles in both human population studies (e.g. anthropological) and medical research. The selected SNPs target the East Asian phylogeny, including its Native American derived branches. We have validated this multiplex assay by genotyping a sample of East Asians (Taiwanese) and Native Americans (Argentineans). In addition to the coding SNP typing, we have sequenced the complete control region for the same samples. The genotyping results (control region plus SNaPshot profiles) are in good agreement with previous human population genetic studies (based on e.g. complete sequencing) and the known mtDNA phylogeny. We observe that the SNaPshot method is reliable, rapid, and cost effective in comparison with other techniques of multiplex SNP genotyping. We discuss the advantages of our SNP genotyping selection with respect to previous attempts, and we highlight the importance of using the known mtDNA phylogeny as a framework for SNP profile interpretation and as a tool to minimize genotyping errors.
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Affiliation(s)
- V Alvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
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50
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Bandelt HJ, Yao YG, Salas A, Kivisild T, Bravi CM. High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients. Biochem Biophys Res Commun 2006; 352:283-91. [PMID: 17123466 DOI: 10.1016/j.bbrc.2006.10.131] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 10/25/2006] [Indexed: 11/18/2022]
Abstract
For identifying mutation(s) that are potentially pathogenic it is essential to determine the entire mitochondrial DNA (mtDNA) sequences from patients suffering from a particular mitochondrial disease, such as Leber hereditary optic neuropathy (LHON). However, such sequencing efforts can, in the worst case, be riddled with errors by imposing phantom mutations or misreporting variant nucleotides, and moreover, by inadvertently regarding some mutations as novel and pathogenic, which are actually known to define minor haplogroups. Under such circumstances it remains unclear whether the disease-associated mutations would have been determined adequately. Here, we re-analyse four problematic LHON studies and propose guidelines by which some of the pitfalls could be avoided.
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