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Yang Z, Slone J, Huang T. Next-Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy. Curr Protoc 2022; 2:e412. [PMID: 35532282 DOI: 10.1002/cpz1.412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a very important role in many crucial cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondrial genomes. Mutant and wild-type mitochondrial DNA (mtDNA) may co-exist as heteroplasmy and cause human disease. The purpose of the protocols in this article is to simultaneously determine the mtDNA sequence and quantify the heteroplasmy level using parallel sequencing. The protocols include mitochondrial genomic DNA PCR amplification of two full-length products using two distinct sets of PCR primers. The PCR products are mixed at an equimolar ratio, and the samples are then barcoded and sequenced with high-throughput next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree/level of heteroplasmy. © 2022 Wiley Periodicals LLC. Basic Protocol 1: PCR amplification of mitochondrial DNA Basic Protocol 2: Analysis of next-generation sequencing of mitochondrial DNA Basic Protocol 3: Mutect2 pipeline for automated sample processing and large-scale data analysis.
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Affiliation(s)
- Zeyu Yang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jesse Slone
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Taosheng Huang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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2
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Barcia G, Assouline Z, Magen M, Pennisi A, Rötig A, Munnich A, Bonnefont JP, Steffann J. Improving post-natal detection of mitochondrial DNA mutations. Expert Rev Mol Diagn 2020; 20:1003-1008. [PMID: 32902337 DOI: 10.1080/14737159.2020.1820326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Currently, genetic testing of mitochondrial DNA mutations includes screening for single-nucleotide variants, several base pair insertions or deletions, large-scale deletions, or relative depletion of total mitochondrial DNA content. Within the last decade, next-generation sequencing (NGS) has resulted in remarkable advances in the field of mitochondrial diseases (MD) and has become a routine step of the diagnostic workup. AREAS COVERED We aimed to present an overview of current technologies employed in molecular diagnosis of mitochondrial DNA diseases. We report on the recent contributions of NGS testing to the diagnosis and understanding of MD. EXPERT OPINION The progress of NGS technologies allows the simultaneous detection of mutations and quantification of the heteroplasmy level, ensuring sensitivity and specificity requested for the detection of mitochondrial DNA point mutations. NGS protocols enabling the simultaneous analysis of mitochondrial and nuclear DNA are now efficient and cost-saving approaches, and have become the gold-standard technique in diagnostic laboratories.
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Affiliation(s)
- Giulia Barcia
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Zahra Assouline
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Maryse Magen
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Alessandra Pennisi
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Agnès Rötig
- Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Arnold Munnich
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Jean-Paul Bonnefont
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Julie Steffann
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
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3
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Yin C, Liu Y, Guo X, Li D, Fang W, Yang J, Zhou F, Niu W, Jia Y, Yang H, Xing J. An Effective Strategy to Eliminate Inherent Cross-Contamination in mtDNA Next-Generation Sequencing of Multiple Samples. J Mol Diagn 2019; 21:593-601. [PMID: 31026598 DOI: 10.1016/j.jmoldx.2019.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/25/2018] [Accepted: 02/19/2019] [Indexed: 12/29/2022] Open
Abstract
Heteroplasmic mutations in mitochondrial DNA (mtDNA) play critical roles in mitochondrial disease, aging, and cancer. Recently, next-generation sequencing (NGS) has been widely used to detect mtDNA mutations for diagnosis and monitoring of the above-mentioned diseases. However, little attention is paid on inherent cross-contamination generated during mtDNA capture and sequencing of mixed samples, which may seriously reduce the detection accuracy of mtDNA heteroplasmic mutations. In this study, a novel sequencing strategy based on a unique double-barcode design was established. The results showed that when single barcode-based analysis strategy was used, cross-contamination level of 20 DNA samples ranged from 0.27% to 11.90% on HiSeq 2500 and from 0.93% to 17.70% on HiSeq X ten, whereas double barcode-based strategy could effectively eliminate cross-contamination. Moreover, the data indicated that cross-contamination was mainly derived from capture process and was significantly affected by different NGS platforms. In addition, contamination level was negatively related to sequencing depth. Moreover, cross-contamination significantly increased the false-positive calling of mtDNA heteroplasmic mutations and remarkably affected the heteroplasmy level of mtDNA mutations. In contrast, cross-contamination had no notable effect on classification of mtDNA haplogroup. Taken together, our novel double barcode-based sequencing strategy is effective in eliminating cross-contamination, enhancing the detection accuracy of mtDNA NGS, and improving its application in diagnosis or monitoring of diseases associated with mtDNA mutations.
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Affiliation(s)
- Chun Yin
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Deyang Li
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Wan Fang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Jin Yang
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi'an, China
| | - Feng Zhou
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China; Department of General Surgery, Huaihai Hospital, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wancheng Niu
- Department of General Surgery, Huaihai Hospital, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, China
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China.
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Zhang Y, Kaynak A, Huang T, Esfandiari L. A rapid bioanalytical tool for detection of sequence-specific circular DNA and mitochondrial DNA point mutations. Anal Bioanal Chem 2019; 411:1935-1941. [PMID: 30810791 DOI: 10.1007/s00216-019-01683-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/04/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023]
Abstract
Mutations in mitochondrial DNA (mtDNA) have been an essential cause of numerous diseases, making their identification critically important. The majority of mtDNA screening techniques require polymerase chain reaction (PCR) amplification, enzymatic digestion, and denaturation procedures, which are laborious and costly. Herein, we developed a sensitive PCR-free electrokinetic-based sensor combined with a customized bis-peptide nucleic acid (bis-PNA) and gamma-PNA (γ-PNA) probes immobilized on beads, for the detection of mtDNA point mutations and sequence-specific supercoiled plasmid DNA at the picomolar range. The probes are capable of invading the double-stranded circular DNA and forming a stable triplex structure. Thus, this method can significantly reduce the sample preparation and omit the PCR amplification steps prior to sensing. Further, this bioanalytical tool can open up a new paradigm in clinical settings for the screening of double-stranded circular nucleic acids with a single-base mismatch specificity in a rapid and sensitive manner.
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Affiliation(s)
- Yuqian Zhang
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Ahmet Kaynak
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Taosheng Huang
- Department of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Leyla Esfandiari
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA. .,Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA.
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5
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Palozzi JM, Jeedigunta SP, Hurd TR. Mitochondrial DNA Purifying Selection in Mammals and Invertebrates. J Mol Biol 2018; 430:4834-4848. [DOI: 10.1016/j.jmb.2018.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/20/2018] [Accepted: 10/25/2018] [Indexed: 01/19/2023]
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6
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Abicht A, Scharf F, Kleinle S, Schön U, Holinski-Feder E, Horvath R, Benet-Pagès A, Diebold I. Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method. Mol Genet Genomic Med 2018; 6:1188-1198. [PMID: 30406974 PMCID: PMC6305657 DOI: 10.1002/mgg3.500] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/21/2023] Open
Abstract
Background The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next‐Generation Sequencing (NGS) technology offers a robust high‐throughput platform for nuclear and mitochondrial DNA (mtDNA) analyses. Method We developed a custom Agilent SureSelect Mitochondrial and Nuclear Disease Panel (Mito‐aND‐Panel) capture kit that allows parallel enrichment for subsequent NGS‐based sequence analysis of nuclear mitochondrial disease‐related genes and the complete mtDNA genome. Sequencing of enriched mtDNA simultaneously with nuclear genes was compared with the separated sequencing of the mitochondrial genome and whole exome sequencing (WES). Results The Mito‐aND‐Panel permits accurate detection of low‐level mtDNA heteroplasmy due to a very high sequencing depth compared to standard diagnostic procedures using Sanger sequencing/SNaPshot and WES which is crucial to identify maternally inherited mitochondrial disorders. Conclusion We established a NGS‐based method with combined sequencing of the complete mtDNA and nuclear genes which enables a more sensitive heteroplasmy detection of mtDNA mutations compared to traditional methods. Because the method promotes the analysis of mtDNA variants in large cohorts, it is cost‐effective and simple to setup, we anticipate this is a highly relevant method for sequence‐based genetic diagnosis in clinical diagnostic applications.
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Affiliation(s)
- Angela Abicht
- Medical Genetic Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | | | | | - Rita Horvath
- Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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7
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Albayrak L, Khanipov K, Pimenova M, Golovko G, Rojas M, Pavlidis I, Chumakov S, Aguilar G, Chávez A, Widger WR, Fofanov Y. The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. BMC Genomics 2016; 17:1017. [PMID: 27955616 PMCID: PMC5153897 DOI: 10.1186/s12864-016-3375-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 12/05/2016] [Indexed: 02/03/2023] Open
Abstract
Background Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput sequencing technology has significantly improved the heteroplasmy identification process, the ability of this technology to detect low-abundance mutations can be affected by the presence of similar sequences originating from nuclear DNA (nDNA). To determine to what extent nDNA can cause false positive low-abundance heteroplasmy calls, we have identified mitochondrial locations of all subsequences that are common or similar (one mismatch allowed) between nDNA and mitochondrial DNA (mtDNA). Results Performed analysis revealed up to a 25-fold variation in the lengths of longest common and longest similar (one mismatch allowed) subsequences across the mitochondrial genome. The size of the longest subsequences shared between nDNA and mtDNA in several regions of the mitochondrial genome were found to be as low as 11 bases, which not only allows using these regions to design new, very specific PCR primers, but also supports the hypothesis of the non-random introduction of mtDNA into the human nuclear DNA. Conclusion Analysis of the mitochondrial locations of the subsequences shared between nDNA and mtDNA suggested that even very short (36 bases) single-end sequencing reads can be used to identify low-abundance variation in 20.4% of the mitochondrial genome. For longer (76 and 150 bases) reads, the proportion of the mitochondrial genome where nDNA presence will not interfere found to be 44.5 and 67.9%, when low-abundance mutations at 100% of locations can be identified using 417 bases long single reads. This observation suggests that the analysis of low-abundance variations in mitochondria population can be extended to a variety of large data collections such as NCBI Sequence Read Archive, European Nucleotide Archive, The Cancer Genome Atlas, and International Cancer Genome Consortium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3375-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark Rojas
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Ioannis Pavlidis
- Department of Computer Science, University of Houston, Houston, TX, USA
| | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Gerardo Aguilar
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Arturo Chávez
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - William R Widger
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA. .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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8
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Quantitative assessment of heteroplasmy of mitochondrial genome: perspectives in diagnostics and methodological pitfalls. BIOMED RESEARCH INTERNATIONAL 2014; 2014:292017. [PMID: 24818137 PMCID: PMC4003915 DOI: 10.1155/2014/292017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/14/2014] [Indexed: 11/17/2022]
Abstract
The role of alterations of mitochondrial DNA (mtDNA) in the development of human pathologies is not understood well. Most of mitochondrial mutations are characterized by the phenomenon of heteroplasmy which is defined as the presence of a mixture of more than one type of an organellar genome within a cell or tissue. The level of heteroplasmy varies in wide range, and the expression of disease is dependent on the percent of alleles bearing mutations, thus allowing consumption that an upper threshold level may exist beyond which the mitochondrial function collapses. Recent findings have demonstrated that some mtDNA heteroplasmic mutations are associated with widely spread chronic diseases, including atherosclerosis and cancer. Actually, each etiological mtDNA mutation has its own heteroplasmy threshold that needs to be measured. Therefore, quantitative evaluation of a mutant allele of mitochondrial genome is an obvious methodological challenge, since it may be a keystone for diagnostics of individual genetic predisposition to the disease. This review provides a comprehensive comparison of methods applicable to the measurement of heteroplasmy level of mitochondrial mutations associated with the development of pathology, in particular, in atherosclerosis and its clinical manifestations.
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9
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Yen HC, Li SL, Hsu WC, Tang P. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system. PLoS One 2014; 9:e92817. [PMID: 24664244 PMCID: PMC3963942 DOI: 10.1371/journal.pone.0092817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/25/2014] [Indexed: 01/02/2023] Open
Abstract
High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.
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Affiliation(s)
- Hsiu-Chuan Yen
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- * E-mail:
| | - Shiue-Li Li
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Wei-Chien Hsu
- Department and Graduate Institute of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Petrus Tang
- Department of Public Health and Parasitology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
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10
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Barić I, Fumić K, Petković Ramadža D, Sperl W, Zimmermann FA, Muačević-Katanec D, Mitrović Z, Pažanin L, Cvitanović Šojat L, Kekez T, Reiner Z, Mayr JA. Mitochondrial myopathy associated with a novel 5522G>A mutation in the mitochondrial tRNA(Trp) gene. Eur J Hum Genet 2013; 21:871-5. [PMID: 23232693 PMCID: PMC3722682 DOI: 10.1038/ejhg.2012.272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/22/2012] [Accepted: 11/13/2012] [Indexed: 12/31/2022] Open
Abstract
We report a novel pathogenic mutation of the mitochondrial transfer RNA (tRNA) gene for tryptophan in a patient with isolated myopathy and persistently elevated creatine kinase. Muscle studies revealed ragged red fibres and decreased activity of respiratory chain complex I and cytochrome c oxidase (COX). Sequencing of the 22 mitochondrial tRNA genes revealed a mutation m.5522G>A, which alters a conserved base pairing in the D-stem of the tRNA for tryptophan. The mutation was heteroplasmic with a mutational load between 88 and 99% in COX-negative fibres. This case contributes to the genetic heterogeneity of mitochondrial diseases caused by mutations in mitochondrial tRNA genes.
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Affiliation(s)
- Ivo Barić
- Department of Paediatrics, University Hospital Centre Zagreb, Zagreb, Croatia.
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11
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Sobenin IA, Sazonova MA, Postnov AY, Salonen JT, Bobryshev YV, Orekhov AN. Association of mitochondrial genetic variation with carotid atherosclerosis. PLoS One 2013; 8:e68070. [PMID: 23874496 PMCID: PMC3706616 DOI: 10.1371/journal.pone.0068070] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 05/24/2013] [Indexed: 11/26/2022] Open
Abstract
In human pathology, several diseases are associated with somatic mutations in the mitochondrial genome (mtDNA). Even though mitochondrial dysfunction leads to increased oxidative stress, the role of mitochondrial mutations in atherosclerosis has not received much attention so far. In this study we analyzed the association of mitochondrial genetic variation with the severity of carotid atherosclerosis, as assessed by carotid intima-media thickness (cIMT) and the presence of coronary heart disease (CHD) in 190 subjects from Moscow, Russia, a population with high CHD occurrence. cIMT was measured by high-resolution B-mode ultrasonography and mtDNA heteroplasmies by a pyrosequencing-based method. We found that heteroplasmies for several mutations in the mtDNA in leukocytes, including C3256T, T3336C, G12315A, G13513A, G14459A, G14846A, and G15059A mutations, were significantly (p<0.001) associated with both the severity of carotid atherosclerosis and the presence of CHD. These findings indicate that somatic mitochondrial mutations have a role in the development of atherosclerosis.
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Affiliation(s)
- Igor A. Sobenin
- Russian Cardiology Research and Production Complex, Moscow, Russia
- Institute of General Pathology and Pathophysiology, Moscow, Russia
| | | | - Anton Y. Postnov
- Russian Cardiology Research and Production Complex, Moscow, Russia
| | - Jukka T. Salonen
- MAS-Metabolic Analytical Services Oy, Helsinki, Finland
- University of Helsinki, Hjelt Institute, Helsinki, Finland
| | - Yuri V. Bobryshev
- Institute for Atherosclerosis Research, Skolkovo Innovation Center, Moscow, Russia
- Faculty of Medicine, University of New South Wales and St Vincent’s Hospital Sydney, Kensington, New South Wales, Australia
| | - Alexander N. Orekhov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
- Institute for Atherosclerosis Research, Skolkovo Innovation Center, Moscow, Russia
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Dakubo GD. Mitochondrial genome analysis in biofluids for early cancer detection and monitoring. ACTA ACUST UNITED AC 2013; 2:263-75. [PMID: 23495657 DOI: 10.1517/17530059.2.3.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Biofluids collected in a non-invasive fashion are potentially valuable samples for assaying genomic alterations for early detection and monitoring of cancer. The low cellularity and nucleic acid content in biofluids, the high copy number of the mitochondrial genome (mtgenome) and its noted early imprints in cancer make this molecule theoretically more sensitive than nuclear targets to measure for early cancer detection. OBJECTIVE This review explores mtgenome analysis in biofluids and addresses the question of whether targeting the mtgenome in biofluids is superior or equivalent to analysis of nuclear genomic alterations. METHODS The literature was retrieved from PubMed using a combination of the following keywords: mtDNA, mutation, deletion, content, copy number, cancer, biofluids, bodily fluids and the specific cancers described here. Studies that analyzed mtgenome alterations in biofluids were included. Analytical methods available for assaying mtgenome changes in biofluids are discussed. RESULTS Despite the limited data available, mtgenome changes in biofluids have been demonstrated in a wide variety of cancer patients. CONCLUSION Mtgenome analysis in biofluids is feasible and relatively easy. Despite the paucity of data, tumor-specific mtgenome changes are observed in biofluids of cancer patients. Given the multiple copies per cell of the mtgenome, future cancer detection efforts should consider complementary analysis of mtgenome changes in biofluids.
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Affiliation(s)
- Gabriel D Dakubo
- Senior Scientist Genesis Genomics, Inc., 290 Munro Street, Ste 1000, Thunder Bay, Ontario, P7A 7T1, Canada +1 807 768 4516 ; +1 807 346 8105 ;
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13
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Parr RL, Jakupciak JP, Birch-Machin MA, Dakubo GD. The mitochondrial genome: a biosensor for early cancer detection? ACTA ACUST UNITED AC 2013; 1:169-82. [PMID: 23489304 DOI: 10.1517/17530059.1.2.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mutations in the mitochondrial genome have been reported as biomarkers for the detection of cancer. Hallmarks of cancer development include the accumulation of genetic alterations in the mitochondrial and nuclear genomes. Damage to mitochondria affects energy metabolism, generation of reactive oxygen species, apoptosis, cell growth and other processes that contribute to the neoplastic process. Furthermore, mitochondrial DNA mutations occur frequently in cancer. Little work has been done to link a pathway between mitochondrial mutations and cancer etiology. Volumes of work have been reported on the association of mitochondrial mutations and almost all types of cancer including the use of body fluids for early detection. This review examines the measurement of mitochondrial mutations for the application of detecting human tumor tissue.
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Affiliation(s)
- Ryan L Parr
- Vice President of Research, Genesis Genomics, Inc., 290 Munro Street, Ste 1000, Thunder Bay, Ontario, P7A 7T1, Canada +1 807 346 8100; +1 807 346 8105 ;
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Calatayud M, Ramos A, Santos C, Aluja MP. Primer effect in the detection of mitochondrial DNA point heteroplasmy by automated sequencing. ACTA ACUST UNITED AC 2013; 24:303-11. [PMID: 23350969 DOI: 10.3109/19401736.2012.760072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The correct detection of mitochondrial DNA (mtDNA) heteroplasmy by automated sequencing presents methodological constraints. The main goals of this study are to investigate the effect of sense and distance of primers in heteroplasmy detection and to test if there are differences in the accurate determination of heteroplasmy involving transitions or transversions. A gradient of the heteroplasmy levels was generated for mtDNA positions 9477 (transition G/A) and 15,452 (transversion C/A). Amplification and subsequent sequencing with forward and reverse primers, situated at 550 and 150 bp from the heteroplasmic positions, were performed. Our data provide evidence that there is a significant difference between the use of forward and reverse primers. The forward primer is the primer that seems to give a better approximation to the real proportion of the variants. No significant differences were found concerning the distance at which the sequencing primers were placed neither between the analysis of transitions and transversions. The data collected in this study are a starting point that allows to glimpse the importance of the sequencing primers in the accurate detection of point heteroplasmy, providing additional insight into the overall automated sequencing strategy.
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Affiliation(s)
- Marta Calatayud
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
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Mueller EE, Brunner SM, Mayr JA, Stanger O, Sperl W, Kofler B. Functional differences between mitochondrial haplogroup T and haplogroup H in HEK293 cybrid cells. PLoS One 2012; 7:e52367. [PMID: 23300652 PMCID: PMC3530588 DOI: 10.1371/journal.pone.0052367] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 11/15/2012] [Indexed: 12/20/2022] Open
Abstract
Background Epidemiological case-control studies have revealed associations between mitochondrial haplogroups and the onset and/or progression of various multifactorial diseases. For instance, mitochondrial haplogroup T was previously shown to be associated with vascular diseases, including coronary artery disease and diabetic retinopathy. In contrast, haplogroup H, the most frequent haplogroup in Europe, is often found to be more prevalent in healthy control subjects than in patient study groups. However, justifications for the assumption that haplogroups are functionally distinct are rare. Therefore, we attempted to compare differences in mitochondrial function between haplogroup H and T cybrids. Methodology/Principal Findings Mitochondrial haplogroup H and T cybrids were generated by fusion of HEK293 cells devoid of mitochondrial DNA with isolated thrombocytes of individuals with the respective haplogroups. These cybrid cells were analyzed for oxidative phosphorylation (OXPHOS) enzyme activities, mitochondrial DNA (mtDNA) copy number, growth rate and susceptibility to reactive oxygen species (ROS). We observed that haplogroup T cybrids have higher survival rate when challenged with hydrogen peroxide, indicating a higher capability to cope with oxidative stress. Conclusions/Significance The results of this study show that functional differences exist between HEK293 cybrid cells which differ in mitochondrial genomic background.
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Affiliation(s)
- Edith E. Mueller
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Susanne M. Brunner
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Johannes A. Mayr
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Olaf Stanger
- Department of Cardiac Surgery, Paracelsus Medical University, Salzburg, Austria
| | - Wolfgang Sperl
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Barbara Kofler
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
- * E-mail:
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Koh HR, Han KY, Jung J, Kim SK. Quantitative genotyping of single nucleotide polymorphism by single-molecule multi-color fluorescence resonance energy transfer. Chem Commun (Camb) 2011; 47:10362-4. [PMID: 21847490 DOI: 10.1039/c1cc12737c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a new single nucleotide polymorphism (SNP) genotyping method based on single-molecule multi-color fluorescence resonance energy transfer (FRET). We demonstrated that this new method uses less than 1 fmol of sample and is also highly quantitative with a detection level of 1% or lower in the minor allele fraction.
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Affiliation(s)
- Hye Ran Koh
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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Huang T. Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy. CURRENT PROTOCOLS IN HUMAN GENETICS 2011; Chapter 19:19.8.1-19.8.12. [PMID: 21975941 PMCID: PMC4687495 DOI: 10.1002/0471142905.hg1908s71] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This protocol describes the methodology to characterize mitochondrial DNA (mtDNA) heteroplasmy by parallel sequencing. Mitochondria play an important role in essential cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. Mutant and wild-type mtDNA may co-exist as heteroplasmy, and cause human disease. The purpose of this protocol is to simultaneously determine mtDNA sequence and quantify the heteroplasmic level. This protocol includes a two-fragment mitochondrial genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples are then barcoded and sequenced with high-throughput, next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the level of heteroplasmy.
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Affiliation(s)
- Taosheng Huang
- Division of Human Genetics/Department of Pediatrics; Center for Molecular and Mitochondrial Medicine and Genetics; University of California, Irvine, CA, 92697
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18
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Ancient voyaging and Polynesian origins. Am J Hum Genet 2011; 88:239-47. [PMID: 21295281 DOI: 10.1016/j.ajhg.2011.01.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 01/02/2023] Open
Abstract
The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.
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Pilch J, Asman M, Jamroz E, Kajor M, Kotrys-Puchalska E, Goss M, Krzak M, Witecka J, Gmiński J, Sieroń AL. Surveyor nuclease detection of mutations and polymorphisms of mtDNA in children. Pediatr Neurol 2010; 43:325-30. [PMID: 20933175 DOI: 10.1016/j.pediatrneurol.2010.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 01/27/2010] [Accepted: 05/26/2010] [Indexed: 10/19/2022]
Abstract
Mitochondrial encephalomyopathies are complex disorders with wide range of clinical manifestations. Particularly time-consuming is the identification of mutations in mitochondrial DNA. A group of 20 children with clinical manifestations of mitochondrial encephalomyopathies was selected for molecular studies. The aims were (a) to identify mutations in mtDNA isolated from muscle and (b) to verify detected mutations in DNA isolated from blood, in order to assess the utility of a Surveyor nuclease assay kit for patient screening. The most common changes found were polymorphisms, including a few missense mutations altering the amino acid sequence of mitochondrial proteins. In two boys with MELAS (i.e., mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), a mutation A→G3243 was detected in the tRNALeu gene of mtDNA isolated from muscle and blood. In one boy, the carrier status of his mother was confirmed, based on molecular analysis of DNA isolated from blood. A method using Surveyor nuclease allows systematic screening for small mutations in mtDNA, using as its source blood of the patients and asymptomatic carriers. The method still requires confirmation studying a larger group. In some patients, the use of this method should precede and might limit indications for traumatic muscle and skin biopsy.
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Affiliation(s)
- Jacek Pilch
- Department of Child Neurology, Medical University of Silesia, ul. Medyków 16, Katowice, Poland.
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Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 2010; 87:237-49. [PMID: 20696290 PMCID: PMC2917713 DOI: 10.1016/j.ajhg.2010.07.014] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 11/29/2022] Open
Abstract
Heteroplasmy, the existence of multiple mtDNA types within an individual, has been previously detected by using mostly indirect methods and focusing largely on just the hypervariable segments of the control region. Next-generation sequencing technologies should enable studies of heteroplasmy across the entire mtDNA genome at much higher resolution, because many independent reads are generated for each position. However, the higher error rate associated with these technologies must be taken into consideration to avoid false detection of heteroplasmy. We used simulations and phiX174 sequence data to design criteria for accurate detection of heteroplasmy with the Illumina Genome Analyzer platform, and we used artificial mixtures and replicate data to test and refine the criteria. We then applied these criteria to mtDNA sequence reads for 131 individuals from five Eurasian populations that had been generated via a parallel tagged approach. We identified 37 heteroplasmies at 10% frequency or higher at 34 sites in 32 individuals. The mutational spectrum does not differ between heteroplasmic mutations and polymorphisms in the same individuals, but the relative mutation rate at heteroplasmic mutations is significantly higher than that estimated for all mutable sites in the human mtDNA genome. Moreover, there is also a significant excess of nonsynonymous mutations observed among heteroplasmies, compared to polymorphism data from the same individuals. Both mutation-drift and negative selection influence the fate of heteroplasmies to determine the polymorphism spectrum in humans. With appropriate criteria for avoiding false positives due to sequencing errors, next-generation technologies can provide novel insights into genome-wide aspects of mtDNA heteroplasmy.
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Affiliation(s)
- Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Anna Schönberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Michael Schaefer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Roland Schroeder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Ivane Nasidze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
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Yen HC, Hsu WC, Lin CL, Chen GW, Huang YH. Advantages and considerations in the confirmation of mitochondrial DNA mutations by denaturing HPLC and pyrosequencing. Ann N Y Acad Sci 2010; 1201:13-20. [DOI: 10.1111/j.1749-6632.2010.05626.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. Biotechniques 2010; 48:287-96. [DOI: 10.2144/000113389] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Characterization of human mitochondrial genome sequences is important for the molecular diagnosis of mitochondrial diseases, especially in samples with a low level of mitochondrial DNA (mtDNA) heteroplasmy (≥5%). Currently, no single methodology can simultaneously determine complete mtDNA sequences, identify mitochondrial genome–wide heteroplasmies, and quantify mtDNA heteroplasmy levels. The deep sampling inherent in “next-generation” sequencing approaches should enable the efficient detection of low-level DNA heteroplasmies and address this need. Herein, we used the Illumina Genome Analyzer to re-sequence human mtDNA samples from two subjects that were combined at five different ratios (1:99, 5:95, 10:90, 20:80, and 50:50). We assessed the sensitivity, specificity, and accuracy of this system, and our results show that mtDNA heteroplasmies ≥5% were detected 100% of the time with virtually no false positives and that the estimates of mtDNA heteroplasmy levels were remarkably close to the theoretical values (correlation coefficient = 0.96). Therefore, parallel sequencing provides a simple, high-throughput, and cost-effective platform for mitochondrial genome sequencing with sensitivity and specificity for mtDNA heteroplasmy detection.
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Kato T, Nishigaki Y, Noguchi Y, Ueno H, Hosoya H, Ito T, Kimura Y, Kitamura K, Tanaka M. Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss. J Hum Genet 2010; 55:147-54. [DOI: 10.1038/jhg.2009.143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Extensive screening system using suspension array technology to detect mitochondrial DNA point mutations. Mitochondrion 2010; 10:300-8. [PMID: 20064630 DOI: 10.1016/j.mito.2010.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/25/2009] [Accepted: 01/05/2010] [Indexed: 11/21/2022]
Abstract
We established an extensive and rapid system using suspension array to detect 61 representative mitochondrial DNA (mtDNA) heteroplasmic or homoplasmic point mutations (29 for Series A and 32 for Series B) in 22 genes: 1 each in MT-RNR1, -TV, -ND1, -TQ, -TW, -TC, and -TH genes; 2 each in MT-TN, -TG, -ND4, -TL2, -TE, and -CYB genes; 3 each in MT-ATP6, -ND3, and -ND5 genes; 4 each in MT-CO1 and -TK genes; 5 each in MT-TI, -TS1, and -ND6 genes; and 10 in the MT-TL1 gene. We carefully selected 5'-biotinylated primers and pooled primers for use in two sets of multiplex-PCR amplifications. To detect both mutant and wild-type mtDNA, even when polymorphisms were present near the target mutation sites, we designed specific oligonucleotide probes. By using the mtDNA point mutation detection system of Series A (29 mutations) and Series B (32 mutations), we screened a total of 3103 mutant sites in 107 DNA samples for Series A and 13,101 mutant sites in 397 DNA samples for Series B. We succeeded in determining 99.4% (Series A) and 99.6% (Series B) of the targeted mutant sites by use of the system. The 22 samples with the m.3243A>G heteroplasmic mutation revealed positive signals with both mutant- and wild-type-specific probes in this detection system with a detection limit of approximately 2%. This genetic screening platform is useful to reach a definitive diagnosis for mitochondrial diseases.
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Determination of DNA mutation load in human tissues using denaturing HPLC-based heteroduplex analysis. Methods Mol Biol 2009. [PMID: 19513681 DOI: 10.1007/978-1-59745-521-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Since its introduction more than a decade ago, denaturing HPLC has been widely used to screen nuclear and mitochondrial DNA for mutations. We recently developed a quantitative method based on denaturing HPLC to measure DNA mutation load, using tRNA Leu(UUR) region of the mitochondrial DNA as an example. The mutation load is determined based on the quadratic function that governs DNA reannealing and the formation of heteroduplex and homoduplex DNAs. We have used this assay to measure heteroplasmy level for several mitochondrial mutations in DNAs obtained from human tissue samples. This quantitative DHPLC assay is well suited for simultaneous detection and quantification of DNA mutations.
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Kraytsberg Y, Bodyak N, Myerow S, Nicholas A, Ebralidze K, Khrapko K. Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR. Methods Mol Biol 2009; 554:329-69. [PMID: 19513684 DOI: 10.1007/978-1-59745-521-3_21] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial genome integrity is an important issue in somatic mitochondrial genetics. Development of quantitative methods is indispensable to somatic mitochondrial genetics as quantitative studies are required to characterize heteroplasmy and mutation processes, as well as their effects on phenotypic developments. Quantitative studies include the identification and measurement of the load of pathogenic and non-pathogenic clonal mutations, screening mitochondrial genomes for mutations in order to determine the mutation spectra and characterize an ongoing mutation process. Single-molecule PCR (smPCR) has been shown to be an effective method that can be applied to all areas of quantitative studies. It has distinct advantages over conventional vector-based cloning techniques avoiding the well-known PCR-related artifacts such as the introduction of artificial mutations, preferential allelic amplifications, and "jumping" PCR. smPCR is a straightforward and robust method, which can be effectively used for molecule-by-molecule mutational analysis, even when mitochondrial whole genome (mtWG) analysis is involved. This chapter describes the key features of the smPCR method and provides three examples of its applications in single-cell analysis: di-plex smPCR for deletion quantification, smPCR cloning for clonal point mutation quantification, and smPCR cloning for whole genome sequencing (mtWGS).
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Affiliation(s)
- Yevgenya Kraytsberg
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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Betsalel OT, van de Kamp JM, Martínez-Muñoz C, Rosenberg EH, de Brouwer APM, Pouwels PJW, van der Knaap MS, Mancini GMS, Jakobs C, Hamel BCJ, Salomons GS. Detection of low-level somatic and germline mosaicism by denaturing high-performance liquid chromatography in a EURO-MRX family with SLC6A8 deficiency. Neurogenetics 2008; 9:183-90. [DOI: 10.1007/s10048-008-0125-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 02/25/2008] [Indexed: 11/28/2022]
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Mayr JA, Meierhofer D, Zimmermann F, Feichtinger R, Kögler C, Ratschek M, Schmeller N, Sperl W, Kofler B. Loss of complex I due to mitochondrial DNA mutations in renal oncocytoma. Clin Cancer Res 2008; 14:2270-5. [PMID: 18413815 DOI: 10.1158/1078-0432.ccr-07-4131] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
PURPOSE Many solid tumors exhibit abnormal aerobic metabolism characterized by increased glycolytic capacity and decreased cellular respiration. Recently, mutations in the nuclear encoded mitochondrial enzymes fumarate hydratase and succinate dehydrogenase have been identified in certain tumor types, thus demonstrating a direct link between mitochondrial energy metabolism and tumorigenesis. Although mutations in the mitochondrial genome (mitochondrial DNA, mtDNA) also can affect aerobic metabolism and mtDNA alterations are frequently observed in tumor cells, evidence linking respiratory chain deficiency in a specific tumor type to a specific mtDNA mutation has been lacking. EXPERIMENTAL DESIGN To identify mitochondrial alterations in oncocytomas, we investigated the activities of respiratory chain enzymes and sequenced mtDNA in 15 renal oncocytoma tissues. RESULTS Here, we show that loss of respiratory chain complex I (NADH/ubiquinone oxidoreductase) is associated with renal oncocytoma. Enzymatic activity of complex I was undetectable or greatly reduced in the tumor samples (n = 15). Blue Native gel electrophoresis of the multisubunit enzyme complex revealed a lack of assembled complex I. Mutation analysis of the mtDNA showed frame-shift mutations in the genes of either subunit ND1, ND4, or ND5 of complex I in 9 of the 15 tumors. CONCLUSION Our data indicate that isolated loss of complex I is a specific feature of renal oncocytoma and that this deficiency is frequently caused by somatic mtDNA mutations.
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Affiliation(s)
- Johannes A Mayr
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
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Ballana E, Govea N, de Cid R, Garcia C, Arribas C, Rosell J, Estivill X. Detection of unrecognized low-level mtDNA heteroplasmy may explain the variable phenotypic expressivity of apparently homoplasmic mtDNA mutations. Hum Mutat 2008; 29:248-57. [PMID: 17999439 DOI: 10.1002/humu.20639] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations are an important cause of human disease. Most mtDNA mutations are found in heteroplasmy, in which the proportion of mutant vs. wild-type species is believed to explain some of the observed high phenotypic heterogeneity. However, homoplasmic mutations also observe phenotypic heterogeneity, which may be in part due to undetected low levels of heteroplasmy. In the present report, we have developed two assays, using DHPLC and Pyrosequencing (Biotage AB, Uppsala, Sweden), for reliably and accurately detecting low-level mtDNA heteroplasmy. Using these assays we have identified a three-generation family segregating two mtDNA mutations in heteroplasmy: the deafness-related m.1555A>G mutation in the 12S rRNA gene (MTRNR1) and a new variant (m.15287T>C) in the cytochrome b gene (MTCYB). Both heteroplasmic mtDNA mutations are transmitted through generations in a random manner, thus showing differences in mutation load between siblings within the family. In addition, the developed assays were also used to screen a group of deaf subjects of unknown etiology for the presence of heteroplasmy for both mtDNA variants. Two additional heteroplasmic m.1555A>G samples, previously considered as homoplasmic, and two deaf subjects carrying m.15287T>C variant were identified, thus confirming the high specificity and reliability of the approach. The development of assays for reliably detecting low-level heteroplasmy, together with the study of heteroplasmic mtDNA transmission, are essential steps for a better knowledge and clinical management of mtDNA diseases.
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Affiliation(s)
- Ester Ballana
- Genetic Causes of Disease Group, Genes and Disease Program, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain
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Lim KS, Naviaux RK, Wong S, Haas RH. Pitfalls in the denaturing high-performance liquid chromatography analysis of mitochondrial DNA mutation. J Mol Diagn 2007; 10:102-8. [PMID: 18165269 DOI: 10.2353/jmoldx.2008.070081] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Denaturing high-performance liquid chromatography (DHPLC) purification of heteroduplexes has been reported as a method to increase sensitivity of the detection of low-level heteroplasmy by DNA sequencing, and DHPLC profiling has been suggested as a method to allow the correlation of a characteristic chromatographic profile with a specific sequence alteration. Herein we report pitfalls associated with the use of DHPLC for these purposes. We show that the purified heteroduplex fraction does not contain a 50:50 mix of wild-type and mutant DNA in DNA samples containing low-level mutations, and that with a commonly used protocol, DNA sequencing gave false negative results at the 1% mutation level, potentially leading to misdiagnosis. We improved the protocol to detect low levels of mutations and evaluated the sensitivity of DNA sequencing in the detection of mutation in these fractions. We also studied the DHPLC profiles of several mutations in the tRNALeu(UUR) region of mitochondrial DNA and found a characteristic profile in only one of five mutants tested, whereas four other mutants showed identical chromatographic profiles.
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Affiliation(s)
- Kok Seong Lim
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California, USA.
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Rose G, Passarino G, Scornaienchi V, Romeo G, Dato S, Bellizzi D, Mari V, Feraco E, Maletta R, Bruni A, Franceschi C, De Benedictis G. The mitochondrial DNA control region shows genetically correlated levels of heteroplasmy in leukocytes of centenarians and their offspring. BMC Genomics 2007; 8:293. [PMID: 17727699 PMCID: PMC2014781 DOI: 10.1186/1471-2164-8-293] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 08/29/2007] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Studies on heteroplasmy occurring in the mitochondrial DNA (mtDNA) control region (CR) in leukocytes of centenarians and younger subjects have shown that the C150T somatic transition is over-represented in centenarians. However, whether the occurrence/accumulation of heteroplasmy is a phenotypic consequence of extreme ageing or a genetically controlled event that may favor longevity is a question that deserves further attention. To clarify this point, we set up a Denaturing High Performance Liquid Chromatography (DHPLC) protocol to quantify mtDNA CR heteroplasmy. We then analyzed heteroplasmy in leukocytes of centenarians (100 subjects), their offspring and nieces/nephews (200 subjects, age-range 65-80 years, median age 70 years), and in leukocytes of 114 control subjects sex- and age-matched with the relatives of centenarians. RESULTS The centenarians and their descendants, despite the different ages, showed similar levels of heteroplasmy which were significantly higher than levels in controls. In addition we found that heteroplasmy levels were significantly correlated in parent-offspring pairs (r = 0.263; p = 0.009), but were independent of mtDNA inherited variability (haplogroup and sequence analyses). CONCLUSION Our findings suggest that the high degree of heteroplasmy observed in centenarians is genetically controlled, and that such genetic control is independent of mtDNA variability and likely due to the nuclear genome.
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Affiliation(s)
- Giuseppina Rose
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | | | | | - Giuseppe Romeo
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | - Serena Dato
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | - Dina Bellizzi
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | - Vincenzo Mari
- Italian National Research Center on Ageing (INRCA). 87100 Cosenza, Italy
| | - Emidio Feraco
- Italian National Research Center on Ageing (INRCA). 87100 Cosenza, Italy
| | - Raffaele Maletta
- Regional Neurogenetic Center, ASL 6 Viale Perugini. 88046 Lamezia Terme, Italy
| | - Amalia Bruni
- Regional Neurogenetic Center, ASL 6 Viale Perugini. 88046 Lamezia Terme, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology and Interdepartmental Center L. Galvani, University of Bologna, Bologna, Italy
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Abstract
Abstract
Background: In recent years, denaturing HPLC (DHPLC) has been widely used to screen the whole mitochondrial genome or specific regions of the genome for DNA mutations. The quantification and mathematical modeling of DHPLC results is, however, underexplored.
Methods: We generated site-directed mutants containing some common mutations in the mitochondrial DNA (mtDNA) tRNA(leu) region with different mutation loads and used PCR to amplify the gene segment of interest in these mutants. We then performed restriction digestion followed by slow reannealing to induce heteroduplex formation and analyzed the samples by use of DHPLC.
Results: We observed a quadratic relationship between the heteroduplex peak areas and mutant loads, consistent with the kinetics of heteroduplex formation reported by others. This was modeled mathematically and used to quantify mtDNA mutation load. The method was able to detect a mutation present in a concentration as low as 1% and gave reproducible measurements of the mutations in the range of 2.5%–97.5%.
Conclusion: The quantitative DHPLC assay is well suited for simultaneous detection and quantification of DNA mutations.
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Affiliation(s)
- Kok Seong Lim
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA 92093-0935, USA.
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Oberacher H, Niederstätter H, Pitterl F, Parson W. Profiling 627 mitochondrial nucleotides via the analysis of a 23-plex polymerase chain reaction by liquid chromatography-electrospray ionization time-of-flight mass spectrometry. Anal Chem 2007; 78:7816-27. [PMID: 17105176 DOI: 10.1021/ac061210i] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a rapid and informative mitochondrial DNA profiling system, which has high forensic impact. The assay is based on the analysis of a 23-plex PCR by ion-pair reversed-phase high-performance liquid chromatography online hyphenated to electrospray ionization time-of-flight mass spectrometry (ICEMS). In a single 25-min run, an overall number of 627 nucleotide positions were screened. The vast majority of observed sequence variations were explainable by alterations of the allelic states of the 23 target SNPs, which were selected on their ability to increase forensic discrimination within West Eurasian populations. Within an Austrian population sample comprising 90 unrelated men, 14 different, nontarget SNP-related sequence variations--13 base substitutions and 1 deletion--were detected by ICEMS and confirmed by sequencing. All amplified sequences were located outside of the routinely sequenced hypervariable segments (HVS-I and HVS-II) of the noncoding control region. Accordingly, the genetic information obtained by the 23-plex PCR-ICEMS assay could be combined with HVS-I/HVS-II sequencing results to one highly discriminating mtDNA profile, which covered approximately 7.5% of the total mtDNA genome. With the 23-plex PCR-ICEMS assay, DNA mixtures were detected and the allelic ratios were accurately quantified. The observed robustness and sensitivity underlined the practical applicability of the assay in forensic science, which was proven by typing eight representative casework samples.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
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Wiesbauer M, Meierhofer D, Mayr JA, Sperl W, Paulweber B, Kofler B. Multiplex primer extension analysis for rapid detection of major European mitochondrial haplogroups. Electrophoresis 2007; 27:3864-8. [PMID: 16960846 DOI: 10.1002/elps.200600086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of the human mitochondrial genome is reflected in the existence of ethnically distinct lineages or haplogroups. Alterations of mitochondrial DNA (mtDNA) have been instrumental in studies of human phylogeny, in population genetics, and in molecular medicine to link pathological mutations to a variety of human diseases of complex etiology. For each of these applications, rapid and cost effective assays for mtDNA haplogrouping are invaluable. Here we describe a hierarchical system for mtDNA haplogrouping that combines multiplex PCR amplifications, multiplex single-base primer extensions, and CE for analyzing ten haplogroup-diagnostic mitochondrial single nucleotide polymorphisms. Using this rapid and cost-effective mtDNA genotyping method, we were able to show that within a large, randomly selected cohort of healthy Austrians (n = 1172), mtDNAs could be assigned to all nine major European haplogroups. Forty-four percent belonged to haplogroup H, the most frequent haplogroup in European Caucasian populations. The other major haplogroups identified were U (15.4%), J (11.8%), T (8.2%) and K (5.1%). The frequencies of haplogroups in Austria is within the range observed for other European countries. Our method may be suitable for mitochondrial genotyping of samples from large-scale epidemiology studies and for identifying markers of genetic susceptibility.
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Affiliation(s)
- Martina Wiesbauer
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Salzburg, Austria
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Mayr JA, Moslemi AR, Förster H, Kamper A, Idriceanu C, Muss W, Huemer M, Oldfors A, Sperl W. A novel sporadic mutation G14739A of the mitochondrial tRNA(Glu) in a girl with exercise intolerance. Neuromuscul Disord 2006; 16:874-7. [PMID: 17056256 DOI: 10.1016/j.nmd.2006.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 08/15/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
We describe a 7-year-old girl who presented with loss of appetite, weakness and excercise intolerance. Enzyme investigation of the respiratory chain in muscle tissue revealed a combined complex I, III and IV deficiency. A novel heteroplasmic G-->A exchange at nucleotide position 14739 was found in the MTTE gene of the tRNA glutamic acid. The mutation load in muscle was 72%, urine sediment 38%, blood 31% and fibroblasts 29% and it correlated with COX-negative fibres. Our patient presented with a predominantly myopathic phenotype. The G14739A mutation is the third reported in the mitochondrial tRNA glutamic acid gene, and it occurred in a sporadic case.
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Affiliation(s)
- Johannes A Mayr
- University Children's Hospital, Paracelsus Private Medical University, Müllner Hauptstr 48, A-5020 Salzburg, Austria.
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Meierhofer D, Mayr JA, Fink K, Schmeller N, Kofler B, Sperl W. Mitochondrial DNA mutations in renal cell carcinomas revealed no general impact on energy metabolism. Br J Cancer 2006; 94:268-74. [PMID: 16404428 PMCID: PMC2361126 DOI: 10.1038/sj.bjc.6602929] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previously, renal cell carcinoma tissues were reported to display a marked reduction of components of the respiratory chain. To elucidate a possible relationship between tumourigenesis and alterations of oxidative phosphorylation, we screened for mutations of the mitochondrial DNA (mtDNA) in renal carcinoma tissues and patient-matched normal kidney cortex. Seven of the 15 samples investigated revealed at least one somatic heteroplasmic mutation as determined by denaturating HPLC analysis (DHPLC). No homoplasmic somatic mutations were observed. Actually, half of the mutations presented a level of heteroplasmy below 25%, which could be easily overlooked by automated sequence analysis. The somatic mutations included four known D-loop mutations, four so far unreported mutations in ribosomal genes, one synonymous change in the ND4 gene and four nonsynonymous base changes in the ND2, COI, ND5 and ND4L genes. One renal cell carcinoma tissue showed a somatic A3243G mutation, which is a known frequent cause of MELAS syndrome (mitochondrial encephalomyopathy, lactic acidosis, stroke-like episode) and specific compensatory alterations of enzyme activities of the respiratory chain in the tumour tissue. No difference between histopathology and clinical progression compared to the other tumour tissues was observed. In conclusion, the low abundance as well as the frequently observed low level of heteroplasmy of somatic mtDNA mutations indicates that the decreased aerobic energy capacity in tumour tissue seems to be mediated by a general nuclear regulated mechanism.
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Affiliation(s)
- D Meierhofer
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
| | - J A Mayr
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
| | - K Fink
- Department of Urology, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
| | - N Schmeller
- Department of Urology, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
| | - B Kofler
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria. E-mail:
| | - W Sperl
- Department of Paediatrics, Paracelsus Private Medical University Salzburg, Muellner Hauptstr. 48, A-5020 Salzburg, Austria
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Meierhofer D, Ebner S, Mayr JA, Jones ND, Kofler B, Sperl W. Platelet transfusion can mimic somatic mtDNA mutations. Leukemia 2005; 20:362-3. [PMID: 16357835 DOI: 10.1038/sj.leu.2404070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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