Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing
Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type o...
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Published in | PloS one Vol. 5; no. 8; p. e12295 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
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20.08.2010
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Abstract | Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We "shotgun" sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300x average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20x while heteroplasmic variants required >200x coverage. Several Sanger "misses" were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease. |
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AbstractList | Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We "shotgun" sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300 average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20 while heteroplasmic variants required >200 coverage. Several Sanger "misses" were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease. Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We “shotgun” sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300× average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20× while heteroplasmic variants required >200× coverage. Several Sanger “misses” were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease. Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We "shotgun" sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300x average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20x while heteroplasmic variants required >200x coverage. Several Sanger "misses" were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease. |
Audience | Academic |
Author | Lin, Dawei Diegoli, Marta Zaragoza, Michael V Arbustini, Eloisa Fass, Joseph |
AuthorAffiliation | 1 Genetics & Metabolism Division, Pediatrics Department and Center for Mitochondrial and Molecular Medicine and Genetics (MAMMAG), University of California Irvine, Irvine, California, United States of America Duke University Medical Center, United States of America 2 Bioinformatics Core, UC Davis Genome Center, University of California Davis, Davis, California, United States of America 3 Centre for Inherited Cardiovascular Diseases, IRCCS Foundation Policlinico San Mateo, Pavia, Italy |
AuthorAffiliation_xml | – name: 2 Bioinformatics Core, UC Davis Genome Center, University of California Davis, Davis, California, United States of America – name: 3 Centre for Inherited Cardiovascular Diseases, IRCCS Foundation Policlinico San Mateo, Pavia, Italy – name: Duke University Medical Center, United States of America – name: 1 Genetics & Metabolism Division, Pediatrics Department and Center for Mitochondrial and Molecular Medicine and Genetics (MAMMAG), University of California Irvine, Irvine, California, United States of America |
Author_xml | – sequence: 1 givenname: Michael V surname: Zaragoza fullname: Zaragoza, Michael V email: mzaragoz@uci.edu organization: Genetics & Metabolism Division, Pediatrics Department and Center for Mitochondrial and Molecular Medicine and Genetics, University of California Irvine, Irvine, California, United States of America. mzaragoz@uci.edu – sequence: 2 givenname: Joseph surname: Fass fullname: Fass, Joseph – sequence: 3 givenname: Marta surname: Diegoli fullname: Diegoli, Marta – sequence: 4 givenname: Dawei surname: Lin fullname: Lin, Dawei – sequence: 5 givenname: Eloisa surname: Arbustini fullname: Arbustini, Eloisa |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20808834$$D View this record in MEDLINE/PubMed |
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Copyright | COPYRIGHT 2010 Public Library of Science 2010 Zaragoza et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Zaragoza et al. 2010 |
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Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 ObjectType-Feature-1 Conceived and designed the experiments: MVZ JF DL EA. Performed the experiments: MVZ JF MD. Analyzed the data: MVZ JF MD DL EA. Contributed reagents/materials/analysis tools: MVZ JF MD DL EA. Wrote the paper: MVZ. |
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Snippet | Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In... |
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SubjectTerms | Base Sequence Bioinformatics Cardiac patients Cardiomyopathies - genetics Cardiomyopathy Cardiovascular Disorders/Heart Failure Cardiovascular Disorders/Myopathies Comparative analysis Computational Biology Deoxyribonucleic acid Disease DNA DNA sequencing DNA, Mitochondrial - genetics Evolutionary Biology/Genomics Female Gene mapping Gene sequencing Genetic Variation Genetics and Genomics Genetics and Genomics/Bioinformatics Genetics and Genomics/Genetics of Disease Genetics and Genomics/Genomics Genetics and Genomics/Medical Genetics Genomes Genomics Heart Heart diseases Heteroplasmy Humans Male Medical research Mitochondrial Diseases - genetics Mitochondrial DNA Multiplexing Mutation Nucleotide sequence Patients Phylogenetics Reference materials Sequence Analysis, DNA - methods Serine Simulation Studies Tissues Transfer RNA tRNA Ser |
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Title | Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing |
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