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Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench?

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Abstract
Next-generation sequencing (NGS), an innovative sequencing technology that enables the successful analysis of numerous gene sequences in a massive parallel sequencing approach, has revolutionized the field of molecular biology. Although NGS was introduced in a rather recent past, the technology has already demonstrated its potential and effectiveness in many research projects, and is now on the verge of being introduced into the diagnostic setting of routine laboratories to delineate the molecular basis of genetic disease in undiagnosed patient samples. We tested a benchtop device on retrospective genomic DNA (gDNA) samples of controls and patients with a clinical suspicion of a mitochondrial DNA disorder. This Ion Torrent Personal Genome Machine platform is a high-throughput sequencer with a fast turnaround time and reasonable running costs. We challenged the chemistry and technology with the analysis and processing of a mutational spectrum composed of samples with single-nucleotide substitutions, indels (insertions and deletions) and large single or multiple deletions, occasionally in heteroplasmy. The output data were compared with previously obtained conventional dideoxy sequencing results and the mitochondrial revised Cambridge Reference Sequence (rCRS). We were able to identify the majority of all nucleotide alterations, but three false-negative results were also encountered in the data set. At the same time, the poor performance of the PGM instrument in regions associated with homopolymeric stretches generated many false-positive miscalls demanding additional manual curation of the data.
Keywords
DNA, LACTIC-ACIDOSIS, MUTATION, HETEROPLASMY, MELAS

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Chicago
Seneca, Sara, Kim Vancampenhout, Rudy Van Coster, Joél Smet, Willy Lissens, Arnaud Vanlander, Boel De Paepe, An Jonckheere, Katrien Stouffs, and Linda De Meirleir. 2015. “Analysis of the Whole Mitochondrial Genome: Translation of the Ion Torrent Personal Genome Machine System to the Diagnostic Bench?” European Journal of Human Genetics 23 (1): 41–48.
APA
Seneca, S., Vancampenhout, K., Van Coster, R., Smet, J., Lissens, W., Vanlander, A., De Paepe, B., et al. (2015). Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench? EUROPEAN JOURNAL OF HUMAN GENETICS, 23(1), 41–48.
Vancouver
1.
Seneca S, Vancampenhout K, Van Coster R, Smet J, Lissens W, Vanlander A, et al. Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench? EUROPEAN JOURNAL OF HUMAN GENETICS. 2015;23(1):41–8.
MLA
Seneca, Sara, Kim Vancampenhout, Rudy Van Coster, et al. “Analysis of the Whole Mitochondrial Genome: Translation of the Ion Torrent Personal Genome Machine System to the Diagnostic Bench?” EUROPEAN JOURNAL OF HUMAN GENETICS 23.1 (2015): 41–48. Print.
@article{4358524,
  abstract     = {Next-generation sequencing (NGS), an innovative sequencing technology that enables the successful analysis of numerous gene sequences in a massive parallel sequencing approach, has revolutionized the field of molecular biology. Although NGS was introduced in a rather recent past, the technology has already demonstrated its potential and effectiveness in many research projects, and is now on the verge of being introduced into the diagnostic setting of routine laboratories to delineate the molecular basis of genetic disease in undiagnosed patient samples. We tested a benchtop device on retrospective genomic DNA (gDNA) samples of controls and patients with a clinical suspicion of a mitochondrial DNA disorder. This Ion Torrent Personal Genome Machine platform is a high-throughput sequencer with a fast turnaround time and reasonable running costs. We challenged the chemistry and technology with the analysis and processing of a mutational spectrum composed of samples with single-nucleotide substitutions, indels (insertions and deletions) and large single or multiple deletions, occasionally in heteroplasmy. The output data were compared with previously obtained conventional dideoxy sequencing results and the mitochondrial revised Cambridge Reference Sequence (rCRS). We were able to identify the majority of all nucleotide alterations, but three false-negative results were also encountered in the data set. At the same time, the poor performance of the PGM instrument in regions associated with homopolymeric stretches generated many false-positive miscalls demanding additional manual curation of the data.},
  author       = {Seneca, Sara and Vancampenhout, Kim and Van Coster, Rudy and Smet, Jo{\'e}l and Lissens, Willy and Vanlander, Arnaud and De Paepe, Boel and Jonckheere, An and Stouffs, Katrien and De Meirleir, Linda},
  issn         = {1018-4813},
  journal      = {EUROPEAN JOURNAL OF HUMAN GENETICS},
  language     = {eng},
  number       = {1},
  pages        = {41--48},
  title        = {Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench?},
  url          = {http://dx.doi.org/10.1038/ejhg.2014.49},
  volume       = {23},
  year         = {2015},
}

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