Other formats:
BibTeX
LaTeX
RIS
@article{1120083,
author = {Li, Xinzhong and Buckton, Andrew J. and Wilkinson, Samuel and John, Shibu and Walsh, Roddy and Novotný, Tomáš and Valášková, Iveta and Gupta, Manu and Game, Laurence and Barton, Paul L. and Cook, Stuart A. and Ware, James S.},
article_location = {San Francisco},
article_number = {7},
doi = {http://dx.doi.org/10.1371/journal.pone.0067744},
keywords = {Arrhythmias; Biology; Cardiomyopathies; Cardiovascular; Clinical laboratory sciences; Congenital heart disease; Diagnostic medicine; Genetics; Genome sequencing; Genomics; Medicine; Molecular genetics; Research Article},
language = {eng},
issn = {1932-6203},
journal = {PLoS One},
title = {Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers},
volume = {8},
year = {2013}
}
TY - JOUR
ID - 1120083
AU - Li, Xinzhong - Buckton, Andrew J. - Wilkinson, Samuel - John, Shibu - Walsh, Roddy - Novotný, Tomáš - Valášková, Iveta - Gupta, Manu - Game, Laurence - Barton, Paul L. - Cook, Stuart A. - Ware, James S.
PY - 2013
TI - Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers
JF - PLoS One
VL - 8
IS - 7
SP - e67744
EP - e67744
PB - Public Library of Science
SN - 19326203
KW - Arrhythmias
KW - Biology
KW - Cardiomyopathies
KW - Cardiovascular
KW - Clinical laboratory sciences
KW - Congenital heart disease
KW - Diagnostic medicine
KW - Genetics
KW - Genome sequencing
KW - Genomics
KW - Medicine
KW - Molecular genetics
KW - Research Article
N2 - Background: Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations. Methodology/Principal Findings: We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm), and sequenced on the MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%). At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs), with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS. Conclusions/Significance: MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias, these NGS approaches are faster, less expensive, and yet more comprehensive.
ER -
LI, Xinzhong, Andrew J. BUCKTON, Samuel WILKINSON, Shibu JOHN, Roddy WALSH, Tomáš NOVOTNÝ, Iveta VALÁŠKOVÁ, Manu GUPTA, Laurence GAME, Paul L. BARTON, Stuart A. COOK and James S. WARE. Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers. \textit{PLoS One}. San Francisco: Public Library of Science, 2013, vol.~8, No~7, p.~e67744, 10 pp. ISSN~1932-6203. doi:10.1371/journal.pone.0067744.
|
