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. 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.
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Basic information
Original name Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers
Authors LI, Xinzhong (826 United Kingdom of Great Britain and Northern Ireland), Andrew J. BUCKTON (826 United Kingdom of Great Britain and Northern Ireland), Samuel WILKINSON (826 United Kingdom of Great Britain and Northern Ireland), Shibu JOHN (826 United Kingdom of Great Britain and Northern Ireland), Roddy WALSH (840 United States of America), Tomáš NOVOTNÝ (203 Czech Republic, guarantor, belonging to the institution), Iveta VALÁŠKOVÁ (203 Czech Republic, belonging to the institution), Manu GUPTA (826 United Kingdom of Great Britain and Northern Ireland), Laurence GAME (826 United Kingdom of Great Britain and Northern Ireland), Paul L. BARTON (826 United Kingdom of Great Britain and Northern Ireland), Stuart A. COOK (702 Singapore) and James S. WARE (826 United Kingdom of Great Britain and Northern Ireland).
Edition PLoS One, San Francisco, Public Library of Science, 2013, 1932-6203.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 30201 Cardiac and Cardiovascular systems
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
Impact factor Impact factor: 3.534
RIV identification code RIV/00216224:14110/13:00069082
Organization unit Faculty of Medicine
Doi http://dx.doi.org/10.1371/journal.pone.0067744
UT WoS 000323350700031
Keywords in English Arrhythmias; Biology; Cardiomyopathies; Cardiovascular; Clinical laboratory sciences; Congenital heart disease; Diagnostic medicine; Genetics; Genome sequencing; Genomics; Medicine; Molecular genetics; Research Article
Tags Reviewed
Changed by Changed by: Ing. Mgr. Věra Pospíšilíková, učo 9005. Changed: 13. 11. 2013 13:40.
Abstract
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.
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