Evaluation of Second-Generation Sequencing of 19 Dilated Cardiomyopathy Genes for Clinical Applications
Evaluation of Second-Generation Sequencing of 19 Dilated Cardiomyopathy Genes for Clinical Applications
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DOI：
10.2353/jmoldx.2010.100014
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发表时间：
2010-11-01
影响因子：
4.1
通讯作者：
Funke, Birgit H.
中科院分区：
文献类型：
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作者：
Gowrisankar, Sivakumar;Lerner-Ellis, Jordan P.;Funke, Birgit H.
具有基因座和等位基因异质性的疾病的医学测序受到传统测序技术的高成本和低通量的限制。“第二代”测序（SGS）技术允许并行处理大量基因，因此为医学测序提供了巨大的希望，然而，它们在临床实验室中的应用仍处于起步阶段我们的实验室提供扩张型心肌病（DCM）的临床再测序使用基于阵列的平台，该平台询问已知引起DCM的30多个基因中的19个。我们探索了使用PCR扩增，然后使用SGS技术对一组5个富含已知序列改变的样品中的这19个基因进行测序的可行性和成本效益。（109个独特的取代和27个插入和缺失）虽然取代的分析灵敏度与DCM阵列相当（98%），但SGS技术在插入和缺失方面的表现优于DCM阵列。（90 6% vs 58%）总体而言，SGS的性能明显优于当前基于阵列的测试平台，但运营成本和预计周转时间不符合我们当前的标准。因此，在将该平台应用于常规临床应用之前，需要缩短周转时间并降低试剂和劳动力成本的有效捕获方法和/或样本合并策略（J Mol Diagn 2010，12 818-827，DOI 10.2353/jmoldx.2010.100014）
Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies "Second generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing, however, their use in clinical laboratories is still in its infancy Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array based platform that interrogates 19 of more than 30 genes known to cause DCM We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions) While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90 6% versus 58%) Overall, SGS per formed substantially better than did the current array based testing platform, however, the operational cost and projected turnaround time do not meet our current standards Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and laborcosts are needed before implementing this platform into routine clinical applications (J Mol Diagn 2010, 12 818-827, DOI 10.2353/jmoldx.2010.100014)