Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer.
Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer.
复制标题
DOI：
10.1186/s13742-015-0051-z
复制
发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Minot SS
中科院分区：
文献类型：
--
作者：
Kilianski A;Haas JL;Corriveau EJ;Liem AT;Willis KL;Kadavy DR;Rosenzweig CN;Minot SS
MinION™纳米孔测序仪最近发布给α测试人员社区，用于使用各种测序应用进行评估。最近的报告已经测试了MinION™作为全基因组测序仪的能力，并且已经证明纳米孔测序具有巨大的潜在效用。然而，目前的纳米孔技术在错误率方面仍然存在局限性，并且当试图组装整个基因组而不进行第二轮测序来纠正错误时，这是有问题的。在这项研究中，我们测试了MinION™纳米孔测序仪通过对目标进化枝中广泛共有的特征基因进行定向测序来准确识别和区分细菌和病毒样品的能力。使用6小时测序运行时间，产生足够的数据来鉴定E.大肠杆菌样品的16 S rDNA扩增产物的水平下降到物种水平。鉴定了三种痘病毒（牛痘、牛痘-MVA和牛痘-Lister），并将其区分至毒株水平，尽管牛痘毒株之间的同一性超过98%。尽管观察到的每碱基错误率约为30%，但通过MinION™上的扩增子测序实现了区分菌株的能力。虽然纳米孔测序，特别是使用来自Oxford Nanopore的MinION™平台，继续成熟为商业上可获得的技术，但寻求该技术的当前版本的实际用途。本研究通过证明当前版本的MinION™技术可以通过扩增子测序准确识别和区分生物样品中存在的病毒和细菌物种，提供了扩增子测序实用性的证据。本文的在线版本（doi：10.1186/s13742-015-0051-z）包含补充材料，可供授权用户使用。
The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade. Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%. While nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing. The online version of this article (doi:10.1186/s13742-015-0051-z) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
7.7
作者：
Stoloff DH;Wanunu M
通讯作者：
Wanunu M
影响因子：
14.9
作者：
Loy A;Maixner F;Wagner M;Horn M
通讯作者：
Horn M
DOI：
10.1093/bioinformatics/btt389
发表时间：
2013-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ames SK;Hysom DA;Gardner SN;Lloyd GS;Gokhale MB;Allen JE
通讯作者：
Allen JE
影响因子：
48
作者：
Segata, Nicola;Waldron, Levi;Ballarini, Annalisa;Narasimhan, Vagheesh;Jousson, Olivier;Huttenhower, Curtis
通讯作者：
Huttenhower, Curtis
影响因子：
7
作者：
Naccache SN;Federman S;Veeraraghavan N;Zaharia M;Lee D;Samayoa E;Bouquet J;Greninger AL;Luk KC;Enge B;Wadford DA;Messenger SL;Genrich GL;Pellegrino K;Grard G;Leroy E;Schneider BS;Fair JN;Martínez MA;Isa P;Crump JA;DeRisi JL;Sittler T;Hackett J Jr;Miller S;Chiu CY
通讯作者：
Chiu CY