Shared High-throughput DNA sequencer for the Brown University Community

描述(由申请人提供)： 布朗在生物和医学部拥有近600名教职员工/研究人员；它在2008年获得了美国国立卫生研究院112,884,965美元的支持，它拥有一个强大的翻译和临床研究团队，并专注于基因组应用的基础研究。然而，该机构的DNA测序能力有限，即单一的应用生物系统3130xl遗传分析仪毛细管测序仪。研究前沿已经发生了巨大的变化，现在DNA测序被用于探索、详细分析和定量。现在，与用于分析例如全基因组转录组阵列的许多微阵列方法相比，它甚至具有成本效益。布朗大学的研究人员正经历着对快速、深入和经济有效的DNA测序的迅速增长的需求。对需求的评估已经与高通量DNA测序仪结合在一起；这样的仪器将满足绝大多数研究需要。不幸的是，非现场设施的排队时间从4周(如果调查员自己建造了所有图书馆)到2个多月的全方位服务设施。校外样本也经常因为新的校园项目而被推迟。因此，我们请求获得支持，以获得高通量DNA测序仪，以满足布朗大学生物和医学系对DNA测序的迅速增长的需求。从历史上看，短读测序仪(Solexa，Solid)因其高通量和相对较低的测序成本而颇具吸引力。然而，由于解释和比对长度为25-35个碱基的具有较大序列复杂性的后生动物基因组的短序列读数的困难，它们的潜力一直落后于它们。随着Illumina GAII平台的出现，这种负面影响已降至最低，平均实现了100多个碱基的读取长度，并且该下一代单元包括成对的末端读取功能，读取长度现在接近替代测序格式的长度，例如454个长度，但具有更高的吞吐量和显著更低的成本。事实上，随着新的测序化学和软件功能的进步，从头测序被添加到其功能列表中，使这种类型的仪器满足了布朗大学的研究人员的需求。这个应用程序代表了32个主要用户和9个次要用户的集体DNA测序需求，他们代表了14个不同的研究部门，以及超过70个NIH拨款。它包含了基础和临床研究人员、医学博士和博士。重要的是，它包含了一支强大的计算分子生物学家队伍，他们对更好、更容易地利用这种仪器产生的大型数据集感兴趣。大学致力于通过人员、实验室空间、计算机数据存储能力和延长的服务合同来支持这一仪器，以最大限度地增加仪器的投资，并促进每一名研究人员的产出。

DESCRIPTION (provided by applicant): Brown has almost 600 faculty/researchers in the Division of Biology and Medicine; it received $112,884,965 in NIH support in 2008, it has a strong translational and clinical research group, and a basic research emphasis on genomic applications. Yet this institution has limited DNA sequencing capabilities i.e. a single Applied Biosystems 3130xl Genetic Analyzer capillary sequencer. The research frontier has changed tremendously so that now DNA sequencing is used for exploration, for detailed analysis, and for quantitation. It is even cost effective now compared to many microarray approaches for analysis of e.g. whole genome transcriptome arrays. Investigators at Brown University are experiencing a burgeoning need for rapid, deep, and cost-effective DNA sequencing. An assessment of needs has coalesced to the High Throughput DNA Sequencing instruments; such an instrument would meet the vast majority of research needs. Unfortunately, the queues for off-site facilities ranged from 4 weeks (providing the investigator made all their own libraries), to over 2 months for full-service facilities. An off-campus sample was also subject to consistently getting delayed by new on-campus projects. We therefore request support to acquire a high-throughput DNA sequencer to handle the burgeoning needs for DNA sequencing in the Division of Biology and Medicine at Brown University. Historically, the short read sequencers (Solexa, SOLID) have been attractive for the high throughput and relatively low cost of sequence. However, they have lagged behind in their potential because of the difficulties in interpreting and aligning short sequencing reads, 25-35 bases in length, of metazoan genomes with large sequence complexity. This detraction is minimized now with the Illumina GAII platform, achieving read lengths of over 100 bases on average, and with paired end read capabilities included in this next generation unit, the read lengths now approach the lengths of alternative sequencing formats, e.g. 454 lengths, but with much higher throughput and significantly lower cost. Indeed, with new sequencing chemistries, and advances in software capabilities, de novo sequencing is added to its list of capabilities, making this type of instrument meet the investigator need at Brown University. This application represents the collective DNA sequencing needs of 32 major users and 9 minor users, representing 14 different research departments, and over 70 NIH grants. It contains a mix of basic and clinical researchers, M.D.s and Ph.D.s. Importantly, it contains a strong contingent of computational molecular biologists interested in better, and more easily making use of the large data sets resulting from such an instrument. The University is committed to supporting this instrument through personnel, laboratory space, computer data storage capabilities, and extended service contracts to maximize the investment of the instrument and to facilitate the output of each investigator.