Shared High-throughput DNA sequencer for the Brown University Community

布朗大学社区共享高通量 DNA 测序仪

• 批准号: 7795437
• 负责人: GARY M WESSEL
• 金额: $ 49.98万
• 依托单位: BROWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-03-18 至 2011-03-17
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7795437
• 关键词: Basic Science; Biology; Blood capillaries; Chemistry; Clinical; Clinical Research; Commit; Communities; Computer software; Computers; Contract Services; DNA; DNA Sequence; Data Set; Data Storage and Retrieval; Faculty; Gene Expression Profile; Genetic; Genome; Genomics; Grant; Institution; Investments; Laboratory Personnel; Length; Libraries; Medicine; Minor; Molecular; Needs Assessment; Output; Reading; Research; Research Personnel; Sampling; Services; Site; Solid; United States National Institutes of Health; Universities; base; capillary; cost; cost effective; experience; frontier; instrument; interest; meetings; next generation

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.

描述（由申请人提供）： 布朗大学在生物学和医学部门有近600名教师/研究人员;它在2008年获得了美国国立卫生研究院的112，884，965美元的支持，它拥有强大的翻译和临床研究团队，以及对基因组应用的基础研究重点。然而，该机构具有有限的DNA测序能力，即单个应用生物系统3130 xl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。与许多用于分析例如全基因组转录组阵列的微阵列方法相比，它现在甚至是成本有效的。布朗大学的研究人员正在经历对快速，深入和具有成本效益的DNA测序的迅速增长的需求。对需求的评估已与高通量DNA测序仪器合并;这样一种仪器将满足绝大多数研究需求。不幸的是，场外设施的排队时间从4周（假设研究者自己建立了所有图书馆）到2个月以上的全方位服务设施。一个校外样本也受到不断得到新的校园项目延迟。 因此，我们请求支持获得高通量DNA测序仪，以满足布朗大学生物学和医学部对DNA测序的迅速增长的需求。历史上，短读段测序仪（Solexa，SOLID）由于高通量和相对低的测序成本而具有吸引力。然而，它们在其潜力方面落后，因为难以解释和比对具有大序列复杂性的后生动物基因组的长度为25-35个碱基的短测序读数。现在使用Illumina GAII平台使这种减损最小化，实现了平均超过100个碱基的读取长度，并且在该下一代单元中包括配对末端读取能力的情况下，读取长度现在接近替代测序格式的长度，例如454个长度，但是具有高得多的通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布朗大学研究人员的需求。 该应用程序代表了32个主要用户和9个次要用户的集体DNA测序需求，代表了14个不同的研究部门和70多个NIH赠款。它包括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，他们对更好地、更容易地利用这种仪器产生的大型数据集感兴趣。该大学致力于通过人员，实验室空间，计算机数据存储能力和扩展服务合同来支持该仪器，以最大限度地提高仪器的投资，并促进每个研究人员的产出。