Illumina Genome Analyzer II

描述（由申请人提供）：本提案的总体目标是通过收购最先进的Illumina基因组分析仪II下一代测序仪来支持广泛的基因组学计划，从而显著增强已建立且非常成功的西奈山DNA测序和基因分型共享资源设施（DNAcore）的能力。这一升级对于实现高通量但经济的全基因组重测序项目以及基因调控、DNA基因型变异和表观遗传修饰的分析至关重要，因为它们与理解健康和疾病有关，从而保持DNAcore支持西奈山300多名NIH资助研究人员的能力。1）将DNAcore设施从基于毛细管电泳的测序和基因分型升级为包括Illumina基因组分析仪II的大规模并行测序，以保持该设施提供快速、可靠、经济和现在全基因组高质量DNA测序的能力; 2）提供样品制备、仪器操作和生物信息学支持，使我们的研究人员能够充分利用Illumina Genome Analyzer II，以满足他们基于DNA测序的研究需求; 3）为我们研究者项目的特定应用需求提供咨询支持，包括ChIP-Seq，miRNA表达分析，靶向重测序，DNA甲基化分析等;以及4）教育西奈山研究人员关于下一代测序的可用性和使用，以使他们的NIH资助的研究受益。DNAcore对西奈山调查人员的支持的成功将进一步得到该机构强有力的费用分摊承诺的保证（见Dean Dennis Charney的支持信）提供所需的额外资金，以充分装备DNAcore，通过成本分摊优化使用Illumina基因组分析仪II，以维护仪器，并为专门的FTE DNA核心助理提供支持，以操作仪器。RNA样品制备支持将通过微阵列、PCR和生物信息学共享资源设施主任Stuart Sealfon博士提供（见信函）。此外，对大量输出数据进行有效分析所需的关键生物信息学支持将由西奈山计算生物学共享资源中心和Ravi Sachidanandam博士的资源组合提供，Ravi Sachidanandam博士是冷泉港实验室最近招募的教师，他一直在支持和开发Solexa生物信息学工具，以促进数据操作和结果可视化。 公共卫生相关性：该应用程序要求支持购买超高容量DNA测序仪，Illumina基因组分析仪II，这是新的，复杂的研究技术所需的，以确定导致疾病的基因改变，快速，经济地测序关键小RNA和DNA样品的数十亿个核苷酸，并提供强大的基因调控和修饰的新分析。将这种使能的“下一代”工具放置在已建立的西奈山DNAcore中，这是一个用于DNA测序、基因分型和合成的全机构共享资源设施，将允许使用当前测序设备进行不可能的研究，极大地丰富了资助的研究项目中复杂基因分析的广度和深度，这些研究项目旨在处理我们300多名NIH资助的研究人员的健康和疾病的关键问题。这些项目有可能大大提高社会科普数量不断增加的基因疾病、各种人类癌症、对我们遗传脆弱性的环境挑战以及迅速演变的传染病的能力。

DESCRIPTION (provided by applicant): The overall objective of this proposal is to significantly enhance the capabilities of the established and highly successful Mount Sinai DNA Sequencing and Genotyping Shared Resource Facility (the DNAcore) by acquisition of a state-of-the-art Illumina Genome Analyzer II next-generation sequencer to support a broad array of genomics initiatives. This upgrade is critical to enable high-throughput, yet economical, genome-wide resequencing projects, as well as analyses of gene regulation, DNA genotype variation, and epigenetic modification, as they relate to understanding health and disease, and thus to maintain the DNAcore's ability to support Mount Sinai's over 300 NIH-funded researchers. The specific aims of this proposal are: 1) to upgrade the DNAcore facility from capillary electrophoresis-based sequencing and genotyping to include massively parallel sequencing by the Illumina Genome Analyzer II in order to maintain the facility's ability to provide rapid, reliable, economic, and now genome-wide, high-quality DNA sequencing; 2) to provide sample preparation, instrument operation and bioinformatics support to enable our investigators to make optimal use of the Illumina Genome Analyzer II to fulfill their DNA sequencing-based research needs; 3) to offer consultation support for the application-specific needs of our investigator's projects including ChIP-Seq, miRNA expression analyses, targeted resequencing, DNA methylation analyses, etc; and 4) to educate Mount Sinai researchers about the availability and use of next- generation sequencing to advantage their NIH-funded research. The success of this enhancement to the DNAcore's support of Mount Sinai investigators will be further assured by the strong cost-sharing commitment of the Institution (see Dean Dennis Charney's letter of support) to provide the additional funds needed to fully equip the DNAcore to optimally use the Illumina Genome Analyzer II through cost-sharing, to maintain the instrument, and to provide support for a dedicated FTE DNAcore associate to operate the instrument. RNA sample preparation support will be provided via Dr. Stuart Sealfon, Director of the Microarray, PCR and Bioinformatics Shared Resource Facility (see letter). In addition, the critical bioinformatics support required for effective analyses of the massive amounts of output data will be provided by a combination of resources from Mount Sinai's Computational Biology Shared Resource Center and Dr. Ravi Sachidanandam, a recent Faculty recruit from the Cold Spring Harbor Laboratory who has been supporting and developing Solexa bioinformatic tools to facilitate data manipulation and results visualization. PUBLIC HEALTH RELEVANCE: This application requests support to purchase an ultra-high capacity DNA sequencer, the Illumina Genome Analyzer II, that is required for new, sophisticated research techniques to define gene-based alterations which cause disease, to rapidly and economically sequence billions of nucleotides of critical small RNA and DNA samples, and to provide powerful new analyses of gene regulation and modification. Placement of this enabling "Next Generation" tool in the established Mount Sinai DNAcore, an Institution-wide Shared Resource Facility for DNA Sequencing, Genotyping and Synthesis, will permit studies not possible with the current sequencing equipment, vastly enriching the breadth and depth of sophisticated gene analyses in funded research projects designed to deal with critical issues of health and disease by our over 300 NIH-funded Investigators. These projects have the potential to dramatically improve society's ability to cope with an ever- expanding number of gene-based disorders, a wide variety of human cancers, environmental challenges to our genetic vulnerabilities, and rapidly evolving infectious diseases.