Illumina Genome Analyzer II

Illumina 基因组分析仪 II

• 批准号: 7595397
• 负责人: DAVID Franklin BISHOP
• 金额: $ 33.8万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-01 至 2010-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7595397
• 关键词: Arts; Base Sequence; Bioinformatics; Bioinformatics Shared Resource; Capillary Electrophoresis; Communicable Diseases; Computational Biology; Consultations; Cost Sharing; DNA; DNA Methylation; DNA Resequencing; DNA Sequence; DNA Sequencing Facility; Data; Disease; Economics; Equipment; Faculty; Funding; Gene Expression Regulation; Genes; Genetic Predisposition to Disease; Genome; Genomics; Genotype; Health; Human; Imagery; Institution; Laboratories; Letters; MicroRNAs; Modification; Nucleotides; Operative Surgical Procedures; Output; Preparation; RNA; Recruitment Activity; Request for Applications; Research; Research Personnel; Research Project Grants; Research Technics; Resource Sharing; Resources; Sampling; Small RNA; Societies; base; coping; design; environment related cancer; epigenetic variation; genome-wide; improved; instrument; next generation; public health relevance; success; tool

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.

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下一代测序仪来显著增强已建立并高度成功的西奈山DNA测序和基因分型共享资源设施(DNAcore)的能力，以支持广泛的基因组学计划。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对基因调控、DNA基因变异和表观遗传修饰的分析至关重要，因为它们与了解健康和疾病有关，从而保持DNAcore支持西奈山300多名NIH资助研究人员的能力。这项建议的具体目标是：1)将DNAcore设施从基于毛细管电泳法的测序和基因分型升级到包括Illumina Genome Analyzer II的大规模并行测序，以保持该设施提供快速、可靠、经济的、现在是全基因组范围的高质量DNA测序的能力；2)提供样品准备、仪器操作和生物信息学支持，使我们的研究人员能够最佳地利用Illumina Genome Analyzer II，以满足他们基于DNA测序的研究需求；3)为我们研究人员的项目的特定应用需求提供咨询支持，包括芯片序列、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，以利用他们由NIH资助的研究。DNAcore对西奈山调查人员的大力支持将进一步确保这一改进的成功，因为该机构做出了强有力的成本分担承诺(参见Dennis Charney院长的支持函)，提供所需的额外资金，以全面装备DNAcore，通过成本分担优化使用Illumina基因组分析仪II，维护仪器，并为专门的FTE DNAcore同事提供支持，以操作仪器。RNA样品制备支持将由微阵列、聚合酶链式反应和生物信息学共享资源设施主任斯图尔特·西尔丰博士提供(见信函)。此外，有效分析海量输出数据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最近从冷泉港实验室招聘的Ravi Schidanandam博士提供资源，Ravi Schidanandam博士一直在支持和开发Solexa生物信息工具，以促进数据处理和结果可视化。公共卫生相关性：该应用程序请求支持购买超大容量DNA测序仪，Illumina Genome Analyzer II，这是新的、复杂的研究技术所必需的，以确定导致疾病的基于基因的变化，快速和经济地对关键的小RNA和DNA样本的数十亿个核苷酸进行测序，并提供强大的基因调控和修改的新分析。将这一令人信服的“下一代”工具放置在已建立的Mountain Sinai DNAcore中，这是一个机构范围内的DNA测序、基因分型和合成共享资源设施，将允许进行使用当前测序设备无法进行的研究，极大地丰富了由NIH资助的300多名研究人员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关键的健康和疾病问题。这些项目有可能极大地提高社会应对数量不断增加的基于基因的疾病、各种各样的人类癌症、环境对我们的遗传脆弱性的挑战以及快速演变的传染病的能力。