NEXT GENERATION SEQUENCING

下一代测序

• 批准号: 8559784
• 负责人: Srinivasan Yegnasubramanian
• 金额: $ 21.46万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8559784
• 关键词: Adoption; Appointment; Base Pairing; Base Sequence; Binding Sites; Bioinformatics; Biological; Boxing; Calendar; Clinical; Comprehensive Cancer Center; Consult; Consultations; Core Facility; Custom; DNA; DNA Methylation; DNA Sequencing Facility; Data; Data Analyses; Engineering; Ensure; Epigenetic Process; Equipment; Experimental Designs; Faculty; Gene Expression Profile; Genetic Research; Genome; Genomics; Goals; Gold; Laboratories; Libraries; Malignant Neoplasms; Memory; Molecular Biology; Molecular Genetics; Mutation; Partner in relationship; Preparation; Process; Protocols documentation; Quality Control; Reading; Research; Research Personnel; Resource Sharing; Running; Sampling; Scheme; Sequence Alignment; Services; Sonication; Synapses; Targeted Resequencing; Technology; Time; Translations; Variant; cancer genetics; chromatin modification; computer science; computing resources; cost; design; flexibility; genome-wide; image processing; innovation; instrument; member; new technology; next generation sequencing; oncology; research study; structural genomics; transcription factor

To maintain and build on the Sidney Kimmel Comprehensive Cancer Centers (SKCCC) record of excellence in the fields of cancer genetics and epigenetics, the SKCCC established a new Next Generation Sequencing Core (NGSC) as a shared resource in January 2009. A product of a convergence of advances in molecular biology, engineering, computer science, and bioinformatics. Next Generation Sequencing features the ability to sequence billions of base pairs of DNA in a single run, at a cost that is several orders of magnitude less than previous gold standard sequencing technologies. Next Generation Sequencing is an extremely versatile technology and can be used to investigate a multitude of genomic processes in a previously unimaginable genome-wide and unbiased fashion. In order to facilitate widespread adoption of this relatively new technology, rather than administering the Core as a "black-box" facility, the Core operates as a "collaborative Core" in which users can consult and collaborate with NGSC faculty and staff to: 1) identify the optimal molecular biology approaches (prior to sequencing library construction) to synapse their research questions with the capabilities of the Core, 2) prepare the appropriate libraries and carry out massively parallel sequencing, and 3) carry out the appropriate primary, secondary, and tertiary bioinformatics analyses to analyze and interpret the results. The NGSC features Applied Biosystems SOUD Next Generation Sequencing instruments capable of generating nearly 100 Gigabases of sequencing data in a single run, state-of-the-art equipment for sequencing library preparation and quality control, and powerful computational resources including a server with ten compute nodes (each containing Quad Core Intel Xeon processors and 16 Gigabytes of memory) and 100 terabytes of storage for dedicated bioinformatics analyses. The Core is currently administered by a faculty director overseeing all activities, a faculty Co-Director overseeing bioinformatics support, a laboratory manager, and a bioinformatics manager. The Core's goal is to be as flexible as possible in assisting researchers in exploring all aspects of cancer genetics and epigenetics, including, but not limited to, germline and somatic variation/mutation, genomic structural variations/alterations, transcriptome analysis, transcription factor binding sites, chromatin modifications, and DNA methylation. Lay: The Next Generation Sequencing Core provides cutting edge services that harness the most recent technological advances to allow large scale genomic sequencing of many hundreds of millions of DNA molecules in parallel at about 100,000 times less cost than previous sequencing technologies. These services are poised to rapidly accelerate the pace of discovery and clinical translation in cancer molecular genetics research. SKCCC Managed Shared Resource

为了保持和发展悉尼金梅尔综合癌症中心（SKCCC）在癌症遗传学和表观遗传学领域的卓越记录，SKCCC于2009年1月建立了新的下一代测序核心（NGSC）作为共享资源。是分子生物学、工程学、计算机科学和生物信息学发展的产物。下一代测序技术能够在一次运行中对数十亿个DNA碱基对进行测序，其成本比以前的黄金标准测序技术低几个数量级。下一代测序是一种非常通用的技术，可用于以以前无法想象的全基因组和无偏见的方式研究多种基因组过程。为了促进这种相对较新的技术的广泛采用，而不是将核心作为“黑匣子”设施进行管理，核心作为“协作核心”运行，用户可以与NGSC教职员工进行咨询和协作，以便：1）确定最佳的分子生物学方法（在测序文库构建之前）将他们的研究问题与核心的能力相关联，2）制备适当的文库并进行大规模平行测序，以及3）进行适当的初级、二级和三级生物信息学分析以分析和解释结果。NGSC的特点是应用生物系统SOUD下一代测序仪器能够在一次运行中产生近100千兆字节的测序数据，最先进的测序文库制备和质量控制设备，以及强大的计算资源，包括一台具有10个计算节点的服务器（每个都包含四核英特尔至强处理器和16兆字节的内存）和100 TB的存储空间，用于专门的生物信息学分析。该核心目前由一名负责监督所有活动的教师主任，一名负责监督生物信息学支持的教师联合主任，一名实验室经理和一名生物信息学经理管理。核心的目标是尽可能灵活地协助研究人员探索癌症遗传学和表观遗传学的各个方面，包括但不限于生殖系和体细胞变异/突变，基因组结构变异/改变，转录组分析，转录因子结合位点，染色质修饰和DNA甲基化。铺设：下一代测序核心提供尖端服务，利用最新的技术进步，以比以前的测序技术低约10万倍的成本并行进行数亿个DNA分子的大规模基因组测序。这些服务有望迅速加快癌症分子遗传学研究的发现和临床转化步伐。SKCCC托管共享资源