Core-005

核心005

• 批准号: 10819686
• 负责人: KUNLE O. ODUNSI
• 金额: $ 25.26万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-09-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10819686
• 关键词: Automation; Bioinformatics; Biological Assay; Biological Models; Biological Sciences; Biometry; Budgets; Cancer Center Support Grant; Cells; Chicago; Client; Clinical; Communities; Comprehensive Cancer Center; Consultations; Core Facility; DNA; DNA Microarray Chip; DNA sequencing; Data Analyses; Data Storage and Retrieval; Development; Dideoxy Chain Termination DNA Sequencing; Doctor of Philosophy; Education; Employee; Equipment; Faculty; Fee-for-Service Plans; Feedback; Fees; Financial Support; Floor; Funding; Future; Gene Chips; Gene Expression; Gene Expression Profiling; Generations; Genomic approach; Genomics; Genotype; Goals; High-Throughput Nucleotide Sequencing; Human Genetics; Human Resources; Institution; Leadership; Libraries; Malignant Neoplasms; Marketing; Mediation; Medicine; Methods; Microarray Analysis; Modeling; Modernization; NCI Center for Cancer Research; Needs Assessment; Play; Protocols documentation; Reagent; Recommendation; Research; Research Personnel; Role; Running; Sampling; Scanning; Service delivery model; Services; Specific qualifier value; Speed; Statistical Data Interpretation; Surveys; System; Techniques; Technology; Time; Universities; anticancer research; cost; cost effective; droplet sequencing; genomic data; genomic platform; improved; instrument; instrumentation; member; new technology; next generation sequencing; operation; population based; professor; research facility; satisfaction; synergism; technology development; tool; transcriptome sequencing

ABSTRACT The University of Chicago Medicine Comprehensive Cancer Center (UCCCC) Genomics Core Facility (GCF) is tasked with providing state-of-the-art genomics data generation services to University of Chicago faculty in a fee-for-service model. UCCCC members’ fees are subsidized by the Cancer Center Support Grant (CCSG) via a co-pay mechanism. At present, the GCF main services are next-generation sequencing, DNA microarray analysis, and Sanger sequencing. The GCF also provides data storage services to its clients and partners with the Bioinformatics Core Facility (BiCF) for genomic data analysis. The GCF is organized into two Subcores, Next-Generation Sequencing and Microarrays Subcore, and DNA Sequencing and Genotyping Subcore, and has been located on the first floor of the Knapp Center for Biomedical Discovery (KCBD) since 2009. The GCF is directed scientifically by Yoav Gilad, PhD, Professor of Human Genetics, and operationally by Pieter Faber, PhD, with the assistance of William Buikema, PhD, as Technical Director of the DNA Sequencing and Genotyping Subcore. In addition to the leadership, the GCF employs nine technologists (six in the NextGeneration Sequencing and Microarrays Subcore, and three in the DNA Sequencing and Genotyping Subcore). Core developments in the current funding period include increased emphasis on next-generation sequencing (NGS) services to meet demand and advancements in the field. The main operating instruments of the Facility include Applied Biosystems 3730xl DNA analyzers (DNA Sequencing and Genotyping Subcore), an Illumina HiScan, and an Affymetrix GeneScan3000 microarray scan system, as well as three Illumina nextgeneration sequencing instruments (HiSEQ4000, HiSEQ2500, and a NextSeq500; Next-Generation Sequencing and Microarrays Subcore). The GCF effectively serves users’ needs, and the services provided using these instruments occupy 80-90% of the available instrument and/or personnel time, indicating that staffing and instrumentation are operating and maintained at an appropriate level. UCCCC members receive priority, and projects are prioritized based on sample reception date and project urgency. To direct operations, Drs. Gilad and Faber meet on a biweekly basis, discussing any operational issues, as well as short-term and long-term strategies. Additionally, Drs. Gilad and Faber meet regularly with the GCF Faculty Oversight Committee (FOC) to receive constructive feedback from expert users in the genomics field. To best serve users’ needs and gauge user satisfaction, the University of Chicago Office of Shared Research Facilities under the leadership of George Langan, DVM, conducts annual on-campus user surveys. The most recent survey from August 2016 showed a high approval rating (approximately 80%), with 99% of responders predicting continued use of the Facility in the future. New services will be added as needed (e.g., the Facility intends to add single cell RNA-SEQ to its repertoire (DROP-SEQ protocol) in 2017).

摘要 芝加哥大学医学综合癌症中心（UCCCC）基因组学核心设施（GCF）是 其任务是为芝加哥大学的教师提供最先进的基因组学数据生成服务， 收费服务模式。UCCCC会员的费用由癌症中心支持补助金（CCSG）通过以下方式补贴： 共同付费机制。目前，GCF的主要服务是下一代测序、DNA微阵列 分析和桑格测序。GCF还为客户和合作伙伴提供数据存储服务， 生物信息学核心设施（BiCF）用于基因组数据分析。GCF被组织成两个子核心， 下一代测序和微阵列子核心，DNA测序和基因分型子核心， 自2009年以来一直位于克纳普生物医学发现中心（KCBD）的一楼。绿色气候基金 由人类遗传学教授Yoav Gilad博士科学指导，由Pieter Faber操作， 博士，在William Buikema博士的协助下，作为DNA测序的技术总监， 基因分型子核心。除了领导层，GCF还雇用了9名技术专家（其中6名在Next代测序和微阵列亚核心，以及三代中的DNA测序和基因分型 Subcore）。本供资期的核心发展包括更加重视下一代 测序（NGS）服务，以满足该领域的需求和进步。主要操作仪器 该设施包括应用生物系统公司3730 xl DNA分析仪（DNA测序和基因分型子核心）， Illumina HiScan和Affyscore GeneScan 3000微阵列扫描系统，以及接下来的三个Illumina第二代测序仪器（HiSEQ 4000、HiSEQ 2500和NextSeq 500; Next-Generation测序仪） 测序和微阵列子核心）。全球合作框架有效地满足了用户的需求， 使用这些仪器占用了80-90%的可用仪器和/或人员时间，表明 人员配备和仪器设备的运作和维护处于适当水平。UCCCC成员获得 根据样品接收日期和项目紧迫性确定项目的优先次序。为了指挥行动， Drs.吉拉德和费伯每两周举行一次会议，讨论任何业务问题，以及短期和 长期战略。此外，吉拉德和费伯博士定期会见GCF教师监督 委员会（FOC）从基因组学领域的专家用户那里获得建设性的反馈。最好地服务于 用户的需求和衡量用户的满意度，芝加哥共享研究设施办公室根据 乔治兰根，DVM的领导，进行年度校园用户调查。最近一次调查 从2016年8月开始的调查显示，支持率很高（约80%），99%的受访者预测， 今后继续使用该设施。将根据需要添加新服务（例如，该基金打算 将单细胞RNA-SEQ添加到其库中（2017年DROP-SEQ方案）。