Genomics

基因组学

• 批准号: 10178295
• 负责人: Yoav Gilad
• 金额: $ 0.47万
• 依托单位: UNIVERSITY OF CHICAGO
• 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/10178295
• 关键词: Automation; Bioinformatics; Biological Assay; Biological Models; Biological Sciences; Biometry; Budgets; Cancer Center Support Grant; Cancer Model; 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; Ensure; 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; Leadership; Libraries; Mediation; Medicine; Methods; Microarray Analysis; Modeling; Modernization; NCI Center for Cancer Research; 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; base; 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; single-cell RNA sequencing; 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 Next- Generation 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 next- generation 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).

抽象的 芝加哥大学医学综合癌症中心（UCCCC）基因组学核心设施（GCF）是 任务是为芝加哥大学教职员工提供最先进的基因组数据生成服务 收费服务模型。 UCCCC会员的费用由癌症中心支持补助金（CCSG）通过 共付款机制。目前，GCF主要服务是下一代测序，DNA微阵列 分析和Sanger测序。 GCF还向客户和合作伙伴提供数据存储服务 用于基因组数据分析的生物信息学核心设施（BICF）。 GCF分为两个子核， 下一代测序和微阵列子核，DNA测序和基因分型子核，以及 自2009年以来一直位于Knapp生物医学发现中心（KCBD）的一楼。GCF 由人类遗传学教授的Yoav Gilad博士科学地执导，并由Pieter Faber运营， 博士，在William Buikema博士的协助下，作为DNA测序的技术总监和 基因分型子核。除领导层外，GCF员工还九种技术 生成测序和微阵列子核心，在DNA测序和基因分型中三个 子核）。当前资金期间的核心发展包括对下一代的越来越重视 测序（NGS）服务以满足该领域的需求和进步。主要操作工具的 该设施包括应用生物系统3730xl DNA分析仪（DNA测序和基因分型子核），一个 Illumina Hiscan和Affymetrix Genescan3000微阵列扫描系统以及三个Illumina接下来 - 生成测序仪器（HISEQ4000，HISEQ2500和NEXTSEQ500；下一代 测序和微阵列子核心）。 GCF有效地满足用户的需求，并提供了提供的服务 使用这些仪器占用可用仪器和/或人员时间的80-90％，表明 人员配备和仪器在适当的水平上运行和维护。 UCCCC成员会收到 优先级和项目根据样本接收日期和项目紧迫性进行优先级。直接操作， 博士。吉拉德（Gilad）和法布尔（Faber）每两周开会，讨论任何操作问题，以及短期和 长期策略。另外，博士。吉拉德（Gilad）和法布尔（Faber）定期与GCF教师监督会面 委员会（FOC）接收基因组学领域专家用户的建设性反馈。最好服务 用户的需求和衡量用户满意度，芝加哥大学共享研究设施办公室 DVM乔治·兰加（George Langan）的领导层进行年度校园用户调查。最近的调查 从2016年8月开始，批准率很高（约80％），有99％的响应者预测 将来继续使用该设施。将根据需要添加新服务（例如，设施打算 在2017年将单细胞RNA-Seq添加到其曲目（Drop-Seq协议）中。