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Genomic Analysis Core

基因组分析核心

基本信息

批准号：
10550261
负责人：
TAPAN GANGULY
金额：
--
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
1997
资助国家：
美国
起止时间：
1997-01-15 至 2025-11-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10550261
关键词：
ATAC-seq Abbreviations Biological Blood capillaries Cancer Center Cancer Center Support Grant Cancer Control Cell Culture Techniques Cell Line Cell physiology Characteristics Chromosome abnormality Classification Cloning Community Outreach Computer software Consultations Contracts Copy Number Polymorphism DNA DNA Fragmentation DNA Sequencing Facility DNA Sequencing Shared Resource DNA sequencing Data Data Analyses Developmental Process Dideoxy Chain Termination DNA Sequencing Equipment Experimental Designs Funding Future Gene Chips Gene Expression Profile Generations Genes Genetic Genetic Fingerprintings Genetic study Genomics Genotype Grant Guidelines Human Human Cell Line Immunity Immunotherapy Infrastructure Institution Investments Ions Laboratories Leadership Malignant Neoplasms Massive Parallel Sequencing Microsatellite Repeats Minisatellite Repeats Mission Molecular Molecular Genetics Molecular Profiling Molecular Target Mus Mycoplasma Oncogenes Pathogenesis Pediatric Hospitals Philadelphia Preparation Process Protons Publications Qualifying RNA Radiobiology Reporting Research Research Personnel Resource Sharing Role Sampling Services Site-Directed Mutagenesis Sushi Domain System Technology Time Training acronyms anticancer research cancer cell cancer diagnosis cancer genome community engagement comparative genomic hybridization environmental carcinogenesis equipment acquisition experience gene discovery genome-wide imaging program immune cell infiltrate instrument medical schools member next generation sequencing pancreatic cancer model plasmid DNA programs response risk prediction risk selection screening square foot targeted sequencing tobacco carcinogenesis transcriptome transcriptome sequencing tumor vector whole genome

项目摘要

PROJECT SUMMARY – Genomic Analysis Core The Genomic Analysis Core (GAC) of the Abramson Cancer Center (ACC) provides a spectrum of genomic and molecular biological services with a team of highly experienced and trained professionals. These services are essential to ACC members for studying the role of specific genes in normal or abnormal cellular processes found in cancer cells and tumors. Investigators can observe global gene expression patterns in a sample, and genetic variability in an unaffected or tumor genome. The GAC's configuration dates to 2014 when two NCI CCSG supported Shared Resources – the DNA Sequencing Facility and the Genomics Facility – were consolidated under a single umbrella facility. The resulting Shared Resource was and continues to be directed by Dr. Tapan Ganguly, who directed the DNA Sequencing Facility since 2003. He is assisted by Erik Toorens, Technical Director, with five years of leadership and fifteen years of service at the GAC. This team is supported by seven other FTEs with an average of fifteen years' experience. GAC offers sequencing service on three platforms - Ion Torrent PGM & S5, Illumina MiSeq & NextSeq 500 - and Sanger sequencing on ABI capillary sequencers. The capillary sequencers also enable microsatellite-based genotyping, fragment analysis, and cell line authentication. Whole genome and targeted molecular profiling are performed on multiple platforms. The GAC supports quantitative RNA and DNA profiling on Affymetrix GeneChips and high-throughput GeneTitan, Fluidigm BioMark HD, and ABI QS12 Flex real-time PCR instruments. The molecular biological services include cloning, subcloning, site-directed mutagenesis and vector construction. ACC members benefit from consultations and training available throughout their projects. The range of services along with the expertise of the GAC Director facilitates gene discovery, functional characterization and other research questions to elucidate the molecular pathogenesis of human cancers. In addition, molecular profiling of DNA and RNA, together with targeted sequencing of cancer genes, can help ACC members in cancer diagnosis, subclassifications, risk prediction and selection of appropriate therapy. The GAC contributed to multiple high impact publications, including supporting the generation of RNA-Seq and ATAC-Seq data to elucidate tumor- specific characteristics that underlie variability of immune cell infiltration and response to immunotherapy using a mouse pancreatic cancer model (Li et al., Immunity, 2018; Markosyan et al., J Clin Invest, 2019). ACC members accounted for 102 of 376 investigators (27%) using the Shared Resource during the most recent reporting period (07/01/18-06/30/19). In addition to CCSG support, funding for the GAC comes from chargebacks, grants/contracts and Institutional support, including funding for equipment purchases. The excellent scientific and technical management of this facility, along with highly qualified and stable staff, contribute to the reputation of this well-established and effective Shared Resource as an integral part of the infrastructure necessary for rigorous cancer research.

项目摘要 – 基因组分析核心艾布拉姆森癌症中心 (ACC) 的基因组分析核心 (GAC) 提供了一系列基因组分析和分子生物学服务，拥有一支经验丰富且训练有素的专业人员团队。这些服务对于 ACC 成员研究特定基因在正常或异常细胞过程中的作用至关重要存在于癌细胞和肿瘤中。研究人员可以观察样本中的全局基因表达模式，并且未受影响的基因组或肿瘤基因组中的遗传变异性。 GAC 的配置可以追溯到 2014 年，当时两个 NCI CCSG 支持的共享资源——DNA 测序设施和基因组学设施—— 合并到一个单一的伞式设施下。由此产生的共享资源曾经并将继续被定向由 Tapan Ganguly 博士负责，他自 2003 年起负责 DNA 测序设施。他由 Erik Toorens 协助，技术总监，在 GAC 工作了 5 年和 15 年。这个团队受支持由其他七名平均拥有十五年经验的 FTE 负责。广汽集团提供三项测序服务平台 - Ion Torrent PGM 和 S5、Illumina MiSeq 和 NextSeq 500 - 以及 ABI 毛细管上的 Sanger 测序测序仪。毛细管测序仪还可以进行基于微卫星的基因分型、片段分析和细胞分析线路认证。全基因组和靶向分子分析在多个平台上进行。这 GAC 支持在 Affymetrix GeneChips 和高通量 GeneTitan 上进行定量 RNA 和 DNA 分析， Fluidigm BioMark HD 和 ABI QS12 Flex 实时 PCR 仪器。分子生物学服务包括克隆、亚克隆、定点诱变和载体构建。 ACC 会员受益于在整个项目中提供咨询和培训。服务范围以及专业知识 GAC 主任促进基因发现、功能表征和其他研究问题，以阐明人类癌症的分子发病机制。此外，DNA 和 RNA 的分子分析，结合癌症基因的靶向测序，可以帮助ACC会员进行癌症诊断，子分类、风险预测和适当治疗的选择。 GAC 为多项高额贡献做出了贡献影响出版物，包括支持生成 RNA-Seq 和 ATAC-Seq 数据以阐明肿瘤- 免疫细胞浸润和对免疫治疗反应的可变性的具体特征小鼠胰腺癌模型（Li 等人，Immunity，2018；Markosyan 等人，J Clin Invest，2019）。 ACC 最近一次使用共享资源的 376 名调查员中，有 102 名成员 (27%) 报告期（07/01/18-06/30/19）。除了 CCSG 的支持外，GAC 的资金还来自退款、赠款/合同和机构支持，包括设备采购资金。这该设施卓越的科学技术管理，以及高素质和稳定的员工队伍，为这一完善且有效的共享资源的声誉做出贡献，使其成为该资源不可分割的一部分严格的癌症研究所需的基础设施。