Genomic Analysis Core

基因组分析核心

• 批准号: 10088762
• 负责人: TAPAN GANGULY
• 金额: --
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 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/10088762
• 关键词: ATAC-seq; Abbreviations; Biological; Blood capillaries; Cancer Center; Cancer Center Support Grant; Cancer Control; Cell Culture Techniques; Cell Line; Cell physiology; Cells; Characteristics; Chromosome abnormality; 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; Immune; Immunity; Immunotherapy; Infiltration; Infrastructure; 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; RNA; Radiobiology; Reporting; Research; Research Personnel; Resource Sharing; Role; Sampling; Services; Site-Directed Mutagenesis; Sushi Domain; System; Technology; Time; Training; acronyms; anticancer research; base; cancer cell; cancer diagnosis; cancer genome; community engagement; comparative genomic hybridization; environmental carcinogenesis; equipment acquisition; experience; gene discovery; genome-wide; imaging program; 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

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)提供基因组谱 拥有一支经验丰富、训练有素的专业团队，致力于分子生物学服务。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是必不可少的 在癌细胞和肿瘤中发现。研究人员可以观察样本中的全球基因表达模式，以及 未受影响的或肿瘤基因组中的遗传变异。广汽的配置可以追溯到2014年，当时有两个NCI CCSG支持的共享资源-DNA测序设施和基因组学设施-是 合并在一个单一的保护伞设施下。所产生的共享资源过去和现在都是定向的 Tapan Gangully博士，他自2003年起领导DNA测序设施。他得到了埃里克·图伦斯的协助， 技术总监，领导五年，在广汽服务十五年。这支球队得到了支持 被其他七家平均拥有15年工作经验的全职员工聘用。广汽集团在三个方面提供测序服务 平台-Ion Torrent PGM&S5，Illumina MiSeq和NextSeq 500-以及ABI毛细管上的Sanger测序 测序仪。毛细管测序仪还支持基于微卫星的基因分型、片段分析和细胞 线路身份验证。全基因组和靶向分子图谱在多个平台上进行。这个 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实时聚合酶链式反应分析仪。分子生物学服务 包括克隆、亚克隆、定点突变和载体构建。ACC成员受益于 在其整个项目中提供咨询和培训。一系列服务以及 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的分子图谱， 与癌症基因的定向测序一起，可以帮助ACC成员进行癌症诊断， 分类、风险预测和选择适当的治疗方法。广汽助推多重高位 影响出版物，包括支持RNA-Seq和ATAC-Seq数据的生成，以阐明肿瘤- 免疫细胞浸润和对免疫治疗的反应的变异性基础上的特定特征 小鼠胰腺癌模型(Li等人，免疫力，2018年；Markosyan等人，J Clin Invest，2019)。行政协调会 在最近使用共享资源的376名调查人员中，成员占102人(27%) 报告期(07/01/18-06/30/19)。除了CCSG的支持外，GAC的资金来自 按存储容量使用计费、赠款/合同和机构支助，包括购买设备的资金。这个 该设施优秀的科技管理，以及高素质和稳定的员工， 为这一成熟而有效的共享资源的声誉做出贡献，作为 严格的癌症研究所需的基础设施。