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Genomic Analysis Core

基因组分析核心

基本信息

批准号：
10330982
负责人：
TAPAN GANGULY
金额：
$ 0.21万
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/10330982
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

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.

项目概要-基因组分析核心 Abramson癌症中心（ACC）的基因组分析核心（GAC）提供了一个基因组谱，和分子生物学服务，拥有一支经验丰富、训练有素的专业团队。这些服务是ACC成员研究特定基因在正常或异常细胞过程中的作用所必需的发现于癌细胞和肿瘤中。研究人员可以观察样本中的整体基因表达模式，未受影响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-是整合在一个单一的伞式融资机制下。所产生的共享资源过去是， Tapan Ganguly博士，自2003年以来一直负责DNA测序设施。他由埃里克·图伦斯协助，技术总监，在GAC担任领导职务五年，服务15年。该团队得到支持其他七位平均有十五年经验的全职员工。GAC提供三个测序服务平台-ABI毛细管上的Ion Torrent PGM & S5、Illumina MiSeq & NextSeq 500和桑格测序定序器毛细管测序仪还可以进行基于微卫星的基因分型、片段分析和细胞测序。线路认证。全基因组和靶向分子谱分析在多个平台上进行。的 GAC支持在Affyssin GeneChips和高通量GeneTitan上进行定量RNA和DNA分析， Fluidigm BioMark HD和ABI QS 12 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成员受益于在整个项目中提供咨询和培训。服务范围沿着的专业知识 GAC主任促进基因发现，功能表征和其他研究问题，阐明人类癌症的分子发病机制。此外，DNA和RNA的分子图谱，与癌症基因的靶向测序一起，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。GAC促成了多个高影响出版物，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疗法的应答的可变性的基础的特定特征，小鼠胰腺癌模型（Li等，Immunity，2018; Markosyan等人，J Clin Invest，2019）。ACC 在最近一次使用共享资源的376名调查员中，有102名成员（27%）报告所述期间（2018年1月7日至2019年6月30日）。除了CCSG的支持外，GAC的资金还来自于退款、赠款/合同和机构支持，包括设备采购资金。的该设施的优秀科学和技术管理，沿着高素质和稳定的工作人员，有助于这一良好的和有效的共享资源的声誉，作为一个不可分割的一部分，严格的癌症研究所需的基础设施。