Cancer Bioinformatics Services

摘要：癌症生物信息学服务(CBS) 癌症生物信息学服务(CBS)专注于为UPCI调查人员提供分析专业知识， 支持癌症生物标记物的计算基础设施、专门数据库和研究分析 发现号。这些最先进的生物信息学能力涉及到癌症之间的深度合作 生物信息学服务(CBS)和生物医学信息学系生物信息学系 匹兹堡超级计算中心、个性化医学研究所和匹兹堡大学 仿真建模中心。CBS在下一个续约期的目标是：1)提供 生物信息学分析支持所有微阵列和下一代测序(NGS)平台。这 包括实验设计、差异表达(DE)分析、miRNA靶标分析、拷贝数 分析、查询公共数据库和使用商业(Invenity Path)进行高级路径分析 分析、GeneGo和学术工具(如Cytoscape)。2)对TCGA等进行综合分析 来自所有平台的联合体数据，包括表达、甲基化、体细胞变异和拷贝数。3) 根据共同数据使用协议(DUA)开发和实施匹兹堡基因组资源 存储库(PGRR)，用于存储、分析和归档大型PB大小基因组数据的基础设施 例如来自癌症基因组图谱(TCGA)项目。哥伦比亚广播公司还将开发PGRR信息会议 并开发生物信息学服务，以方便使用。4)开发专门的节目数据库 例如UPCI皮肤孢子，其集成了完全不同临床数据源，使得能够集成基因组学 使用开源信息学将生物学与临床表型相结合的生物标记数据 床边(I2b2)平台和相关技术。5)为癌症基因组学设施提供IT支持 (CGF)高性能计算需求，6)准备数据以供发布，包括向 基因表达总括(GEO)和协助手稿准备，以及7)与卫生局合作 Science Library System(HSLS)用于评估生物信息学工具的许可和季度教学 面向用户社区的生物信息学课程。CBS的目标是提供具有成本效益和效率的 为UPCICCSG社区提供生物信息学分析服务。目前的提案重点是扩大 这些服务对新的癌症生物标志物和治疗方法的科学发现至关重要 目标。在目前的项目期间，所有10个研究方案都使用了哥伦比亚广播公司的服务。

Abstract: Cancer Bioinformatics Services (CBS) Cancer Bioinformatics Service (CBS) focuses on providing UPCI investigators with the analysis expertise, computational infrastructure, specialized databases and research analytics to support cancer biomarker discovery. These state-of-the-art bioinformatics capabilities involve deep collaborations between the Cancer Bioinformatics Service (CBS) and the Department of Biomedical Informatics bioinformatics faculty, the Pittsburgh Supercomputing Center, the Institute of Personalized Medicine and the University of Pittsburgh’s Simulation and Modeling Center. The aims of CBS for the next renewal period are to: 1) Provide bioinformatics analysis support for all microarray and Next Generation Sequencing (NGS) platforms. This includes experimental design, differential expression (DE) analysis, miRNA target analysis, copy number analysis, queries of public databases and advanced pathway analysis using commercial (Ingenuity Pathway analysis, GeneGo, and academic (e.g. Cytoscape) tools. 2) Perform integrative analysis of TCGA and other consortia data from all platforms including expression, methylation, somatic variants and copy number. 3) Develop and implement, under a common Data Use Agreement (DUA), the Pittsburgh Genome Resource Repository (PGRR), an infrastructure for storage, analysis and archiving of large petabyte size genomic data such as from The Cancer Genome Atlas (TCGA) project. CBS will also develop PGRR informational sessions and also develop bioinformatics services to facilitate use. 4) Develop specialized databases for programs such as UPCI Skin SPORE that integrate disparate clinical data sources, enabling integration of genomics biomarker data with clinical phenotypes using the open source Informatics for Integrating Biology to the Bedside (i2b2) platforms and related technologies. 5) Provide IT support for the Cancer Genomics Facility (CGF) high performance computing needs, 6) Prepare data for publication including submitting data to the Gene Expression Omnibus (GEO) and assist with manuscript preparation, and 7) Collaborate with the Health Sciences Library System (HSLS) to evaluate bioinformatics tools for licensing and teach quarterly bioinformatics courses to the user community. The goal of CBS is to provide cost effective and efficient bioinformatics analysis services to the UPCI CCSG community. The current proposal focuses on expanding these services as they are critical to the scientific discovery of new cancer biomarkers and therapeutic targets. During that current project period all 10 Research Programs used CBS services.