Integrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC)

综合分析管道

• 批准号: 8123272
• 负责人: GORDON B. MILLS
• 金额: $ 143.84万
• 依托单位: UNIVERSITY OF TX MD ANDERSON CAN CTR
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-29 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8123272
• 关键词: Address; Algorithms; Architecture; Bioinformatics; Biological; Biological Markers; Biology; Biometry; Cancer Center; Cancer Patient; Clinical; Clinical Research; Confidentiality; Country; Data; Data Analyses; Development; Ensure; Funding; Genome; Goals; Human; Imagery; Institution; Lead; Malignant Neoplasms; Molecular Profiling; Participant; Pathology; Pathway Analysis; Research Personnel; Software Engineering; Source; Specimen; System; Systems Biology; Technology; The Cancer Genome Atlas; Time; University of Texas M D Anderson Cancer Center; Work; base; biological systems; biosignature; cancer Biomedical Informatics Grid; computer based Semantic Analysis; data integration; design; follow-up; innovation; member; novel; programs; software development; tumor; user-friendly

DESCRIPTION (provided by applicant): The proposed Genome Data Analysis Center B (GDAC B) will work cooperatively with other GDACs funded by The Cancer Genome Atlas (TCGA) project to (i) develop an innovative, integrative pipeline for systems- level analysis of TCGA's molecular profiling data on many different types of human tumors and (ii) apply that pipeline and its component modules to TCGA data to address important biological and clinical questions. An overarching goal is to 'personalize' the management of patients' cancers on the basis of new tumor biomarkers and biosignatures. For the first time, it is easier to generate millions of data points on tumors than to analyze or interpret those data, hence the bioinformatic challenge is formidable. The pipeline will be constructed using the Agile software development paradigm and semantic web query architecture. It will be based on novel algorithms and modules developed by participants in the GDAC. Included will be modules for data integration, data visualization, pathway analysis, and systems biological interpretation, all designed to be user-friendly for the bench researcher and clinician. Those modules will be interfaced with additional ones developed by other GDACs, All development will adhere to standards of TCGA and the Cancer Biomedical Informatics Grid (caBIG) and will provide controlled access to ensure confidentiality of personally identifiable data. The proposed GDAC team brings to this project expertise in bioinformatics, biostatistics, software engineering, high-throughput molecular profiling technologies, systems-oriented biology, biomarker studies, pathology, and clinical research. The three co-PIs (for bioinformatics, systems biology, and clinical research) have each participated actively in TCGA since its inception, as have other members of the team, including the lead software engineer. A major strength is the University of Texas M. D. Anderson Cancer Center (MDACC) as an institution. MDACC has been, and presumably will continue to be, the largest source of tumor specimens for TCGA. As one of the country's foremost cancer centers, with by far the largest cancer clinical research program, MDACC has unparalleled expertise for follow up on medically important leads that result from the development and application of the pipeline to TCGA data

描述（申请人提供）：拟议的基因组数据分析中心B（GDAC B）将与癌症基因组图谱（TCGA）项目资助的其他GDAC合作，（i）开发一种创新的，用于TCGA对许多不同类型的人类肿瘤的分子谱数据的系统级分析的集成管道;以及（ii）将该管道及其组件模块应用于TCGA数据，以解决重要的生物学和临床问题。一个首要目标是基于新的肿瘤生物标志物和生物特征“个性化”患者癌症的管理。这是第一次，生成数百万个肿瘤数据点比分析或解释这些数据更容易，因此生物信息学的挑战是巨大的。管道将使用敏捷软件开发范式和语义Web查询架构构建。它将基于GDAC参与者开发的新算法和模块。包括数据集成，数据可视化，途径分析和系统生物学解释模块，所有这些模块都旨在为实验室研究人员和临床医生提供用户友好性。这些模块将与其他GDAC开发的其他模块接口，所有开发都将遵守TCGA和癌症生物医学信息网格（caBIG）的标准，并将提供受控访问，以确保个人身份数据的机密性。拟议的GDAC团队为该项目带来了生物信息学，生物统计学，软件工程，高通量分子分析技术，系统导向生物学，生物标志物研究，病理学和临床研究方面的专业知识。三个co-PI（生物信息学，系统生物学和临床研究）自成立以来都积极参与TCGA，团队的其他成员也是如此，包括首席软件工程师。一个主要的优势是得克萨斯大学M。D.安德森癌症中心（MDACC）作为一个机构。MDACC一直是，并可能继续是TCGA的最大肿瘤标本来源。作为该国最重要的癌症中心之一，拥有迄今为止最大的癌症临床研究计划，MDACC拥有无与伦比的专业知识，可以跟踪TCGA数据管道的开发和应用所产生的医学重要线索