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

综合分析管道

• 批准号: 7942759
• 负责人: GORDON B. MILLS
• 金额: $ 149.18万
• 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/7942759
• 关键词: Address; Algorithms; Architecture; Atlases; 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; Time; University of Texas M D Anderson Cancer Center; Work; base; biological systems; biosignature; cancer Biomedical Informatics Grid; cancer genome; 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（由申请人提供）：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) 开发创新的综合管道，用于对许多不同类型的人类肿瘤的 TCGA 分子谱数据进行系统级分析，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。总体目标是基于新的肿瘤生物标志物和生物特征对患者的癌症进行“个性化”管理。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，因此生物信息学挑战是巨大的。该管道将​​使用敏捷软件开发范例和语义网络查询架构来构建。它将基于 GDAC 参与者开发的新颖算法和模块。其中包括数据集成、数据可视化、路径分析和系统生物学解释的模块，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的体验。这些模块将与其他 GDAC 开发的其他模块相连接，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 团队将为该项目带来生物信息学、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。自 TCGA 成立以来，三位联合 PI（生物信息学、系统生物学和临床研究）以及团队的其他成员（包括首席软件工程师）都积极参与了 TCGA。德克萨斯大学 MD 安德森癌症中心 (MDACC) 是一个主要优势机构。 MDACC 一直是并且可能将继续是 TCGA 肿瘤标本的最大来源。作为全国最重要的癌症中心之一，MDACC 拥有迄今为止最大的癌症临床研究项目，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重要医学线索