OHSU Center for Specialized Data Analysis as part of the GDAN

OHSU 专业数据分析中心作为 GDAN 的一部分

• 批准号: 10689802
• 负责人: Kyle Ellrott
• 金额: $ 36.22万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10689802
• 关键词: Acceleration; Address; Algorithms; Area; Bioinformatics; Biological; Cancer Biology; Cancer Center; Charge; Clinical; Clinical Trials; Clinical Trials Design; Communities; Competence; Computer software; Data; Data Analyses; Data Set; Detection; Development; Disease; Distributed Systems; Dreams; Ensure; Evolution; Future; Genetic Heterogeneity; Genomic approach; Genomics; Goals; Heterogeneity; Individual; Infrastructure; Intervention; Knowledge; Learning; Malignant Neoplasms; Malignant neoplasm of prostate; Manuals; Messenger RNA; Methodology; Methods; Mutation; Neoplasm Metastasis; Pathway Analysis; Pathway interactions; Patients; Pharmacologic Substance; Prevention strategy; Process; Prognostic Marker; Quality Control; Research; Research Personnel; Resistance; Running; Sampling; Services; Site; Specialized Center; Survival Rate; System; Systems Integration; The Cancer Genome Atlas; Therapeutic; Therapeutic Intervention; Training; Update; Variant; Visualization; Work; bioinformatics tool; cancer genomics; cancer initiation; cancer prevention; cell free DNA; clinical care; cluster computing; complex data; computer infrastructure; computerized tools; data analysis pipeline; data integration; diagnostic biomarker; experience; genetic evolution; genomic data; improved; innovation; multidisciplinary; novel; novel diagnostics; novel strategies; patient subsets; precision medicine; programs; response; single-cell RNA sequencing; success; therapy resistant; transcriptome sequencing; treatment strategy; tumor; tumor DNA; working group

Project Summary Recent advances in therapeutics have improved survival rates for many cancers. However, nearly all metastatic tumors are incurable, and resistance to therapeutic interventions is nearly universal. There are many reasons for our lack of progress-foremost of which is lack of understanding of mechanisms of response and resistance and lack of markers to identify subsets of patients ideally-suited for specific treatments. Our team brings enormous experience in TCGA and other multi-disciplinary coordinated projects, such as BEAT-AML, and the Stand Up to Cancer West Coast Prostate Cancer Dream Team. The Cancer Genome Atlas (TCGA) was successful because multi-disciplinary teams worked together to create new and innovative knowledge about cancer and we intend to ensure that the GDAN is equally successful. In this application, we have assembled a team of proven investigators from four of the different TCGA groups to extend the successes of TCGA to the projects managed by the Center for Cancer Genomics. Our team will continue our outstanding capabilities at analyzing and interpreting cancer genomic data by deploying data analysis pipelines that support the key capabilities of the network. In addition to the our experience in coordinated network studies, we bring experience with clinical trial design and interpretation. Further, the team has deep expertise at building the computational infrastructure necessary for the GDAN to succeed. For example, in the domain of distributed computing we have deploy pipelines for execution at many sites. We also bring novel methods for integrative pathways and analysis. Finally, we bring our experiences with competitive challenges that ensure that we can identify and deploy the most effective methods for genomic data analyses. Using these strengths we will support the GDAN and the Analysis Working Groups (AWGs) that it serves with two principal objectives. The first objective and second objective, per the RFA, are the “Development of innovative bioinformatics and computational tools and methodologies”, which will allow us to make clinical and biological correlations and to “Conduct Integrative analysis of data sets generated by GCCs using the bioinformatics tools developed by each GDAC.” We will achieve these objectives in five specific aims, one administrative aim to support the GDAN and four aims, one for each of the areas where we propose a competency.

项目摘要 最近的治疗进展提高了许多癌症的存活率。然而，几乎所有 转移性肿瘤是不可治愈的，并且对治疗干预的抗性几乎是普遍的。有 我们缺乏进展的原因很多，其中最重要的是缺乏对反应机制的理解 以及缺乏标记物来鉴定理想地适合于特定治疗的患者子集。 我们的团队在TCGA和其他多学科协调项目方面拥有丰富的经验，例如 BEAT-AML和西海岸前列腺癌梦之队。癌症基因组 Atlas（TCGA）之所以成功，是因为多学科团队共同努力， 我们希望确保GDAN同样成功。在本申请中，我们 已经组建了一个由来自四个不同TCGA小组的经过验证的调查人员组成的团队， TCGA的成功，由癌症基因组学中心管理的项目。我们的团队将继续 通过部署数据分析管道，分析和解释癌症基因组数据的出色能力 支持网络的关键功能。 除了我们在协调网络研究方面的经验外，我们还带来了临床试验设计方面的经验 和解释。此外，该团队在构建必要的计算基础设施方面拥有深厚的专业知识 为了GDAN的成功例如，在分布式计算领域，我们部署了管道， 在许多地方执行。我们还带来了整合途径和分析的新方法。最后，我们带来 我们应对竞争挑战的经验，确保我们能够识别和部署最有效的 基因组数据分析方法。 利用这些优势，我们将支持GDAN及其服务的分析工作组（AWG） 两个主要目标。根据RFA，第一个目标和第二个目标是“发展 创新的生物信息学和计算工具和方法”，这将使我们能够进行临床和 生物相关性，并“使用 每个GDAC开发的生物信息学工具。我们将通过五个具体目标实现这些目标， 行政目标，以支持GDAN和四个目标，每个领域，我们提出了一个 能力