Center for comprehensive proteogenomic data analysis

综合蛋白质组数据分析中心

• 批准号: 10440579
• 负责人: GAD A GETZ
• 金额: $ 79.11万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-15 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10440579
• 关键词: Affect; Affinity; Algorithmic Analysis; Algorithms; Antineoplastic Agents; Big Data; Biochemical; Bioinformatics; Biological; Biological Models; Cancer Biology; Clinical; Collaborations; Collection; Complex; Computational Biology; Copy Number Polymorphism; Data; Data Analyses; Data Commons; Data Set; Databases; Decision Aid; Decision Making; Disease; Dose; Drug Targeting; Drug resistance; Encapsulated; Foundations; Genes; Genetic; Genome; Genomics; HLA Antigens; Human; Immune; Individual; Leadership; Ligase; Light; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Measurement; Methodology; Methods; Modeling; Multiomic Data; Mutate; Mutation; Normal tissue morphology; Pathway Analysis; Pathway interactions; Peptides; Pharmacotherapy; Phase; Phosphotransferases; Post Translational Modification Analysis; Post-Translational Modification Site; Post-Translational Protein Processing; Process; Prognostic Marker; Proteins; Proteome; Proteomics; Publications; RNA; Reporting; Reproducibility; Retrieval; Sampling; Scientist; Signal Transduction; Site; Source; Specific qualifier value; Standardization; Subgroup; System; Systems Biology; Techniques; Therapeutic; Therapeutic Intervention; Transcript; Translational Research; Ursidae Family; Validation; antigen binding; base; cancer biomarkers; cancer subtypes; cancer type; cloud based; cohort; computerized data processing; data repository; differential expression; disease prognostic; flexibility; genomic data; improved; individual patient; insight; interest; laboratory experiment; metabolomics; multiple omics; neoantigens; new therapeutic target; next generation sequencing; novel; personalized medicine; phenotypic data; proteogenomics; response; therapeutic target; tool; transcriptomics; translational pipeline; tumor

Project Summary Proteogenomics involves the integrative multi-omic analysis of genomic, transcriptomic, proteomic and post- translational modification data produced by next-generation sequencing and mass spectrometry-based proteomics. Several publications by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and others have highlighted the impact of proteogenomics in enabling deeper insight into the biology of cancer and identification of potential drug targets. Integrative analysis of multi-omic data requires the deployment of complex algorithms and data processing techniques, which are generally inaccessible to scientists without a background in bioinformatics and computational biology. Our proposed center for comprehensive proteogenomic data analysis will encapsulate a comprehensive set of analysis methods in a platform that will be (i) simple to use (ii) flexible (iii) automated, facilitating the routine application to all CPTAC proteogenomic datasets as they become available, and (iv) able to incorporate new methods with minimal effort. We will leverage PANOPLY--a cloud-based platform for automated and reproducible proteogenomic data analysis--as the foundation, with specific, carefully chosen algorithms targeted for addition to provide an expansive set of analysis capabilities that can be easily harnessed to provide a rapid and extensive baseline analysis for proteogenomic studies, leading to many disease specific hypotheses that can be explored further using additional computational and wet-lab experiments. Our collection of tools, algorithms and interactive reports will enable unprecedented, automated and integrative systems-biology level analyses of proteome, post-translational modification and metabolomic data combined with genomic data for individual disease cohorts and pan-cancer analysis across cohorts, leading to deeper understanding of cancer biology and enabling identification of therapeutic targets and disease/prognostic biomarkers.

项目概要 蛋白质组学涉及基因组学、转录组学、蛋白质组学和后处理的综合多组学分析。 基于下一代测序和质谱法产生的翻译修饰数据 蛋白质组学。临床蛋白质组学肿瘤分析联盟 (CPTAC) 等的多篇出版物 强调了蛋白质基因组学在更深入地了解癌症生物学方面的影响， 识别潜在的药物靶点。多组学数据的综合分析需要部署 复杂的算法和数据处理技术，如果没有专业知识，科学家通常无法获得这些技术 生物信息学和计算生物学背景。 我们提议的综合蛋白质组数据分析中心将囊括全面的 平台中的一组分析方法将 (i) 使用简单 (ii) 灵活 (iii) 自动化，促进 对所有可用的 CPTAC 蛋白质组数据集进行常规应用，并且 (iv) 能够 以最小的努力融入新方法。我们将利用 PANOPLY——一个基于云的平台 自动化且可重复的蛋白质组数据分析——作为基础，以特定的、精心选择的 针对加法的算法提供了一组广泛的分析功能，可以轻松地 利用它为蛋白质组学研究提供快速而广泛的基线分析，从而导致许多 可以使用额外的计算和湿实验室进一步探索的疾病特定假设 实验。 我们的工具、算法和交互式报告集合将实现前所未有的自动化和集成 蛋白质组、翻译后修饰和代谢组数据相结合的系统生物学水平分析 具有单个疾病队列的基因组数据和跨队列的泛癌分析，从而导致更深入的研究 了解癌症生物学并能够识别治疗靶点和疾病/预后 生物标志物。