Advanced Development of Informatics Technologies for Cancer Research and Management (U24 Clinical Trial Optional)

癌症研究和管理信息学技术的先进发展（U24临床试验可选）

• 批准号: 10447021
• 负责人: James Gregory Caporaso
• 金额: $ 73.72万
• 依托单位: NORTHERN ARIZONA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-15 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10447021
• 关键词: Address; Advanced Development; Advanced Malignant Neoplasm; Architecture; Archives; Area; Bioinformatics; Cancer Detection; Cancer Prognosis; Clinical Trials; Collaborations; Colon Carcinoma; Communities; Computer software; Conflict (Psychology); Data; Data Pooling; Data Provenance; Decentralization; Deposition; Development; Diet; Ecosystem; Educational process of instructing; Educational workshop; Ensure; Environment; Environmental Exposure; Etiology; Galaxy; Genes; Genotype; Health; Human; Human Microbiome; Human body; Immune; Immune system; Improve Access; Individual; Informatics; Malignant Neoplasms; Malignant neoplasm of cervix uteri; Metabolic; Metadata; Metagenomics; Methods; Modeling; Multiomic Data; Online Systems; Prognosis; Publications; R programming language; Reproducibility; Research; Research Personnel; Resources; Ribosomal RNA; Role; Running; Sampling; Series; Smoking Status; Systems Analysis; Taxonomy; Technology; The Cancer Genome Atlas; Time; Translating; Treatment Efficacy; Work; anticancer research; base; bioinformatics tool; cancer therapy; carcinogenesis; community engagement; data access; data integrity; data repository; data submission; driving force; epigenome; graphical user interface; improved; insight; malignant stomach neoplasm; metabolome; metabolomics; metagenome; metaproteomics; metatranscriptome; metatranscriptomics; microbial; microbiome; microbiome research; microbiota; microorganism; multiple omics; neoplasm resource; pathogenic microbe; pathogenic virus; preference; repository; research and development; skills; success; symposium; tool

In the past two decades, we have taken large strides towards understanding the role of the microbiota (the trillions of microorganisms inhabiting the human body) and the microbiome (their genes) in human health. Individual microbial or viral pathogens are implicated in the etiology of many cancers, including gastric, colon, and cervical cancer. Still more cancers likely arise from the interplay of many different microbial taxa, their metabolic activities, the host’s genotype and immune system activity, and factors such as host diet, current and former smoking status, and environmental exposures. We propose to advance cancer microbiome research through three specific aims. This work will be performed in the context of the popular QIIME 2 microbiome bioinformatics platform and the Qiita public microbiome data repository and pooled analysis system. In our first aim, we will improve access to cancer microbiome bioinformatics methods and data through the creation of a Galaxy interface for QIIME 2, improved support for working with QIIME 2 in the R programming language and Galaxy GUI ecosystem, popular for cancer research, the development of a resource for cancer microbiome pooled analysis, the development of a cancer- focused microbiome bioinformatics workshop series, and by making QIIME 2 and cancer microbiome data accessible from within the NCI Cloud Resources. Our second aim will develop a microbiome multi-omics bioinformatics platform driven by the needs of the cancer research community through creating QIIME 2 plugins for metabolomics, metatranscriptomics, metagenomics, and metaproteomics with developers working in these areas. Many important cancer microbiome projects have made advances by integrating these different data types, yet considerable technical hurdles remain to making microbiome multi-omics bioinformatics accessible by all researchers whose projects would benefit from these methods. To facilitate this, we will create a microbiome multi-omics bioinformatics developer conference, following the model of our recent Teaching and Developing QIIME 2 conference. Our third aim will improve the reproducibility of cancer microbiome bioinformatics methods, and the reliability of cancer microbiome bioinformatics results, by expanding several features related to tracking data provenance in QIIME 2, and helping users submit their microbiome multi-omics raw data to archival repositories. Much of this work will occur in collaboration with NCI Informatics Technology for Cancer Research (ITCR) and Cloud Resources project teams, several of whom we’re already beginning to collaborate with.

在过去的二十年里，我们在理解微生物群的作用方面取得了很大的进步（ 数万亿的微生物居住在人体）和微生物组（他们的基因）在人类健康。 个别微生物或病毒病原体与许多癌症的病因学有关，包括胃癌、结肠癌、 和宫颈癌。还有更多的癌症可能是由许多不同的微生物类群的相互作用引起的，它们 代谢活动，宿主的基因型和免疫系统活动，以及诸如宿主饮食，当前和 以前的吸烟状况和环境暴露。 我们建议通过三个具体目标推进癌症微生物组研究。这项工作将在 在流行的QIIME 2微生物组生物信息学平台和Qiita公共微生物组数据的背景下 存储库和汇集分析系统。在我们的第一个目标中，我们将改善癌症微生物组的获取 通过为QIIME 2创建Galaxy接口，改进对生物信息学方法和数据的支持， 在R编程语言和Galaxy GUI生态系统中使用QIIME 2， 研究，开发用于癌症微生物组汇总分析的资源，癌症的发展- 重点微生物组生物信息学研讨会系列，并通过制作QIIME 2和癌症微生物组数据， 可从NCI云资源中访问。我们的第二个目标是开发微生物组多组学 通过创建QIIME 2，由癌症研究社区的需求驱动的生物信息学平台 用于代谢组学、元转录组学、元基因组学和元蛋白组学的插件， 在这些领域。许多重要的癌症微生物组项目通过整合这些不同的 数据类型，但使微生物组多组学生物信息学仍然存在相当大的技术障碍 所有项目将受益于这些方法的研究人员都可以访问。为了促进这一点，我们将 创建一个微生物组多组学生物信息学开发者会议，按照我们最近的模型， 教学和开发QIIME 2会议。我们的第三个目标是提高癌症的可再生性 微生物组生物信息学方法，以及癌症微生物组生物信息学结果的可靠性， 扩展了QIIME 2中与跟踪数据来源相关的几个功能，并帮助用户提交他们的 微生物组多组学原始数据到档案库。这项工作的大部分将与NCI合作进行 癌症研究信息技术（ITCR）和云资源项目团队，其中一些人 我们已经开始合作了。