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

在过去的二十年里，我们在理解微生物区系( 数以万亿计的微生物)和微生物群(它们的基因)对人类健康的影响。 单独的微生物或病毒病原体与许多癌症的病因有关，包括胃、结肠、 和宫颈癌。还有更多的癌症可能是由于许多不同的微生物分类群的相互作用而产生的，他们的 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。这项工作将被执行 在流行的QIIME 2微生物组生物信息学平台和齐塔公共微生物组数据的背景下 存储库和池分析系统。在我们的第一个目标中，我们将改善获得癌症微生物组的机会 通过为QIIME 2创建Galaxy接口的生物信息学方法和数据，改进了对 在R编程语言和Galaxy图形用户界面生态系统中使用QIIME 2，这是癌症的常见病 研究，开发用于癌症微生物群池分析的资源，开发一种癌症- 聚焦微生物组生物信息学系列研讨会，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发展微生物组多组学 由癌症研究界需求驱动的生物信息学平台通过创建QIIME 2 用于代谢组学、元转录组学、元基因组学和元蛋白质组学的插件，与开发人员合作 在这些地区。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，然而在进行微生物组多组学生物信息学方面仍然存在相当大的技术障碍 其项目将从这些方法中受益的所有研究人员都可以访问。为了促进这一点，我们将 创建一次微生物组多组学生物信息学开发者会议，遵循我们最近的模式 QIIME第二届教学与发展大会。我们的第三个目标是提高癌症的再生性 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，由 在QIIME 2中扩展了几个与跟踪数据来源相关的功能，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，其中几个 我们已经开始与之合作。

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.