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: 10665002
• 负责人: James Gregory Caporaso
• 金额: $ 74.72万
• 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/10665002
• 关键词: Address; Advanced Development; Advanced Malignant Neoplasm; Architecture; Area; Bioinformatics; Cancer Detection; Cancer Prognosis; Clinical Trials; Collaborations; Colon Carcinoma; Communities; Computer software; 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; Plug-in; 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; Translating; Treatment Efficacy; Work; anticancer research; bioinformatics tool; cancer therapy; carcinogenesis; community engagement; data access; data integrity; data repository; data submission; driving force; epigenomic profiling; 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; 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.

在过去的二十年中，我们在了解微生物群（微生物群）的作用方面取得了长足的进步。 居住在人体中的数万亿微生物）以及人类健康中的微生物组（它们的基因）。 个别微生物或病毒病原体与许多癌症的病因有关，包括胃癌、结肠癌、 还有更多的癌症可能是由许多不同的微生物相互作用引起的。 代谢活动、宿主的基因型和免疫系统活动以及宿主饮食、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来推进癌症微生物组研究。 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 我们的第一个目标是改善癌症微生物组的获取。 通过为 QIIME 2 创建 Galaxy 界面，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，该生态系统在癌症领域很受欢迎 研究、开发癌症微生物组汇集分析资源、开发癌症- 重点关注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 我们的第二个目标是开发微生物组多组学。 通过创建 QIIME 2 来满足癌症研究界的需求驱动的生物信息学平台 与开发人员合作的代谢组学、宏转录组学、宏基因组学和宏蛋白质组学插件 许多重要的癌症微生物组项目通过整合这些不同的领域取得了进展。 数据类型，但实现微生物组多组学生物信息学仍存在相当大的技术障碍 所有项目将从这些方法中受益的研究人员都可以访问。为了促进这一点，我们将 按照我们最近的模型，创建一个微生物组多组学生物信息学开发者会议 QIIME 2 教学和发展会议我们的第三个目标是提高癌症的可重复性。 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，通过 与跟踪数据相关的多项功能已在 QIIME 2 中得到扩展，并帮助用户提交他们的数据 微生物组多组学原始数据到档案库的大部分工作将与 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 我们已经开始合作。

项目成果

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.

• DOI: 10.1371/journal.pcbi.1011676
• 发表时间: 2023-11
• 期刊: PLoS computational biology
• 影响因子: 4.3

Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References.

• DOI: 10.1128/msystems.00758-22
• 发表时间: 2022-10-26
• 期刊: mSystems
• 影响因子: 6.4

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

• DOI: 10.1371/journal.pcbi.1009056
• 发表时间: 2021-06
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Dillon MR;Bolyen E;Adamov A;Belk A;Borsom E;Burcham Z;Debelius JW;Deel H;Emmons A;Estaki M;Herman C;Keefe CR;Morton JT;Oliveira RRM;Sanchez A;Simard A;Vázquez-Baeza Y;Ziemski M;Miwa HE;Kerere TA;Coote C;Bonneau R;Knight R;Oliveira G;Gopalasingam P;Kaehler BD;Cope EK;Metcalf JL;Robeson Ii MS;Bokulich NA;Caporaso JG
• 通讯作者: Caporaso JG

The Oral Microbiome and Lung Cancer Risk: An Analysis of 3 Prospective Cohort Studies.

口腔微生物组和肺癌风险：3 项前瞻性队列研究的分析。

• DOI: 10.1093/jnci/djac149
• 发表时间: 2022
• 期刊: Journal of the National Cancer Institute
• 作者: Vogtmann,Emily;Hua,Xing;Yu,Guoqin;Purandare,Vaishnavi;Hullings,AutumnG;Shao,Dantong;Wan,Yunhu;Li,Shilan;Dagnall,CaseyL;Jones,Kristine;Hicks,BelyndaD;Hutchinson,Amy;Caporaso,JGregory;Wheeler,William;Sandler,DaleP;BeaneFr
• 通讯作者: BeaneFr

Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey.

美国人口的代表性口腔微生物组数据：国家健康和营养检查调查。

• DOI: 10.1016/s2666-5247(22)00333-0
• 发表时间: 2023
• 期刊: The Lancet. Microbe
• 作者: Vogtmann,Emily;Chaturvedi,AnilK;Blaser,MartinJ;Bokulich,NicholasA;Caporaso,JGregory;Gillison,MauraL;Hua,Xing;Hullings,AutumnG;Knight,Rob;Purandare,Vaishnavi;Shi,Jianxin;Wan,Yunhu;Freedman,NealD;Abnet,ChristianC
• 通讯作者: Abnet,ChristianC