Omics and Technology Core

组学和技术核心

• 批准号: 9795001
• 负责人: Rima F Kaddurah-Daouk
• 金额: $ 175.59万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9795001
• 关键词: Address; Algorithms; Alzheimer' s Disease; Archaea; Area; Bacteria; Biochemical; Biochemistry; Bioinformatics; Biological; Biological Models; Biotechnology; Blood; Brain; Brain imaging; Canada; Clinical; Collection; Communities; Complex; Computational Biology; Computational algorithm; Computer software; DNA; Data; Data Analyses; Data Provenance; Data Quality; Databases; Diet; Dimensions; Disease; Ensure; Environment; Feces; Funding; Generations; Genomics; Gold; Health Insurance Portability and Accountability Act; Human; Human Microbiome; Image; Indiana; Individual; Infrastructure; Institution; Institutional Review Boards; Investigation; Investments; Knowledge; Laboratories; Learning; Libraries; Magnetic Resonance Imaging; Mass Spectrum Analysis; Measurement; Medicine; Metagenomics; Methods; Molecular; Netherlands; Output; Pacific Northwest; Participant; Peripheral; Pharmaceutical Preparations; Phenotype; Problem Solving; Procedures; Process; Protocols documentation; Research; Research Personnel; Resolution; Sampling; Sampling Studies; Scanning; Secure; Ships; Shotguns; Site; Specialist; Specimen; Standardization; Structure; Systems Biology; Taxon; Technology; United States National Institutes of Health; Universities; Virus; Work; base; clinical phenotype; data integration; data management; data mining; experience; fecal metabolome; fungus; gut microbiome; gut microbiota; host microbiota; human model; imaging informatics; informatics infrastructure; innovation; interest; member; metabolome; metabolomics; metagenome; metagenomic sequencing; microbial; microbial community; microbiome; microbiome composition; microbiota profiles; multidisciplinary; relational database; sample collection; success

ABSTRACT – Core 1: Omics and Technology Core The Omics and Technology Core will act as a portal that interconnects all parts of the project, and will provide them with high-quality genomics, metabolomics and imaging data, to be integrated with the clinical and phenotyping information. To ensure maximal scientific output from the study samples, analysis will be conducted by leaders in each field and centers of excellence. The core will work closely with NCRAD, that will implement standardized procedures for collection of samples across the Alzheimer Centers, will coordinate shipment to our technology hubs for sample analysis, and enable tracking of chain of custody. The core will also work closely with the bioinformatics core and the Duke team to ensure gold-standard data management and to enable comprehensive data mining for the whole scientific community. The first sub-core will conduct state of the art metagenomics analysis of collected fecal samples to profile the entire microbial community inhabiting the gut. Genomic microbial DNA will be extracted and purified from the specimens using a commercially-available DNA kit, previously validated by the Human Microbiome Project. The culture- independent molecular methods will consist of shotgun metagenomic sequencing that provides the most comprehensive microbiota profile (bacteria, viruses, archaea, fungi). Rigorous sequence data analysis will utilize a set of advanced computational algorithms, according to the taxon-based or function-based data matrices. The second sub-core will conduct metabolomics analysis of blood and feces, to profile the host and gut-microbiota metabolomes. Comprehensive metabolome coverage is best achieved via combination of complementary approaches, and here we will apply various advanced methods of untargeted and targeted metabolomics. Untargeted metabolomics will utilize very high-resolution mass spectrometry (MS) to detect many thousands of compound spectra per sample, and employ complex algorithms and extensive data mining for identity elucidation. Conversely, targeted metabolomics platforms will utilize more sensitive and quantitative MS/MS measurement of only hundreds of compounds chosen according to existing evidence, biological interest and specifically the gut microbiome activity. Global metabolomics will be a cross-over between the two approaches, producing a full-scan high-resolution MS measurement of a few thousands of compounds, some identifiable via authentic standards, while others continuously added to the dynamic learning database of detected compounds, for further investigation. The third sub-core will gather quantitative magnetic resonance imaging of the brain, which contributes an additional layer to the phenotyping of the study participants. Building from the success of the ADNI project, a T1-weighted volumetric imaging will be utilized, to allow harmonization across the multiple sites. The imaging sub-core will coordinate the collection and aggregation of three- dimensional T1 imaging, and utilize existing ADCS image informatics infrastructure for high-throughput data capture, upload, and review.

摘要 - 核心1：OMICS和技术核心 OMICS和Technology Core将充当互连项目所有部分的门户，并将提供 它们具有高质量的基因组学，代谢组学和成像数据，将与临床和 表型信息。为了确保研究样本中的最大科学输出，分析将是 由每个领域和卓越中心的领导人进行。核心将与Ncrad紧密合作，这将 实施标准化程序，以收集整个阿尔茨海默氏症中心的样品，将协调 运送到我们的技术枢纽以进行样本分析，并可以跟踪监护链。核心意愿 还与生物信息学核心和杜克团队紧密合作，以确保黄金标准的数据管理 并为整个科学界提供全面的数据挖掘。第一个子核将进行 收集到的粪便样品的最新核类核学分析，以介绍整个微生物群落 居住在肠道上。基因组微生物DNA将被提取并从样品中纯化 商业上可用的DNA试剂盒，以前通过人类微生物组项目验证。文化 - 独立的分子方法将包括shot弹枪宏基因组测序，提供最多 全面的微生物群（细菌，病毒，古细菌，真菌）。严格的序列数据分析将 根据基于分类单元或基于功能的数据，利用一组高级计算算法 矩阵。第二个子核将对血液和粪便进行代谢组学分析，以介绍宿主和 肠菌菌属代谢组。通过组合，最好实现全面的代谢覆盖范围 完全方法 代谢组学。未靶向的代谢组学将利用非常高分辨率的质谱（MS）来检测 每个样品和员工复杂算法和大量数据挖掘的数千种化合物光谱 阐明身份。相反，有针对性的代谢组学平台将利用更敏感和定量的 仅根据现有证据选择的数百种化合物的MS/MS测量 兴趣，特别是肠道微生物组活性。全球代谢组学将是两者之间的交叉 方法，产生几千种化合物的全扫描高分辨率MS测量，有些 通过真实标准可识别，而其他标准则不断添加到动态学习数据库中 检测到的化合物，以进行进一步研究。第三个子核将收集定量磁共振 大脑的成像，这为研究参与者的表型贡献了一层。建筑 从ADNI项目的成功来看，将利用T1加权体积成像，以允许协调 跨多个站点。成像子核将协调三核的收集和聚集 尺寸T1成像，并利用现有的ADC图像信息基础架构进行高通量数据 捕获，上传和审查。