Stanford/Salk MoTrPAC Site for Genomes, Epigenomes and Transcriptomes

斯坦福/索尔克 MoTrPAC 基因组、表观基因组和转录组网站

• 批准号: 10318103
• 负责人: Stephen Montgomery
• 金额: $ 273.67万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-12-13 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10318103
• 关键词: ATAC-seq; Adipose tissue; Age; Algorithms; Alleles; Animals; Athletic; Bioinformatics; Biological; Blood; Body Composition; Cells; Characteristics; Chemicals; Chromatin; Chronic; Communities; Coordination and Collaboration; DNA Methylation; Data; Data Analyses; Data Set; Disease; Environment; Exercise; Generations; Genes; Genetic; Genetic Polymorphism; Genetic study; Genome; Genomics; Genotype-Tissue Expression Project; Goals; Health; Health Benefit; Human; Individual; Investigation; Maps; Measures; Medical; Metabolic; Methods; Methylation; Molecular; Molecular Profiling; Muscle; Nucleic Acids; Outcomes Research; Output; Participant; Pathway interactions; Persons; Physical activity; Physiological; Pilot Projects; Procedures; Process; Production; Publications; Quality Control; Reporting; Research; Research Activity; Research Design; Research Personnel; Risk Factors; Robotics; Sampling; Science; Signal Transduction; Site; Technology; Therapeutic; Time; Tissue Banks; Tissues; Transducers; Urine; Variant; Veterans; Work; circulating microRNA; cohort; cost; data access; data format; data sharing; differential expression; epigenome; epigenomics; exosome; expectation; experience; extracellular vesicles; fitness; functional genomics; gene environment interaction; high throughput technology; human study; improved; innovation; insertion/deletion mutation; interest; loss of function; multiple omics; new therapeutic target; novel; nucleic acid mapping; physical inactivity; preservation; promoter; public health relevance; response; sedentary; sedentary lifestyle; sex; tool; transcriptome; transcriptomics; whole genome

Lack of physical activity is central to numerous health problems. Despite this, we have limited understanding of the molecular components which confer the benefit of physical activity and their diverse impacts across tissues with respect to age, sex, genetics, environment and other objective physiologic, morphometric, and metabolic measures. Identifying these molecular signatures offers to provide new opportunities for treatment and therapeutics. The goal of the Molecular Transducers of Physical Activity in Humans Consortium (MoTrPAC) is to assemble a comprehensive map of the molecular changes that occur in response to physical activity and, when possible, relate these changes to the benefits of physical activity. This map will be greatly facilitated by the application of –omics technologies to identify exercise-responsive genes and to relate their benefits across multiple tissues and contexts. We propose to aid in the construction of this map as the Stanford/Salk MoTrPAC Genome, Epigenome and Transcriptome (GET) Chemical Analysis Center. We will leverage our production and analysis experience to engage in MoTrPAC study design, enable the production of high quality and low cost genomes, epigenomes and transcriptomes and facilitate and engage in bioinformatics analysis with the MoTrPAC Bioinformatics Center. Key activities will include coordination and collaboration with all the MoTrPAC sites from tissue management to data delivery. Through these activities we will sequence 3000 genomes and at least 40000 epigenomes and 40000 transcriptomes for samples collected at MoTrPAC animal and human study sites. Our site will engage in multiple levels of quality control from tissue collection to sequence mapping. Generated data in common data formats will be immediately available to MoTrPAC investigators and the Bioinformatics Center through the Google Cloud. In addition, as part of our proposed site, and in coordination with both the MoTrPAC Steering Committee and investigators, we will leverage our expertise in both studies of exosomes and chromatin accessibility sequencing with ATAC-seq to conduct two early pilots that aim to elucidate the systemic and molecular changes in response to physical activity. Additional features of our proposed site are analytical opportunities that include leveraging multiple exercise-related –omics data sets, such as the DGN study where we have genetic data, transcriptomes and exercise activity recorded for 922 people and have already identified multiple differentially expressed genes and gene-by-environment variants in response to exercise, and diverse and novel -omics methods for gene-by-environment, multi-omics and longitudinal data analysis. Our expectation is that this combination of production experience, exercise-relevant data and novel methods will support diverse and impact research outcomes in the MoTrPAC.

缺乏身体活动是许多健康问题的核心，尽管如此，我们的身体活动仍然有限。 了解赋予身体活动益处的分子成分及其作用 不同组织对年龄、性别、遗传、环境和其他目标的不同影响 识别这些分子特征可以提供生理、形态测量和代谢测量。 为治疗和治疗提供新的机会。分子传感器的目标。 人类体力活动联盟 (MoTrPAC) 旨在绘制一份关于人类体力活动的综合地图 因身体活动而发生的分子变化，并在可能的情况下将这些变化联系起来 组学的应用将极大地促进身体活动的益处。 识别运动反应基因并在多个组织中关联其益处的技术 我们建议斯坦福/索尔克 MoTrPAC 协助构建此地图。 我们将利用我们的基因组、表观基因组和转录组 (GET) 化学分析中心。 从事MoTrPAC研究设计的生产和分析经验，使生产高 高质量和低成本的基因组、表观基因组和转录组，并促进和参与 与 MoTrPAC 生物信息学中心进行生物信息学分析 关键活动将包括协调。 以及与所有 MoTrPAC 站点从组织管理到数据交付的协作。 我们将对 3000 个基因组、至少 40000 个表观基因组和 40000 个转录组进行测序 对于在 MoTrPAC 动物和人类研究地点收集的样本，我们的网站将涉及多个层面。 从组织采集到序列图谱生成的通用数据格式的质量控制。 将立即通过 MoTrPAC 研究人员和生物信息学中心获取 此外，作为我们提议的网站的一部分，并与 MoTrPAC 协调。 指导委员会和研究人员，我们将利用我们在外泌体研究和 使用 ATAC-seq 进行染色质可及性测序，进行两项早期试点，旨在阐明 我们提出的响应身体活动的系统和分子变化。 网站提供分析机会，包括利用多个与运动相关的组学数据集，例如 第 922 章 人类并已经鉴定出多个差异表达基因和不同环境的基因 对运动的反应变异，以及针对不同环境的基因的多样化和新颖的组学方法， 我们的期望是多组学和纵向数据分析的结合。 经验、与运动相关的数据和新颖的方法将支持多样化和影响力的研究 MoTrPAC 中的成果。

项目成果

Leveraging Mobile Technology for Public Health Promotion: A Multidisciplinary Perspective.

利用移动技术促进公共卫生：多学科视角。

• 发表时间: 2023-04-03
• 作者: Hicks, Jennifer L;Boswell, Melissa A;Althoff, Tim;Crum, Alia J;Ku, Joy P;Landay, James A;Moya, Paula M L;Murnane, Elizabeth L;Snyder, Michael P;King, Abby C;Delp, Scott L
• 通讯作者: Delp, Scott L

Dynamic DNA methylation: In the right place at the right time.

动态 DNA 甲基化：在正确的时间发生在正确的位置。

• 发表时间: 2018-09-28
• 作者: Luo, Chongyuan;Hajkova, Petra;Ecker, Joseph R
• 通讯作者: Ecker, Joseph R

Nonsense-mediated decay is highly stable across individuals and tissues.

无义介导的衰变在个体和组织中高度稳定。

• 发表时间: 2021
• 影响因子: 9.8
• 作者: Teran, Nicole A;Nachun, Daniel C;Eulalio, Tiffany;Ferraro, Nicole M;Smail, Craig;Rivas, Manuel A;Montgomery, Stephen B
• 通讯作者: Montgomery, Stephen B