Epigenomics Data Analysis and Coordination Center at Baylor College of Medicine

描述(申请人提供)：高密度微阵列和下一代测序技术，加上注释的人类基因组序列的可用性，正在开辟一条通向分子表观遗传模式的全面图谱的道路。预计对表观遗传模式的全面绘制和研究将提供对人类发育、生理和疾病的洞察。表观遗传模式既可以沿基因组序列“水平”绘制，也可以“垂直”跨越多个分化和发育阶段以及生理条件。表观基因组学的这一愿景呼吁既适合高通量数据驱动的科学的新组织模式，也适合创新的联网网络基础设施。该项目旨在开发这种联网的网络基础设施，并利用它来整合和协调数据分析和数据管道，这些数据分析和数据管道涉及指定的参考表观基因组测绘中心(REMC)、NCBI和其他参与者。该基础设施建立在现已建立的Genboree系统的基础上，该系统是在许多基因组项目的背景下开发的，最近被用于协调癌症基因组图谱项目的试点阶段。该基础设施将为进一步整合新的表观基因组学技术提供可扩展性和适应性，以适应日益多样化的实验和计算方法。使用软件即服务模式、Web服务和语义网技术，基础设施将有助于整合和协调REMC、NCBI以及跨地理位置工作的表观基因组学领域越来越多的合作机构和多学科小组的努力。公共卫生相关性：表观基因组学是研究未在基因组DNA中编码的人类细胞的可遗传或稳定变化。表观基因组变化在肥胖症、自闭症和癌症等多种疾病中的作用正在显现。重要的是，由于表观基因组现象受到营养和环境的影响，包括孕期的母体营养，因此增加对表观基因组学的理解可能会通过改变人类的营养和行为来促进健康。为了更好地了解人类健康和疾病中的表观基因组现象，美国国立卫生研究院表观基因组学路线图倡议建议全面绘制和研究不同发育阶段和生理条件下人类组织的表观基因组模式。高密度微阵列和下一代测序技术，加上注释的人类基因组序列的可获得性，正在开辟一条通向这种模式的全面图谱的道路。产生的数据量和多样性将非常大，需要信息基础设施才能进行适当的分析。该项目以已建立的通过互联网进行协作基因组研究的Genboree系统为基础，旨在开发这样一个网络基础设施，并利用它来整合和协调数据分析和数据管道，这些数据分析和数据管道涉及指定的参考表观基因组绘制中心和NIH表观基因组学路线图倡议的其他参与者。

DESCRIPTION (provided by applicant): High-density microarrays and next-generation sequencing technologies, coupled with the availability of the annotated human genomic sequence, are opening a road toward a comprehensive mapping of molecular epigenetic patterns. It is anticipated that comprehensive mapping and study of epigenetic patterns both "horizontally" along the genomic sequence and "vertically" across multiple differentiation and developmental stages and physiological conditions, will provide insights into human development, physiology, and disease. This vision of epigenomics calls both for novel organizational models suitable for high-throughput data-driven science and for innovative networked cyberinfrastructure. This project aims to develop such networked cyberinfrastructure and employ it to integrate and coordinate data analyses and data pipelines involving designated Reference Epigenome Mapping Centers (REMCs), NCBI, and other participants. The infrastructure builds on the now well established Genboree system which was developed in the context of numerous genome projects and has most recently been employed to coordinate the pilot stage of The Cancer Genome Atlas Project. The infrastructure will provide both scalability for further integration of new epigenomic technologies with increasing data production throughputs and adaptability to accommodate an increasing diversity of experimental and computational methodologies. Using the software-as-a-service model, web services, and semantic web technologies, the infrastructure will help integrate and coordinate efforts of REMCs, NCBI, and an increasing number of collaborating institutions and multi-disciplinary groups in the field of epigenomics working across geographic locations. PUBLIC HEALTH RELEVANCE: Epigenomics is the study of heritable or stable changes in human cells that are not coded in the genomic DNA. The role of epigenomic changes in diseases as diverse as obesity, autism, and cancer is coming to light. Importantly, because epigenomic phenomena are affected by nutrition and environment, including maternal nutrition during pregnancy, increased understanding of epigenomics may lead to better health through changes in human nutrition and behavior. To better understand epigenomic phenomena in human health and disease, the NIH Roadmap Initiative in Epigenomics proposes comprehensive mapping and study of epigenomic patterns in human tissues at different developmental stages and physiological conditions. High-density microarrays and next-generation sequencing technologies, coupled with the availability of the annotated human genomic sequence, are opening a road toward a comprehensive mapping of such patterns. The amount and diversity of data produced will be very large and will require an informatic infrastructure for proper analysis. Building on the established Genboree system for collaborative genomic research over the Internet, this project aims to develop such a networked infrastructure, and employ it to integrate and to coordinate data analyses and data pipelines involving designated Reference Epigenome Mapping Centers and other participants in the NIH Roadmap Initiative in Epigenomics.