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.
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.
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