Genboree System for Translational Studies of Genome Variation

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DESCRIPTION (provided by applicant): We propose to develop the Genboree system to enable collaborative translational studies of genome variation on any scale. By employing an innovative combination of information technologies such as Life Science Identifiers, XML, Distributed Annotation System and web services, Genboree will minimize technical barriers to collaboration by interdisciplinary research groups including clinicians, biologists, and genome scientists. Two independently NIH-funded projects, "Identification of Nonsyndromic Hearing Impairment Genes" ("NSHI") and "Parallel Sequence Profiling of Ion Channels in Epilepsy" ("Epilepsy") will be employed to drive development and enhance usability of Genboree software. Genboree system will enable the study of genetic susceptibility factors to complex yet prevalent diseases such as NSHI and Epilepsy. An improved understanding of causative patterns of genome variation that is anticipated to emerge from these efforts will produce predictive and diagnostic tests and will help elucidate pathological mechanisms. The understanding of mechanisms will in turn point to means of disease prevention and to targets for therapeutic intervention. This program of research has the potential to propel the 21st century medicine from a diagnose-and-treat to a predict-and-prevent paradigm. One of the main informatic challenges facing this program of research is the integration of clinical and genomic information. Another challenge is the integration of collaborative efforts involving clinicians, biologists, and genome scientists. Yet another challenge is extreme scalability required to handle the torrent of genome variation information that will surpass by orders of magnitude the amounts generated by genome projects in the past. None of these three challenges are adequately addressed at this time. The general aim of this proposal is to address these challenges through the development of the Genboree system. Genboree prototype was initially developed to support collaborative genome annotation and comparative genomic projects at the Human Genome Sequencing Center at Baylor College of Medicine. One of the key features of Genboree is the ability to integrate data using assembled genome sequences as a reference by projecting any experimentally or computationally derived data elements onto the reference genomic sequence in the form of annotations. Due to built-in .access control features, Genboree is within reach of HIPAA compliance and thus capable of integrating both patient information and the genomic information obtained from patient samples. Building on the current Genboree prototype, a system will be developed to integrate data, tools, and discovery pipelines to support collaborative translational studies of genome variation.