High Throughput Genome Sequencer for Organ Building

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DESCRIPTION (provided by applicant): The Human Genome Project affords an unrivaled opportunity to advance our understanding of the genetic basis of organismal biology. The potential impact of genomic sequence information includes not only understanding the contribution of genetic variation to complex disease, but also discovery of the genetic regulatory networks (GRNs) that control the development of organisms and their body parts. This shared instrumentation grant (SIG) specifically addresses this latter challenge, by requesting key high throughput DNA sequencing capability for a user group of interdisciplinary scientists who are actively working at the forefront of regenerative biology. The Genome Analyzer II requested is ideally suited to support the extensive SAGE and ChIP-Seq analyses now commencing as part of this Consortium effort. The Major Users are pursuing three major projects that rely critically on the proposed instrumentation, and they are also Principal Investigators and co-Principal Investigators on an NIH Interdisciplinary Research Consortium, one of nine such U54 grants awarded by the NIH in the fall of 2007. The central premise of the Systems-Based Consortium for Organ Design and Engineering, or SysCODE (http://www.SysCODE.org), is that fundamental genetic information, in the form of genetic regulatory networks (GRNs), can be determined from endogenous development about how nature builds organs. This information, in turn, can be used to fabricate organ parts from stem cells to repair organ damage and replace organ loss. A major challenge facing this Consortium is to acquire and use genomic data sets representing: (1) temporally dynamic and spatially defined gene expression data (e.g., SAGE) from both endogenous organ development and in vitro stem cell systems induced to differentiate to specific organ fates, and (2) genome wide location data (e.g., ChIP-Seq) for key transcription factors that are either necessary or sufficient for organ development, as proven by mutational analysis in humans and mice. These large data sets will be integrated at the computational level to construct gene regulatory networks (GRNs) that can be used by tissue engineers to build three organ parts, the tooth germ, the pancreatic islet, and the heart valve. These organ parts embody common developmental principles, but represent distinct structural, physiologic and mechanical endpoints. High throughput DNA sequencing instrumentation will be essential to the success of the Consortium projects that require this underlying genomic data, and to the success of the Consortium as a whole. We are therefore requesting the Illumina Genome Analyzer II to enable the construction of comprehensive RNA profiles (using SAGE libraries) and genome-wide maps of transcription factor-DNA interactions (using ChIP-Seq). Lastly, to further ensure optimal use of this valuable instrument and to extend its benefits to a broader community, we have enlisted a talented set of Other Users with scientifically compelling projects to our user group. PUBLIC HEALTH RELEVANCE: Advances in genome science make possible to postulate that fundamental genetic information, in the form of genetic regulatory networks, can be determined from endogenous development about how nature builds organs. This information, which can be obtained via the high throughput DNA sequencer being requested, can be used to fabricate organ parts to repair organ damage. Our long term goal is to construct a "molecular blueprint" that contains gene regulatory network and other information to build three organ parts: (1) the tooth germ, to replace tooth loss and provide a tractable model system for rapid clinical translation; (2) pancreatic islet cells, for treatment of Type I diabetes; and (3) cardiac outflow valves, to provide a long- term therapy for valvular heart disease, a major cause of childhood death and adult morbidity.