High Throughput Genome Sequencer for Organ Building

描述(申请人提供)：人类基因组计划提供了一个无与伦比的机会，以促进我们对生物生物学的遗传学基础的理解。基因组序列信息的潜在影响不仅包括了解遗传变异对复杂疾病的贡献，还包括发现控制生物体及其身体部分发育的遗传调控网络(GRN)。这项共享仪器拨款(SIG)通过为活跃在再生生物学前沿的跨学科科学家用户群体申请关键的高通量DNA测序能力，专门解决了后一项挑战。所要求的基因组分析仪II非常适合于支持广泛的SAGE和芯片序列分析，该分析现已作为该联盟工作的一部分开始。主要用户正在进行严重依赖于拟议仪器的三个主要项目，他们也是国家卫生研究院跨学科研究联盟的首席调查员和联合首席调查员，这是国家卫生研究院在2007年秋季授予的九项此类U54赠款之一。基于系统的器官设计与工程联盟(http://www.SysCODE.org)，)的核心前提是，以遗传调控网络(GRN)形式存在的基本遗传信息可以从关于自然如何构建器官的内源性发展中确定。反过来，这些信息可以用来用干细胞制造器官部件，以修复器官损伤和取代器官损失。该联盟面临的一个主要挑战是获取和使用基因组数据集，这些数据集包括：(1)来自内源器官发育和体外干细胞系统的时间动态和空间定义的基因表达数据(例如SAGE)，以及(2)人类和小鼠突变分析证明的对器官发育必需或足够的关键转录因子的全基因组位置数据(例如ChIP-Seq)。这些大型数据集将在计算水平上进行整合，以构建基因调控网络(GRN)，组织工程师可以利用GRN构建牙胚、胰岛和心脏瓣膜三个器官部分。这些器官部分体现了共同的发育原则，但代表了不同的结构、生理和机械终点。高通量DNA测序仪器将是联盟项目成功的关键，这些项目需要基础基因组数据，并对联盟整体的成功至关重要。因此，我们要求Illumina基因组分析仪II能够构建全面的RNA图谱(使用SAGE文库)和全基因组转录因子-DNA相互作用图(使用CHIP-SEQ)。最后，为了进一步确保这一宝贵工具的最佳利用，并将其惠及更广泛的社区，我们招募了一批具有科学说服力的项目的其他有才华的用户加入我们的用户群体。与公共健康相关：基因组科学的进步使人们有可能假设，以基因调控网络的形式，基本的遗传信息可以通过关于自然如何构建器官的内源性发育来确定。这些信息可以通过所要求的高通量DNA测序仪获得，可以用来制造器官部分来修复器官损伤。我们的长期目标是构建一个包含基因调控网络和其他信息的“分子蓝图”，以构建三个器官部分：(1)牙胚，以取代牙齿缺失，并为快速临床移植提供一个易于处理的模型系统；(2)胰岛细胞，用于治疗I型糖尿病；(3)心脏流出瓣膜，为瓣膜心脏病提供长期治疗，瓣膜心脏病是儿童死亡和成人发病率的主要原因。

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.