Genboree System for Translational Studies of Genome Variation

用于基因组变异转化研究的 Genboree 系统

• 批准号: 7275266
• 负责人: Aleksandar Milosavljevic
• 金额: $ 56.81万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-15 至 2009-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7275266
• 关键词: Address; Automatic Data Processing; Biological Assay; Biological Sciences; Clinical; Clinical Data; Collaborations; Communication; Complex; Computer software; Custom; DNA; DNA Resequencing; Data; Data Display; Data Element; Data Set; Databases; Derived Data Element; Development; Diagnosis; Diagnostic tests; Disease; Disease Association; Electronic Mail; Epilepsy; Event; Exons; Extensible Markup Language; Funding; Gene Mutation; Genes; Genetic Predisposition to Disease; Genome; Genomics; Haplotypes; Health Insurance Portability and Accountability Act; Human; Informatics; Information Technology; Interdisciplinary Study; Internet; Ion Channel; Medicine; Mus; Mutation; Notification; Nucleic Acid Regulatory Sequences; Online Systems; Patients; Pattern; Phenotype; Process; Publications; Research; Research Personnel; Role; Sampling; Scientist; Score; Services; Site; System; Therapeutic Intervention; Time; Tissues; Update; Validation; Variant; access control features; base; college; comparative; computerized data processing; computerized tools; data integration; design; disorder prevention; genome sequencing; hearing impairment; improved; innovation; interoperability; prevent; programs; protein structure function; prototype; research study; tool; translational study; usability

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.

描述（由申请人提供）：我们建议开发 Genboree 系统，以实现任何规模的基因组变异的协作转化研究。通过采用生命科学标识符、XML、分布式注释系统和网络服务等信息技术的创新组合，Genboree 将最大限度地减少包括临床医生、生物学家和基因组科学家在内的跨学科研究小组合作的技术障碍。 NIH 独立资助的两个项目“非综合征性听力损伤基因的识别”（“NSHI”）和“癫痫离子通道的并行序列分析”（“癫痫”）将用于推动 Genboree 软件的开发和增强可用性。 Genboree 系统将使研究 NSHI 和癫痫等复杂而流行的疾病的遗传易感因素成为可能。这些努力预计将提高对基因组变异致病模式的理解，从而产生预测和诊断测试，并有助于阐明病理机制。对机制的理解反过来将指向疾病预防的手段和治疗干预的目标。该研究计划有可能推动 21 世纪医学从诊断和治疗范式转向预测和预防范式。该研究计划面临的主要信息挑战之一是临床和基因组信息的整合。另一个挑战是临床医生、生物学家和基因组科学家的协作努力的整合。另一个挑战是处理大量基因组变异信息所需的极大可扩展性，这些信息将比过去基因组项目产生的信息量高出几个数量级。目前这三个挑战都没有得到充分解决。该提案的总体目标是通过开发 Genboree 系统来应对这些挑战。 Genboree 原型最初开发是为了支持贝勒医学院人类基因组测序中心的协作基因组注释和比较基因组项目。 Genboree 的关键功能之一是能够使用组装的基因组序列作为参考，通过将任何实验或计算得出的数据元素以注释的形式投影到参考基因组序列上来整合数据。由于内置的​​访问控制功能，Genboree 符合 HIPAA 合规性，因此能够集成患者信息和从患者样本中获得的基因组信息。在当前 Genboree 原型的基础上，将开发一个系统来集成数据、工具和发现管道，以支持基因组变异的协作转化研究。