JH/CIDR Genotyping for Genome-Wide Association Studies

用于全基因组关联研究的 JH/CIDR 基因分型

• 批准号: 7479370
• 负责人: DAVID VALLE
• 金额: $ 247.78万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-06 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7479370
• 关键词: Arts; Bioinformatics; Biological Assay; Cataloging; Catalogs; Communities; Complex; Computer software; Confidentiality of Patient Information; Contracts; Copy Number Polymorphism; Custom; DNA; Data; Data Analyses; Data Quality; Databases; Disease; Ensure; Environment; Evaluation; Failure; Frequencies; Generations; Genes; Genetic; Genetic Medicine; Genetic Services; Genetic Variation; Genetics and Medicine; Genome; Genomics; Genotype; Goals; Human Genetics; Individual; Inherited; Institutes; Laboratories; Manuscripts; Maps; Methods; Metric; Numbers; Performance; Population; Population Study; Privacy; Procedures; Process; Public Health Schools; Rate; Reporting; Research; Research Design; Research Ethics Committees; Research Personnel; Resources; Risk; SNP genotyping; Sampling; Science; Security; Services; Specific qualifier value; To specify; United States National Institutes of Health; Universities; Ursidae Family; Variant; Work; cost; data integrity; design; experience; gene environment interaction; genetic epidemiology; genome sequencing; genome wide association study; human disease; medical schools; response; trait

DESCRIPTION (provided by applicant): The recent tremendous progress in genomics provides biomedical science with a remarkable opportunity to unravel the complex interactions between genetic variation and environmental variables (Gene and Environment Interactions or GEI) responsible for common complex human disease. Some of the advances contributing to this opportunity include availability of high quality whole genome sequence from > 30 vertebrate species including our own plus a growing catalog of human genetic variation provided by HapMap and the fledgling projects aimed at understanding common structural variation. This opportunity is accompanied by a host of challenges including optimal study design, selection and utilization of a genotyping platform appropriate for each study, generation of high quality genotypic data and efficient and comprehensive downstream data analysis for genome wide association studies. The Johns Hopkins University Center for Inherited Disease Research (JH/CIDR) proposes to provide state-of- the-art whole genome association SNP genotyping for 12,000 samples over 3 years that will capture at least 80% of the genetic variation in the relevant study population as well as flexible regional genotyping that will enable custom fine mapping of genomic regions shown to harbor genes contributing risk for complex traits. We will also provide ancillary services as needed for individual projects including DNA isolation, whole genome amplification, assistance in study design and data analysis and provision of genotypic data in study-specific formats to the investigators and to the specified central database. Finally, we will work with the GEI Coordinating Committee in the planning and performance of this project. To achieve these aims we will build on the ten-year experience of JH/CIDR releasing more than 30 million high quality STRP and 1.2 billion high quality SNP genotypes for 128 projects and ~165,000 DNA samples. In this effort, we have interacted with >125 investigators providing genetic epidemiology expertise to assist with study design and analysis. Additionally, we will continue our commitment to evaluation of the rapidly evolving technological environment to provide the genetics community with the most robust, reliable and cost-effective genotyping platforms available. We will also take advantage of the rich scientific environment provided by the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine and the greater Johns Hopkins School of Medicine and School of Public Health environment to maximize the broad expertise we bring to bear on this project.

描述（由申请人提供）：基因组学的最新进展为生物医学科学提供了一个非凡的机会，可以揭示遗传变异与环境变量（基因和环境相互作用或GEI）之间的复杂相互作用，负责常见的复杂人类疾病。有助于这一机会的一些进步包括从> 30种脊椎动物物种中提供高质量的整个基因组序列，包括我们自己的脊椎动物，以及HAPMAP提供的人类遗传变异的日益增长的目录以及旨在理解常见结构变异的刚起步的项目。这个机会伴随着许多挑战，包括适合每项研究的基因分型平台的最佳研究设计，选择和利用，高质量基因型数据的产生以及用于基因组广泛关联研究的有效且全面的下游数据分析。 约翰·霍普金斯大学继承疾病研究中心（JH/CIDR）建议在3年内提供12,000个样本的整个基因组协会SNP基因分型，这些样本将在相关研究人群中捕获至少80％的遗传变异，并将为柔性区域型，以及对港口的定制型号造成的秘密映射，以供港口撰写，以造成基因的贡献。我们还将根据需要为各个项目提供辅助服务，包括DNA隔离，整个基因组扩增，研究设计和数据分析方面的帮助，以及针对研究人员和指定的中央数据库的研究特定格式中基因型数据的提供。最后，我们将与GEI协调委员会合作该项目的计划和绩效。 为了实现这些目标，我们将基于JH/CIDR的十年经验，可为128个项目和约165,000个DNA样品发布超过3000万高品质的股东股东立人士和12亿高质量的SNP基因型。在这项工作中，我们与> 125个研究人员进行了互动，提供遗传流行病学专业知识以协助研究设计和分析。此外，我们将继续致力于评估快速发展的技术环境，以为遗传学社区提供最强大，可靠和成本效益的基因分型平台。我们还将利用约翰·霍普金斯·麦克库西克·纳坦人遗传医学研究所和大约翰·霍普金斯医学院和公共卫生环境学院提供的丰富科学环境，以最大程度地提高我们对该项目的广泛专业知识。