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（申请人提供）：基因组学最近取得的巨大进展为生物医学科学提供了一个非凡的机会，以揭示遗传变异和环境变量（基因和环境相互作用或GEI）之间的复杂相互作用，导致常见的复杂人类疾病。促成这一机会的一些进展包括来自包括我们自己在内的30多个脊椎动物物种的高质量全基因组序列的可用性，以及由HapMap提供的不断增长的人类遗传变异目录和旨在了解常见结构变异的新兴项目。这一机遇伴随着一系列挑战，包括最佳研究设计，选择和利用适合每项研究的基因分型平台，生成高质量的基因型数据，以及对全基因组关联研究进行有效和全面的下游数据分析。 约翰霍普金斯大学遗传疾病研究中心（JH/CIDR）建议在3年内为12，000个样本提供最先进的全基因组关联SNP基因分型，这将捕获相关研究人群中至少80%的遗传变异，以及灵活的区域基因分型，这将使基因组区域的定制精细定位显示出具有复杂性状风险的基因。我们还将为个别项目提供所需的辅助服务，包括DNA分离、全基因组扩增、协助研究设计和数据分析，以及以研究特定格式向研究者和指定的中央数据库提供基因型数据。最后，我们将与GEI协调委员会合作，规划和实施该项目。 为了实现这些目标，我们将在JH/CIDR十年经验的基础上，为128个项目和约165，000个DNA样本发布超过3000万个高质量STRP和12亿个高质量SNP基因型。在这项工作中，我们与超过125名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，为遗传学界提供最强大，可靠和具有成本效益的基因分型平台。我们还将利用约翰霍普金斯麦库西克-内森遗传医学研究所和大约翰霍普金斯医学院和公共卫生学院提供的丰富的科学环境，最大限度地发挥我们在这个项目上的广泛专业知识。