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）：基因组学最近的巨大进展为生物医学科学提供了一个绝佳的机会来揭示遗传变异与环境变量（基因与环境相互作用或 GEI）之间的复杂相互作用，这些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步包括来自超过 30 个脊椎动物物种的高质量全基因组序列，包括我们自己的物种，加上 HapMap 提供的不断增长的人类遗传变异目录，以及旨在了解常见结构变异的新兴项目。这一机遇也伴随着一系列挑战，包括优化研究设计、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用于全基因组关联研究的高效且全面的下游数据分析。 约翰·霍普金斯大学遗传病研究中心 (JH/CIDR) 计划在 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，捕获相关研究群体中至少 80% 的遗传变异，并提供灵活的区域基因分型，从而实现对基因组区域进行定制精细绘图，这些区域显示出包含导致复杂性状风险的基因。我们还将根据各个项目的需要提供辅助服务，包括 DNA 分离、全基因组扩增、研究设计和数据分析方面的协助以及以研究特定格式向研究人员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执行该项目。 为了实现这些目标，我们将借鉴 JH/CIDR 十年的经验，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、最可靠和最具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以及更大的约翰·霍普金斯医学院和公共卫生学院提供的丰富的科学环境，最大限度地利用我们在该项目中发挥的广泛专业知识。