JH/CIDR Genotyping for Genome-Wide Association Studies

描述(由申请人提供)：基因组学最近的巨大进步为生物医学科学提供了一个极好的机会来揭示导致常见复杂人类疾病的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。为这一机会做出贡献的一些进展包括可获得包括我们自己在内的30种脊椎动物的高质量全基因组序列，以及由HapMap提供的不断增长的人类遗传变异目录，以及旨在了解共同结构变异的羽翼未丰的项目。这一机遇随之而来的是一系列挑战，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、生成高质量的基因分型数据以及为全基因组关联研究进行高效和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)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，这将捕捉到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，这将使定制精细绘制包含复杂特征风险基因的基因组区域成为可能。我们亦会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，以及向研究人员和指定的中央资料库提供特定研究格式的基因分型数据。最后，我们将与全球环境倡议协调委员会合作，规划和执行这一项目。 为了实现这些目标，我们将建立在JH/CIDR十年经验的基础上，为128个项目和约16.5万个DNA样本发布3000多万个高质量STRP和12亿个高质量SNP基因型。在这项工作中，我们与提供遗传流行病学专业知识的125名研究人员进行了互动，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，为遗传学社区提供最强大、可靠和成本效益最高的基因分型平台。我们还将利用约翰霍普金斯大学麦库西克-纳桑斯遗传医学研究所以及约翰霍普金斯大学医学院和公共卫生学院所提供的丰富的科学环境，最大限度地利用我们在这个项目中运用的广泛专业知识。

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.