High-throughput characterization of cis-acting polymorphisms in the human genome

描述（由申请人提供）：人类遗传学研究的一个主要目标是在功能上表征人类基因组中的多态性。最近的两个项目--HapMap和1000个基因组计划--在构建不同人群中常见变异和连锁不平衡的目录方面取得了巨大的成功。事实上，人类基因组单体型图的数据使得全基因组关联研究（GWAS）得以发展，该研究已经发现了与多种疾病相关的2000多个基因座。到该项目的资助期开始时，1000个基因组计划将基本上确定人类中所有~107个常见（>1%的次要等位基因频率）多态性。有了这个目录，该领域的下一个巨大挑战将是从功能上描述这一巨大的遗传变异景观。这107种变异几乎都不会产生可检测到的功能性后果，这是很有可能的--尽管不管哪一部分具有功能性影响，确定确实影响表型的特定变异将是未来十年人类遗传学研究的一个重要目标。我们的目标是开发一种实验和计算工具的组合，将允许高通量分配的功能后果，以数千人的多态性，包括许多涉及GWAS。通过对标准染色质免疫沉淀和测序（“ChIP-seq”）方法的简单修改，包括合并样品，我们将能够将分子性状遗传映射到单个核苷酸的水平，与替代方法相比，效率和成本效益提高约100倍。将所得到的功能多态性图谱与eSNP和GWAS结果相结合，将允许同时精确定位和功能表征影响基因表达或疾病风险的许多多态性。 公共卫生相关性：我们的项目将通过大大加快查明各种人类疾病背后的因果多态性的过程，对人类健康产生切实和广泛的影响。鉴定因果多态性是重要的，原因有很多，例如，研究人员进行有针对性的后续研究和功能测定，以更好地了解多态性的作用机制，及其对疾病的影响。此外，了解因果多态性将允许其在病例/对照队列中的基因分型，以揭示该关联的真实人群归因风险和比值比，这两者对于我们理解每个多态性在疾病中的重要性至关重要;使用其他SNP作为代理可能会大大低估多态性对疾病的贡献。

DESCRIPTION (provided by applicant): A major goal of research in human genetics is to functionally characterize polymorphisms in the human genome. Two recent projects - the HapMap and the 1000 Genomes Project - have achieved tremendous success in constructing a catalog of common variants and linkage disequilibrium in diverse populations. Indeed, the HapMap data allowed the development of genome-wide association studies (GWAS), which have already implicated over two thousand loci associated with a wide range of diseases. By the beginning of this project's funding period, the 1000 Genomes Project will have identified essentially all ~107 common (>1% minor allele frequency) polymorphisms in humans. With this catalog in hand, the next great challenge for the field will be to functionally characterize this vast landscape of genetic variation. It is quite possible that nearly all of these 107 variants will have no detectable functional consequences - though regardless of what fraction have functional effects, identifying the specific variants that do affect phenotypes will be a significant goal for human genetics research in the coming decade. Our objective is to develop a combination of experimental and computational tools that will allow the high-throughput assignment of functional consequences to thousands of human polymorphisms, including many of those implicated by GWAS. With a simple modification to standard chromatin immunoprecipitation and sequencing ("ChIP-seq") methods involving pooling of samples, we will be able to genetically map molecular traits down to the level of single nucleotides with ~100-fold gains in efficiency and cost-effectiveness compared to alternative methods. Integrating the resulting functional polymorphism maps with eSNP and GWAS results will allow many polymorphisms affecting gene expression or disease risk to be simultaneously pinpointed and functionally characterized. PUBLIC HEALTH RELEVANCE: Our project will have tangible and wide-reaching effects on human health by greatly accelerating the process of pinpointing causal polymorphisms underlying diverse human diseases. Identifying causal polymorphisms is important for a number of reasons, e.g. for investigators to perform targeted follow-up studies and functional assays to better understand the polymorphism's mechanism of action, and its effects on disease. In addition, knowing the causal polymorphism will allow its genotyping in case/control cohorts to reveal the true population-attributable risk and odds ratio of the association, both of which are crucial to our understanding of each polymorphism's importance in disease; using other SNPs as proxies may substantially underestimate a polymorphism's contribution to disease.