Identification and characterization of inflammatory bowel disease causal variants

项目摘要/摘要 炎症性肠病(IBD)是一组慢性、衰弱的胃肠道疾病， 发病高峰在青春期和成年期早期。美国有300多万人受到影响， 估计每年的直接医疗成本为63亿美元。IBD具有高度的遗传性，因此，研究其遗传基础 IBD的发生是阐明IBD发病机制的一条自然途径，目前对IBD的发病机制知之甚少。 全基因组关联研究已经确定了240多个与IBD相关的基因座。这些协会 由于连锁不平衡(LD)，通常涉及具有数百个变异的大基因组区域。这个 最新的IBD精细定位研究解决了LD，并将45个IBD关联映射到单变异分辨率， 提供对遗传变异如何以组织特有的方式促进IBD发病机制的洞察。尽管 在这一最初的成功中，迄今为止大多数IBD关联和假定的因果变异都来自欧洲 不确定是否可以移植到非欧洲祖先的祖先；以及对大多数 IBD的因果变异，特别是非编码变异，目前尚不清楚。 这项拟议的研究通过一种综合战略来弥合这些差距，该战略结合了对 大规模多家系IBD队列和精心设计的功能实验研究遗传基础 IBD的症状。这一队列包括四个祖先群体的受试者，包括非洲人、混血美国人、东方人 亚洲和欧洲，样本规模史无前例地超过192,600例IBD，其中3倍、12倍、5倍和3倍 分别为每个祖先的当前IBD样本量。大量外显子组测序(WES)数据将 ，使我们能够研究罕见的编码变体的贡献，这些变体已经被证明是 对IBD很重要，并有助于将非编码变体与其基因靶标联系起来。广泛的质量控制和 将执行协调以生成高质量、高覆盖率的个人级别数据集 跨祖先、技术和批次的异质性。将开发一种新的精细映射方法来 利用跨祖先的基因组多样性和WES数据，目标是加强精细作图 尤其是在编码基因组中的分辨率。这项研究预计会有200多个新的IBD因果变异， 包括许多有很大影响并直接扰乱蛋白质功能的物质。这些变种将被描述为 用CRISPR联合激活和CRISPR研究其在人T细胞IBD中的分子和细胞机制 干扰实验，以及编码变体对静息和运动中基因调控的影响 刺激的细胞。 这项研究的新的IBD因果变异和生物学将为IBD的发病机制提供新的见解。 对IBD的新疗法产生重要的积极影响，并成为其基本资源和基础。

PROJECT SUMMARY/ABSTRACT Inflammatory bowel diseases (IBD) are a group of chronic, debilitating disorders of the gastrointestinal tract with peak onset in adolescence and early adulthood. More than 3 million people are affected in U.S., with an estimated direct healthcare cost of $6.3 billion per year. IBD are highly heritable, thus, studying the genetic basis of IBD is a natural path towards elucidating the IBD pathogenesis, which is poorly understood at present. Genome-wide association studies have identified over 240 loci associated with IBD. These associations typically implicate large genomic regions with hundreds of variants due to the linkage disequilibrium (LD). The latest IBD fine-mapping study resolved the LD and mapped 45 IBD associations to single-variant resolution, providing insights into how genetic variants contribute to IBD pathogenesis in a tissue specific manner. Despite of this initial success, most IBD associations and putative causal variants to date were derived from European ancestries with uncertainty in their transferability to non-European ancestries; and the functional impact for most IBD causal variants, especially the noncoding variants, is unclear. This proposed study bridges these gaps through an integrative strategy combining fine-mapping on a large-scale multi-ancestry IBD cohort and well-designed functional experiments to investigate the genetic basis of IBD. This cohort includes subjects of four ancestral populations including African, admixed American, East Asian and European, with an unprecedented sample size of over 192,600 IBD cases, 3x, 12x, 5x and 3x of the current IBD sample size for each ancestry respectively. A large amount of exome sequencing (WES) data will be included, allowing us to investigate the contribution from rare coding variants which have been shown to be important to IBD and help to link noncoding variants to their gene targets. Extensive quality control and harmonization will be performed to generate a high quality, high coverage individual-level dataset with minimal heterogeneity across ancestries, technologies, and batches. A novel fine-mapping method will be developed to leverage the genomic diversity across ancestries and the WES data with the goal to enhance the fine-mapping resolution especially in the coding genome. Over 200 new IBD causal variants are expected from this study, including many that have large effects and directly disrupt protein functions. These variants will be characterized for their molecular and cellular mechanism in IBD in human T cells using pooled CRISPR activation and CRISPR interference experiments, and knockins of coding variants for their effects on gene regulation in resting and stimulated cells. The new IBD causal variants and biology from this study will provide new insights into IBD pathogenesis, make important positive impact and serve as the fundamental resource and basis toward novel IBD therapeutics.