An ethnically diverse genomic reference resource for the human heavy and light chain immunoglobulin loci

项目摘要/摘要 我们对免疫球蛋白(IG)重(IGH)的生殖系变异的理解存在一个根本的差距 人群中的轻链(IGK；IGL)基因座影响功能性抗体(Ab)的产生 健康和疾病方面的反应。然而，越来越多的人意识到IG基因多态有助于 抗体谱系的可变性，表明免疫球蛋白基因数据的整合有可能告诉我们 了解抗体在不同临床环境中的作用。取得进展的一个关键障碍是现有的 IG基因座的基因组资源缺乏，且不能很好地代表人类群体的多样性。免疫球蛋白 区域结构复杂，由大段重复组成，并且是最多的 基因组具有多态，具有大拷贝数变异(CNV)，提高了核苷酸多样性，以及 特定于群体的单倍型变异。这些复杂性长期以来使IG基因座的研究变得困难 使用标准高通量方法的基因组和种群水平，对遗传产生直接负面影响 疾病关联研究以及最近对表达的抗体谱系数据的分析。因此，我们的 对人类免疫球蛋白种系多样性(特别是在非高加索人中)及其对疾病的贡献的知识滞后 远远落后于其他研究得很好的免疫位点。这突显了对公共可用井的直接需求- 描述了IG单倍型参考和来自不同种族背景的准确变异目录 促进设计和集成更准确的基因分型工具、分析管道及其解释。 为了满足这一需求，我们开发了几种可靠的方法，我们将在这里利用这些方法来建立关键的 IG基因座的社区资源。我们将首先列举多达16部小说中的IGH/K/L单倍型参考文献 来自非洲、亚洲和欧洲血统的个人的现有8个Fosmid库的集合。 我们还将使用一种新的多单倍型信息基因分型管道来分析IgH/K/L基因变异。 来自这三个群体的180名有亲缘关系和无关的人组成的队列。这将代表最大的 IG种系多样性的综合种群调查，包括变量、多样性、连接、 和持续的基因变异，以及全区单核苷酸多态(SNPs)和CNV，允许 疾病关联研究的不同归罪小组的精细评估。最后，为了促进 将这些数据用作长期资源、所有序列、工具/方法和分析管道 向公众开放。我们将与已建立的数据库合作，以确保所有序列都存储在RAW和RAW中 和带注释的表格。这将包括将组装整合到未来发布的人类基因组中 供基因组学社区使用的参考，以及对现有生殖系基因/等位基因数据库的更新 对表达的抗体谱系分析至关重要。该项目建立了急需的基因组资源 人类免疫球蛋白基因座，这将在未来几年更好地服务于免疫学社区。这些将作为一种 为未来确定免疫球蛋白种系变异在抗体功能、健康和疾病中的作用奠定了基础。

Project Summary/Abstract There is a fundamental gap in our understanding of how germline variation in immunoglobulin (IG) heavy (IGH) and light chain (IGK; IGL) loci in the human population impacts the development of the functional antibody (Ab) response in health and disease. However, there is a growing appreciation that IG polymorphism contributes to variability in the Ab repertoire, indicating that the integration of IG genetic data has the potential to inform our understanding of Ab function in various clinical contexts. A critical barrier to progress has been that existing genomic resources for IG loci are lacking and poorly represent diversity found across human populations. IG regions are structurally complex, consisting of large segmental duplications, and are among the most polymorphic in the genome, with large copy number variants (CNVs), elevated nucleotide diversity, and population-specific haplotype variants. These complexities have long made IG loci difficult to study at the genomic and population level using standard high-throughput methods, with direct negative impacts on genetic disease association studies and more recently the analysis of expressed Ab repertoire data. As a result, our knowledge of human IG germline diversity (particularly in non-Caucasians) and its contribution to disease lags far behind that of other well studied immune loci. This highlights a direct need for publically available well- characterized IG haplotype references and accurate variant catalogues from diverse ethnic backgrounds to facilitate the design and integration of more accurate genotyping tools, analysis pipelines, and their interpretation. To meet this need, we have developed several robust approaches, which we will utilize here to establish critical community resources for the IG loci. We will first enumerate up to 16 novel IGH/K/L haplotype reference assemblies from an existing set of 8 fosmid libraries from individuals of African, Asian, and European descent. We will also use a novel multi-haplotype informed genotyping pipeline to profile IGH/K/L genetic variation in a cohort of 180 familial and unrelated individuals from these same three populations. This will represent the most comprehensive population survey of IG germline diversity, including descriptions of variable, diversity, joining, and constant gene variation, and locus-wide single nucleotide polymorphisms (SNPs) and CNVs, allowing for fine-scale assessment of variant imputation panels for disease association studies. Finally, to facilitate the utility of these data as long-term resources, all sequences, tools/methods, and analysis pipelines will be made publically available. We will work with established databases to ensure all sequences are deposited in both raw and annotated form. This will include the integration of assemblies into future releases of the human genome reference for use by the genomics community, as well as updates to existing germline gene/allele databases critical to expressed Ab repertoire analysis. This project establishes desperately needed genomic resources for the human IG loci, which will better serve the immunology community for years to come. These will stand as a foundation for future efforts to define the role of IG germline variation in Ab function, health, and disease.