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

项目总结/摘要 我们对免疫球蛋白（IG）重链（IGH）中生殖系变异的理解存在根本性的差距。 和轻链（IGK; IGL）基因座影响功能性抗体（Ab）的发展 健康和疾病的反应。然而，越来越多的人认识到IG多态性有助于 Ab库的变异性，表明IG遗传数据的整合有可能为我们提供信息。 了解各种临床背景下的Ab功能。取得进展的一个关键障碍是， IG基因座的基因组资源缺乏，并且不能很好地代表在人群中发现的多样性。IG 区域结构复杂，由大片段重复组成，是最重要的区域之一。 在基因组中具有多态性，具有大拷贝数变体（CNVs），核苷酸多样性升高， 群体特异性单倍型变异。这些复杂性长期以来使IG基因座难以在 使用标准高通量方法，在基因组和群体水平上， 疾病关联研究以及最近表达的Ab库数据的分析。结果我们的 人类IG生殖系多样性（特别是非高加索人）及其对疾病的贡献的知识滞后 远远落后于其他研究充分的免疫基因座。这突出表明，直接需要化学上可用的良好- 来自不同种族背景的特征性IG单倍型参考和准确的变体目录， 促进更准确的基因分型工具、分析管道及其解释的设计和集成。 为了满足这一需求，我们开发了几种强大的方法，我们将在这里利用它们来建立关键的 IG基因座的社区资源。我们将首先列举多达16个新的IGH/K/L单倍型参考 来自非洲、亚洲和欧洲血统的个体的现有8个fosmid库的集合。 我们还将使用一种新的多单倍型知情基因分型管道，以分析IGH/K/L遗传变异， 来自这三个相同人群的180个家族性和无关个体的队列。这将代表最 IG生殖系多样性的全面人群调查，包括变量，多样性，连接， 和恒定的基因变异，以及基因座范围的单核苷酸多态性（SNP）和CNV， 疾病关联研究中变量插补组的精细尺度评估。最后，为了方便 这些数据作为长期资源的效用，所有序列、工具/方法和分析管道都将 免费提供。我们将与已建立的数据库，以确保所有序列存放在两个原始 注释的形式。这将包括将组装集成到人类基因组的未来版本中 供基因组学界使用的参考，以及对现有生殖系基因/等位基因数据库的更新 对表达的Ab库分析至关重要。该项目建立了急需的基因组资源， 人类IG基因座，这将更好地服务于免疫学社区在未来几年。这些将作为一个 为今后确定IG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.