Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
Front Immunol. 2021 Oct 26;12:739179. doi: 10.3389/fimmu.2021.739179. eCollection 2021.
Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel allele candidates (NACs) using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the NACs detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies Ig-seq.
详细了解各种免疫球蛋白胚系基因对于研究体液免疫至关重要。通过分析抗体库测序（Rep-seq 或 Ig-seq）数据，已经发现了数百个等位基因，这些数据是利用多种新型等位基因检测工具（NADTs）发现的。然而，这些 NADTs 在具有内在体细胞超突变（SHMs）的抗体序列中的性能尚不清楚。在这里，我们开发了一种工具，通过整合抗体库的全谱特征，如胚系基因使用、连接修饰、位置特异性 SHM 和克隆扩增，来模拟库，该工具是基于 2152 个高质量数据集开发的。然后，我们使用模拟和真实的 Ig-seq 数据集系统地评估了这些 NADTs。最后，我们应用这些 NADTs 分析了 687 个 Ig-seq 数据集，并使用定义的标准鉴定了 43 个新的等位基因候选物（NACs）。通过其他来源的发现，有 25 个等位基因得到了验证。除了检测到的 NACs 外，我们的模拟工具、比较结果以及该过程的流程都可能有助于进一步的体液免疫研究和 Ig-seq。
