DKMS Life Science Lab, Dresden, Germany.
DKMS, Tübingen, Germany.
Methods Mol Biol. 2024;2809:157-169. doi: 10.1007/978-1-0716-3874-3_11.
The Immuno Polymorphism Database (IPD) plays a pivotal role for immunogenetics. Due to technical limitations, genotyping often focuses on specific key regions like the antigen recognition domain (ARD) for HLA genotyping, and the databases are populated accordingly. More recently, though, modern next generation sequencing (NGS) assays allow using larger gene segments or even complete genes for genotyping. It is therefore essential that the databases are updated with complete genetic reference sequences to fully serve current and future applications. However, the process of manually annotating and submitting full-length allele sequences to IPD is time-consuming and error-prone, which may discourage HLA-genotyping laboratories or researchers from submitting full-length sequences of novel alleles.Here, we detail the process of preparing and submitting novel HLA, MIC, and KIR alleles to ENA and IPD using TypeLoader2, a convenient software tool developed to streamline this process by automating the sequence annotation, the creation of all necessary files, as well as parts of the submission process itself. The software is freely available from GitHub ( https://github.com/DKMS-LSL/typeloader ).
免疫多态性数据库（IPD）在免疫遗传学中起着至关重要的作用。由于技术限制，基因分型通常集中在特定的关键区域，如 HLA 基因分型的抗原识别域（ARD），并且相应地填充了数据库。然而，最近，现代下一代测序（NGS）检测可以使用更大的基因片段甚至完整的基因进行基因分型。因此，至关重要的是，数据库应使用完整的遗传参考序列进行更新，以充分满足当前和未来的应用需求。然而，手动注释和向 IPD 提交全长等位基因序列的过程既耗时又容易出错，这可能会阻碍 HLA 基因分型实验室或研究人员提交新型等位基因的全长序列。在这里，我们详细介绍了使用 TypeLoader2 向 ENA 和 IPD 准备和提交新型 HLA、MIC 和 KIR 等位基因的过程，TypeLoader2 是一个方便的软件工具，用于通过自动化序列注释、创建所有必要的文件以及部分提交过程本身来简化此过程。该软件可从 GitHub（https://github.com/DKMS-LSL/typeloader）免费获得。
