Lin Mao-Jan, Langmead Ben, Safonova Yana
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Cell Rep Methods. 2025 May 19;5(5):101033. doi: 10.1016/j.crmeth.2025.101033. Epub 2025 May 1.
High-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, LCLs pose technical challenges for profiling immunoglobulin (IG) genes, as their IG loci contain a mixture of germline and somatically recombined haplotypes, making genotyping and assembly difficult with widely used frameworks. To address this, we introduce IGLoo, a software tool that analyzes sequence data and assemblies derived from LCLs, characterizing somatic V(D)J recombination events and identifying breakpoints and missing IG genes in the assemblies. Furthermore, IGLoo implements a reassembly framework to improve germline assembly quality by integrating information on somatic events and population structural variations in IG loci. Applying IGLoo to the assemblies from the Human Pangenome Reference Consortium, we gained valuable insights into the mechanisms, gene usage, and patterns of V(D)J recombination and the causes of assembly artifacts in the IG heavy-chain (IGH) locus, and we improved the representation of IGH assemblies.
源自淋巴母细胞系（LCLs）的高质量人类基因组组装为基因组学研究提供了参考基因组和泛基因组。然而，LCLs在分析免疫球蛋白（IG）基因时带来了技术挑战，因为它们的IG基因座包含种系和体细胞重组单倍型的混合物，使得使用广泛的框架进行基因分型和组装变得困难。为了解决这个问题，我们引入了IGLoo，这是一种软件工具，可分析源自LCLs的序列数据和组装，表征体细胞V(D)J重组事件，并识别组装中的断点和缺失的IG基因。此外，IGLoo实施了一个重新组装框架，通过整合IG基因座中体细胞事件和群体结构变异的信息来提高种系组装质量。将IGLoo应用于人类泛基因组参考联盟的组装中，我们对V(D)J重组的机制、基因使用和模式以及IG重链（IGH）基因座中组装假象的原因有了宝贵的见解，并且我们改进了IGH组装的代表性。
