IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads.

IF 4.3 Q1 BIOCHEMICAL RESEARCH METHODS

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-01 DOI:10.1016/j.crmeth.2025.101033

Mao-Jan Lin, Ben Langmead, Yana Safonova

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Abstract

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.

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使用PacBio高保真读数，IGLoo能够全面分析和组装淋巴母细胞样细胞系中的免疫球蛋白重链位点。

来自淋巴母细胞样细胞系（LCLs）的高质量人类基因组组合为基因组学研究提供了参考基因组和泛基因组。然而，LCLs给免疫球蛋白（IG）基因分析带来了技术挑战，因为它们的IG基因座包含种系和体细胞重组的单倍型的混合物，使得广泛使用的框架难以进行基因分型和组装。为了解决这个问题，我们引入了IGLoo，这是一种软件工具，可以分析来自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实现了一个重组框架，通过整合IG位点的体细胞事件和群体结构变化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（Human Pangenome Reference Consortium）的组装，我们获得了关于V(D)J重组的机制、基因使用和模式以及IG重链（IGH）位点组装伪像的原因的有价值的见解，并改进了IGH组装的表示。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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