Fahad Ahmed S, Gutiérrez-Gonzalez Matías F, Madan Bharat, DeKosky Brandon J
The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA.
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Cold Spring Harb Protoc. 2025 Jan 2;2025(1):pdb.prot108628. doi: 10.1101/pdb.prot108628.
Antibodies consist of unique variable heavy (V) and variable light (V) chains, and both are required to fully characterize an antibody. Methods to detect paired heavy and light chain variable regions (V:V) using high-throughput sequencing (HTS) have recently enabled large-scale analysis of complete functional antibody responses. Here, we describe an HTS computational pipeline to analyze paired V:V antibody sequences and obtain a comprehensive profile of immune diversity landscapes, including gene usage, antibody isotypes, and clonal lineage analysis. This protocol uses Illumina MiSeq 2 × 300-bp sequencing data and integrates with several different computational tools for flexible analyses of paired V:V gene repertoire data to enable efficient antibody discovery.
抗体由独特的重链可变区（V）和轻链可变区（V）组成，两者对于全面表征抗体都是必需的。最近，利用高通量测序（HTS）检测重链和轻链可变区配对（V:V）的方法使得对完整功能性抗体反应进行大规模分析成为可能。在此，我们描述了一种HTS计算流程，用于分析V:V抗体配对序列，并获得免疫多样性图谱的全面概况，包括基因使用情况、抗体亚型和克隆谱系分析。该方案使用Illumina MiSeq 2×300 bp测序数据，并与几种不同的计算工具集成，以便对V:V基因库数据进行灵活分析，从而实现高效的抗体发现。
