Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains

Ahmed S Fahad; Matías F Gutiérrez-Gonzalez; Bharat Madan; Brandon J DeKosky

doi:10.1101/pdb.prot108628

Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains

Cold Spring Harb Protoc. 2025 Jan 2;2025(1):pdb.prot108628. doi: 10.1101/pdb.prot108628.

Authors

Ahmed S Fahad^#^{1

2}, Matías F Gutiérrez-Gonzalez^#^{1

2}, Bharat Madan¹, Brandon J DeKosky^{3

2}

Affiliations

¹ The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA.
² Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
³ The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA dekosky@mit.edu.

^# Contributed equally.

PMID: 39586682
DOI: 10.1101/pdb.prot108628

Abstract

Antibodies consist of unique variable heavy (V_H) and variable light (V_L) chains, and both are required to fully characterize an antibody. Methods to detect paired heavy and light chain variable regions (V_H:V_L) 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_H:V_L 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_H:V_L gene repertoire data to enable efficient antibody discovery.

MeSH terms

Computational Biology / methods
Genetic Variation
High-Throughput Nucleotide Sequencing* / methods
Humans
Immunoglobulin Heavy Chains* / genetics
Immunoglobulin Light Chains* / genetics
Immunoglobulin Variable Region / genetics

Substances

Immunoglobulin Light Chains
Immunoglobulin Heavy Chains
Immunoglobulin Variable Region