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.