Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains
- 1The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA
- 2Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- ↵4Correspondence: dekosky{at}mit.edu
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↵3 These authors contributed equally to this work
Abstract
Antibodies consist of unique variable heavy (VH) and variable light (VL) chains, and both are required to fully characterize an antibody. Methods to detect paired heavy and light chain variable regions (VH:VL) 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 VH:VL 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 VH:VL gene repertoire data to enable efficient antibody discovery.
Footnotes
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From the Advances in Phage Display collection, edited by Gregg J. Silverman, Christoph Rader, and Sachdev S. Sidhu.
