Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains
Antibodies consist of unique variable heavy (V<sub>H</sub>) and variable light (V<sub>L</sub>) chains, and both are required to fully characterize an antibody. Methods to detect paired heavy and light chain variable regions (V<sub>H</sub>:V<sub>L</sub>) 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<sub>H</sub>:V<sub>L</sub> 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<sub>H</sub>:V<sub>L</sub> gene repertoire data to enable efficient antibody discovery.
Authors
- Ahmed S. Fahad (ORCID: https://orcid.org/0000-0002-5088-9333)
- Bharat Madan (ORCID: https://orcid.org/0000-0002-7376-9991)
- Matías Gutiérrez-González (ORCID: https://orcid.org/0000-0002-9729-6850)
- Brandon J. DeKosky (ORCID: https://orcid.org/0000-0001-6406-0836)
Institutions
- Ragon Institute of MGH, MIT and Harvard (US)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Cold Spring Harbor Protocols
- Published
- 2024-11-25
- DOI
- https://doi.org/10.1101/pdb.prot108628
- Citations
- 1
- Primary Topic
- Monoclonal and Polyclonal Antibodies Research
- Type
- article
Funders
- National Institutes of Health