{"doi":"10.1101/pdb.prot108628","title":"Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains","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.","journal":"Cold Spring Harbor Protocols","year":2024,"id":492468,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9517,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":236781,"name":"Matías Gutiérrez-González","orcid":"0000-0002-9729-6850","position":1,"is_corresponding":false},{"id":302419,"name":"Bharat Madan","orcid":"0000-0002-7376-9991","position":2,"is_corresponding":false},{"id":108827,"name":"Brandon J. DeKosky","orcid":"0000-0001-6406-0836","position":3,"is_corresponding":false},{"id":302417,"name":"Ahmed S. Fahad","orcid":"0000-0002-5088-9333","position":0,"is_corresponding":true}],"reference_count":11,"raw_metadata":null,"created_at":"2026-07-19T02:08:56.210382Z","pmid":"39586682","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}