{"doi":"10.1016/j.crmeth.2025.101033","title":"IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads","abstract":null,"journal":"Cell Reports Methods","year":2025,"id":613414,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":18148,"name":"Ben Langmead","orcid":"0000-0003-2437-1976","position":1,"is_corresponding":false},{"id":51320,"name":"Yana Safonova","orcid":"0000-0002-9634-4216","position":2,"is_corresponding":false},{"id":1222597,"name":"Mao-Jan Lin","orcid":"0000-0003-1860-7786","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads","abstract":"High-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, LCLs pose technical challenges for profiling immunoglobulin (IG) genes, as their IG loci contain a mixture of germline and somatically recombined haplotypes, making genotyping and assembly difficult with widely used frameworks. To address this, we introduce IGLoo, a software tool that analyzes sequence data and assemblies derived from LCLs, characterizing somatic V(D)J recombination events and identifying breakpoints and missing IG genes in the assemblies. Furthermore, IGLoo implements a reassembly framework to improve germline assembly quality by integrating information on somatic events and population structural variations in IG loci. Applying IGLoo to the assemblies from the Human Pangenome Reference Consortium, we gained valuable insights into the mechanisms, gene usage, and patterns of V(D)J recombination and the causes of assembly artifacts in the IG heavy-chain (IGH) locus, and we improved the representation of IGH assemblies.","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40315852","pmcid":"PMC12146632","openalex_id":"https://openalex.org/W4409995522","authors":[],"funders":[{"funder_name":"NHGRI","grant_id":"R01HG011392","title":null},{"funder_name":"National Science Foundation","grant_id":"OAC 1920103","title":null},{"funder_name":"NIGMS","grant_id":"R35GM139602","title":null}],"total_grants":3,"fwci":2.0369,"citation_percentile":0.86120862,"influential_citations":0,"citation_trend":[{"year":2025,"count":5}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1016/j.crmeth.2025.101033","host_type":"journal"},{"url":"https://doi.org/10.1016/j.crmeth.2025.101033","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S2667237525000694?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S2667237525000694?httpAccept=text/plain","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40315852","host_type":"repository"},{"url":"https://doaj.org/article/425efa35a9214353a166873af3606c25","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12146632","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC12146632","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC12146632?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Glycosylation and Glycoproteins Research","Blood groups and transfusion","Immunodeficiency and Autoimmune Disorders","Humans","Immunoglobulin Heavy Chains","Software","Cell Line","V(D)J Recombination","Genetic Loci","High-Throughput Nucleotide Sequencing","Sequence Analysis, DNA","Genome, Human"],"mesh_terms":["Cell Line","Humans","Immunoglobulin Heavy Chains","Software","Genome, Human","Sequence Analysis, DNA","Genetic Loci","High-Throughput Nucleotide Sequencing","V(D)J Recombination"],"keywords":["Fidelity","Immunoglobulin heavy chain","Heavy chain","Computational biology","Immunoglobulin light chain","Lymphoblast","Antibody","Biology","Computer science","Cell culture","Genetics","Assembly","Ig","Igh","Lymphoblastoid Cell Line","Lcl","Cp: Systems Biology","Immunoglobulin Gene Loci","Cp: Genetics"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"igsr"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T08:01:28.280862Z","pmid":null,"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":[]}