{"id":"https://openalex.org/W4225810652","doi":"https://doi.org/10.7554/elife.73475","title":"Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities","display_name":"Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities","publication_year":2022,"publication_date":"2022-01-18","ids":{"openalex":"https://openalex.org/W4225810652","doi":"https://doi.org/10.7554/elife.73475","pmid":"https://pubmed.ncbi.nlm.nih.gov/35315770","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8940181"},"language":"en","primary_location":{"id":"doi:10.7554/elife.73475","doi":"https://doi.org/10.7554/elife.73475","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.73475","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7554/elife.73475","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011568627","display_name":"Magdalena L Russell","orcid":"https://orcid.org/0000-0002-1068-1968","observed_orcids":["https://orcid.org/0000-0002-1068-1968"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Magdalena L Russell","raw_affiliation_strings":["Computational Biology Program, Fred Hutch Cancer Research Center","Molecular and Cellular Biology Program, University of Washington"],"raw_orcid":"https://orcid.org/0000-0002-1068-1968","affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutch Cancer Research Center","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Molecular and Cellular Biology Program, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090261568","display_name":"Aisha Hegab Souquette","orcid":"https://orcid.org/0000-0001-6197-5870","observed_orcids":["https://orcid.org/0000-0001-6197-5870"]},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]},{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aisha Souquette","raw_affiliation_strings":["Department of Immunology, St. Jude Children\u2019s Research Hospital","Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, St. Jude Children\u2019s Research Hospital","institution_ids":["https://openalex.org/I1313298211"]},{"raw_affiliation_string":"Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center","institution_ids":["https://openalex.org/I160606119"]}]},{"author_position":"middle","author":{"id":null,"display_name":"David M Levine","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David M Levine","raw_affiliation_strings":["Department of Biostatistics, University of Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Stefan A Schattgen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefan A Schattgen","raw_affiliation_strings":["Department of Immunology, St. Jude Children\u2019s Research Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, St. Jude Children\u2019s Research Hospital","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":null,"display_name":"E Kaitlynn Allen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E Kaitlynn Allen","raw_affiliation_strings":["Department of Immunology, St. Jude Children\u2019s Research Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, St. Jude Children\u2019s Research Hospital","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Guillermina Kuan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210137671","display_name":"Sustainable Sciences Institute","ror":"https://ror.org/02y8mb071","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210137671"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guillermina Kuan","raw_affiliation_strings":["Centro Nacional de Diagn\u00f3stico y Referencia, Ministry of Health","Sustainable Sciences Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de Diagn\u00f3stico y Referencia, Ministry of Health","institution_ids":[]},{"raw_affiliation_string":"Sustainable Sciences Institute","institution_ids":["https://openalex.org/I4210137671"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087655518","display_name":"Noah Simon","orcid":"https://orcid.org/0000-0002-8985-2474","observed_orcids":["https://orcid.org/0000-0002-8985-2474"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah Simon","raw_affiliation_strings":["Department of Biostatistics, University of Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Angel Balmaseda","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210137671","display_name":"Sustainable Sciences Institute","ror":"https://ror.org/02y8mb071","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210137671"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angel Balmaseda","raw_affiliation_strings":["Centro Nacional de Diagn\u00f3stico y Referencia, Ministry of Health","Sustainable Sciences Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de Diagn\u00f3stico y Referencia, Ministry of Health","institution_ids":[]},{"raw_affiliation_string":"Sustainable Sciences Institute","institution_ids":["https://openalex.org/I4210137671"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Aubree Gordon","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aubree Gordon","raw_affiliation_strings":["Department of Epidemiology, University of Michigan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, University of Michigan","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Paul G Thomas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul G Thomas","raw_affiliation_strings":["Department of Immunology, St. Jude Children\u2019s Research Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, St. Jude Children\u2019s Research Hospital","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084752404","display_name":"Frederick A. Matsen IV","orcid":"https://orcid.org/0000-0003-0607-6025","observed_orcids":["https://orcid.org/0000-0003-0607-6025"]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick A Matsen","raw_affiliation_strings":["Computational Biology Program, Fred Hutch Cancer Research Center","Department of Genome Sciences, University of Washington","Department of Statistics, University of Washington","Howard Hughes Medical Institute"],"raw_orcid":"https://orcid.org/0000-0003-0607-6025","affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutch Cancer Research Center","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Department of Genome Sciences, University of Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Statistics, University of Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Howard Hughes Medical Institute","institution_ids":["https://openalex.org/I1344073410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067744380","display_name":"Philip H Bradley","orcid":"https://orcid.org/0000-0002-0224-6464","observed_orcids":["https://orcid.org/0000-0002-0224-6464"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Philip Bradley","raw_affiliation_strings":["Computational Biology Program, Fred Hutch Cancer Research Center","Institute for Protein Design, Department of Biochemistry, University of Washington"],"raw_orcid":"https://orcid.org/0000-0002-0224-6464","affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutch Cancer Research Center","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Institute for Protein Design, Department of Biochemistry, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5011568627","https://openalex.org/A5067744380","https://openalex.org/A5084752404"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":3000,"currency":"USD","value_usd":2500},"apc_paid":{"value":3000,"currency":"USD","value_usd":2500},"fwci":2.0024,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.87174991,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"11","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.7231000065803528,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.7231000065803528,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.18860000371932983,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.02370000071823597,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tcr-repertoire","display_name":"T cell receptor repertoire","score":0.906000018119812},{"id":"https://openalex.org/keywords/v-d-j-recombination","display_name":"V(D)J recombination","score":0.9909999966621399},{"id":"https://openalex.org/keywords/genetic-loci","display_name":"genetic loci","score":0.7630000114440918},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"major histocompatibility complex","score":0.9850000143051147},{"id":"https://openalex.org/keywords/artemis","display_name":"Artemis","score":0.8629999756813049},{"id":"https://openalex.org/keywords/terminal-deoxynucleotidyl-transferase","display_name":"terminal deoxynucleotidyl transferase","score":0.921999990940094},{"id":"https://openalex.org/keywords/junctional-diversity","display_name":"junctional diversity","score":0.8740000128746033},{"id":"https://openalex.org/keywords/t-cell-receptor-diversity","display_name":"T cell receptor diversity","score":0.5180000066757202},{"id":"https://openalex.org/keywords/genetic-variants","display_name":"genetic variants","score":0.31299999356269836}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7782999873161316},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.7185999751091003},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6772000193595886},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.5978000164031982},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.5300999879837036},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.522599995136261},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.5116000175476074},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.4465999901294708},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.4343999922275543},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.42179998755455017},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.41339999437332153},{"id":"https://openalex.org/C103474210","wikidata":"https://www.wikidata.org/wiki/Q142851","display_name":"Immune receptor","level":3,"score":0.4120999872684479},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.3871999979019165},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.3806000053882599},{"id":"https://openalex.org/C40583040","wikidata":"https://www.wikidata.org/wiki/Q1502105","display_name":"Human genetic variation","level":5,"score":0.3650999963283539},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34459999203681946},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.34369999170303345},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.33570000529289246},{"id":"https://openalex.org/C101434241","wikidata":"https://www.wikidata.org/wiki/Q211675","display_name":"Genetic recombination","level":4,"score":0.32710000872612},{"id":"https://openalex.org/C2780254951","wikidata":"https://www.wikidata.org/wiki/Q1093098","display_name":"V(D)J recombination","level":4,"score":0.32170000672340393},{"id":"https://openalex.org/C102744134","wikidata":"https://www.wikidata.org/wiki/Q22280388","display_name":"Homologous recombination","level":3,"score":0.3179999887943268},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.31049999594688416},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.29670000076293945},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.29440000653266907},{"id":"https://openalex.org/C26589402","wikidata":"https://www.wikidata.org/wiki/Q7068267","display_name":"Nucleotide diversity","level":5,"score":0.2858999967575073},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.2858000099658966},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.28040000796318054},{"id":"https://openalex.org/C2992511266","wikidata":"https://www.wikidata.org/wiki/Q1093098","display_name":"Gene rearrangement","level":3,"score":0.26989999413490295},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.26969999074935913},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2612000107765198},{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.2535000145435333}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060152","descriptor_name":"V(D)J Recombination","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.7554/elife.73475","doi":"https://doi.org/10.7554/elife.73475","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.73475","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},{"id":"doi:10.1101/2021.09.17.460747","doi":"https://doi.org/10.1101/2021.09.17.460747","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2021.09.17.460747","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:8940181","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8940181","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"Text"},{"id":"pmid:35315770","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35315770","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:95bf64a4fda74d50b1793c5c3f136e61","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/95bf64a4fda74d50b1793c5c3f136e61","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"eLife, Vol 11 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.7554/elife.73475","doi":"https://doi.org/10.7554/elife.73475","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.73475","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4043000042438507}],"study_designs":[],"awards":[{"id":"https://openalex.org/G151485645","display_name":null,"funder_award_id":"AI33484","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1928169366","display_name":"Genetic Analysis of Airflow Obstruction After Stem Cell Transplantation","funder_award_id":"R01HL088201","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G1946125661","display_name":"Biomarker Discovery in Chronic Graft-vs-Host Disease","funder_award_id":"R01HL094260","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2087537607","display_name":"High-Performance Compute Cluster for Comprehensive Cancer and Infectious Diseases Research","funder_award_id":"1s10od028685-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2124356687","display_name":"Genetic epidemiology of TLR4 alleles and bacteremia","funder_award_id":"K23HL069860","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2203814738","display_name":"Whole Genome Association Analysis of Hematopoietic Cell Transplant Outcome","funder_award_id":"R01HL087690","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2395463226","display_name":null,"funder_award_id":"HL094260","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G273506865","display_name":null,"funder_award_id":"HL088201","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2817879615","display_name":"Immunobiology of Tolerance FF Allogeneic Hematopoietic Cell Transplantation","funder_award_id":"P01AI033484","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4266498966","display_name":null,"funder_award_id":"CA015704","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4431735618","display_name":null,"funder_award_id":"AI149213","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5728891395","display_name":null,"funder_award_id":"HL105914","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G666892057","display_name":"Whole Genome Association Analysis of Hematopoietic Cell Transplant (HCT)  Outcome","funder_award_id":"R01HL105914","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7314510119","display_name":null,"funder_award_id":"75N93021C00016","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8019673204","display_name":"Mechanisms to diversify repertoire and modify T cell activity after infection","funder_award_id":"R01AI107625","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8285517188","display_name":"Blending deep learning with probabilistic mechanistic models to predict and understand the evolution and function of adaptive immune receptors","funder_award_id":"R01AI146028","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8504575983","display_name":"Dynamics of Influenza Transmission in Nicaraguan Households","funder_award_id":"R01AI120997","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000859741","display_name":"Decoding the interactions between T cell receptors and peptide-MHC","funder_award_id":"R01AI136514","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000880613","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA015704","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G918065593","display_name":null,"funder_award_id":"HL087690","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G921956316","display_name":null,"funder_award_id":"HHSN 272201400006C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1520434148","https://openalex.org/W1526919179","https://openalex.org/W1563668677","https://openalex.org/W1566952847","https://openalex.org/W1840379775","https://openalex.org/W1964372737","https://openalex.org/W1969192442","https://openalex.org/W1970429567","https://openalex.org/W1972313386","https://openalex.org/W1973310934","https://openalex.org/W1989223689","https://openalex.org/W1997056099","https://openalex.org/W2005127588","https://openalex.org/W2008047653","https://openalex.org/W2009144436","https://openalex.org/W2009588715","https://openalex.org/W2011522975","https://openalex.org/W2011730671","https://openalex.org/W2017044557","https://openalex.org/W2019794729","https://openalex.org/W2022396117","https://openalex.org/W2033450927","https://openalex.org/W2037517612","https://openalex.org/W2050812646","https://openalex.org/W2051241958","https://openalex.org/W2055519354","https://openalex.org/W2082579696","https://openalex.org/W2086771595","https://openalex.org/W2100213817","https://openalex.org/W2100442196","https://openalex.org/W2103425962","https://openalex.org/W2115122333","https://openalex.org/W2140323624","https://openalex.org/W2143078668","https://openalex.org/W2144504271","https://openalex.org/W2154173051","https://openalex.org/W2172893229","https://openalex.org/W2226732401","https://openalex.org/W2310172832","https://openalex.org/W2319163584","https://openalex.org/W2327212272","https://openalex.org/W2494982315","https://openalex.org/W2605177850","https://openalex.org/W2671261300","https://openalex.org/W2797380951","https://openalex.org/W2951959160","https://openalex.org/W2962685339","https://openalex.org/W2968498576","https://openalex.org/W2988276547","https://openalex.org/W2990427812","https://openalex.org/W2997084988","https://openalex.org/W3042906360","https://openalex.org/W3083225904","https://openalex.org/W3092794318","https://openalex.org/W3092917676","https://openalex.org/W3131255047","https://openalex.org/W3173481701","https://openalex.org/W4205890290","https://openalex.org/W4243563432","https://openalex.org/W4285719527","https://openalex.org/W6869071466","https://openalex.org/W6869487523"],"related_works":["https://openalex.org/W2090794626","https://openalex.org/W2009591180","https://openalex.org/W2143513209","https://openalex.org/W1972750844","https://openalex.org/W3111056735","https://openalex.org/W2170279709","https://openalex.org/W7204187337","https://openalex.org/W2403966431","https://openalex.org/W2140323624","https://openalex.org/W7163737007"],"abstract_inverted_index":{"Abstract":[0],"Every":[1],"T":[2,21],"cell":[3],"receptor":[4],"(TCR)":[5],"repertoire":[6,54,66,157],"is":[7,48],"shaped":[8],"by":[9,159],"a":[10,24,30,63,75],"complex":[11,120],"probabilistic":[12],"tangle":[13],"of":[14,154,169,178],"genetically":[15],"determined":[16],"biases":[17,158],"and":[18,37,134,146,161,173],"immune":[19,200],"exposures.":[20],"cells":[22],"combine":[23],"random":[25],"V(D)J":[26,86,96,170],"recombination":[27,87],"process":[28,32],"with":[29,50,70,85,102,141,185],"selection":[31],"to":[33,42,58,138],"generate":[34],"highly":[35],"diverse":[36],"functional":[38,112],"TCRs.":[39],"The":[40],"extent":[41],"which":[43,182],"an":[44],"individual\u2019s":[45],"genetic":[46,82,167,180],"background":[47],"associated":[49,84,101,140,184],"their":[51],"resulting":[52],"TCR":[53,113,156],"diversity":[55],"has":[56],"yet":[57],"be":[59,139],"fully":[60],"explored.":[61],"Using":[62],"previously":[64],"published":[65],"sequencing":[67],"dataset":[68],"paired":[69],"high-resolution":[71],"genome-wide":[72,90],"genotyping":[73],"from":[74],"large":[76],"human":[77],"cohort,":[78],"we":[79,123],"infer":[80],"specific":[81,125],"loci":[83],"probabilities":[88],"using":[89],"association":[91],"inference.":[92],"We":[93],"show":[94],"that":[95],"gene":[97,171],"usage":[98,172],"profiles":[99],"are":[100,183],"variation":[103,115],"in":[104,116,127],"the":[105,111,117,128,131,135,166,175,193],"TCRB":[106],"locus":[107],"and,":[108],"specifically":[109],"for":[110,195],"repertoire,":[114],"major":[118],"histocompatibility":[119],"locus.":[121],"Further,":[122],"identify":[124],"variations":[126],"genes":[129],"encoding":[130],"Artemis":[132],"protein":[133,137],"TdT":[136],"biasing":[142],"junctional":[143,187],"nucleotide":[144],"deletion":[145],"N-insertion,":[147],"respectively.":[148],"These":[149],"results":[150],"refine":[151],"our":[152],"understanding":[153],"genetically-determined":[155],"confirming":[160],"extending":[162],"previous":[163],"studies":[164],"on":[165],"determinants":[168],"providing":[174],"first":[176],"examples":[177],"trans":[179],"variants":[181],"modifying":[186],"diversity.":[188],"Together,":[189],"these":[190],"insights":[191],"lay":[192],"groundwork":[194],"further":[196],"explorations":[197],"into":[198],"how":[199],"responses":[201],"vary":[202],"between":[203],"individuals.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2022-05-05T00:00:00"}