OGRDB: a reference database of inferred immune receptor genes

Abstract High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germl...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nucleic acids research 2020-01, Vol.48 (D1), p.D964-D970
Hauptverfasser: Lees, William, Busse, Christian E, Corcoran, Martin, Ohlin, Mats, Scheepers, Cathrine, Matsen, Frederick A, Yaari, Gur, Watson, Corey T, Collins, Andrew, Shepherd, Adrian J
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page D970
container_issue D1
container_start_page D964
container_title Nucleic acids research
container_volume 48
creator Lees, William
Busse, Christian E
Corcoran, Martin
Ohlin, Mats
Scheepers, Cathrine
Matsen, Frederick A
Yaari, Gur
Watson, Corey T
Collins, Andrew
Shepherd, Adrian J
description Abstract High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.
doi_str_mv 10.1093/nar/gkz822
format Article
fullrecord <record><control><sourceid>proquest_swepu</sourceid><recordid>TN_cdi_swepub_primary_oai_swepub_ki_se_476713</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkz822</oup_id><sourcerecordid>2299447172</sourcerecordid><originalsourceid>FETCH-LOGICAL-c631t-b74d676d5854a74f947c381eb04893702be6a30222d5c15f71e1a64aa4648dfe3</originalsourceid><addsrcrecordid>eNp9kltrFTEUhYMo9lh98QfIvAgijM1lJ5kIClq1CgcKos8hM7PnOHZuTWYU_fXuw5xW-1AfQsLOt1ZWks3YY8FfCO7UyRDiye7idyHlHbYRysgcnJF32YYrrnPBoThiD1L6zrkAoeE-O1JCGyOl3rBX52ef3719mYUsYoMRhwqzOsyhDAmzscnagaoR66zt-2VAoiqc5jFmOxwwPWT3mtAlfHSYj9nXD--_nH7Mt-dnn07fbPPKKDHnpYXaWFPrQkOw0DiwlSoElhTNKctliSYoLqWsdSV0YwWKYCAEMFDUDapjlq--6SdOS-mn2PYh_vJjaP2hdEEr9GCNFYp4dys_xbH-K7oSClAABRhD2u2t2m6ZaJQ09hrtFAUOxgew2gMvnacL1t6AwVCIhp57H_31akdePdYVDnMM3c1EN3aG9pvfjT-8caC4Lcjg2cEgjpcLptn3baqw68KA45K8lM4BWGEloc9XtIpjSvSh18cI7vet4qlV_NoqBD_5N9g1etUbBDxdgZFu_R-jP4onx4Y</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2299447172</pqid></control><display><type>article</type><title>OGRDB: a reference database of inferred immune receptor genes</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>SWEPUB Freely available online</source><source>Oxford Journals Open Access Collection</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Lees, William ; Busse, Christian E ; Corcoran, Martin ; Ohlin, Mats ; Scheepers, Cathrine ; Matsen, Frederick A ; Yaari, Gur ; Watson, Corey T ; Collins, Andrew ; Shepherd, Adrian J</creator><creatorcontrib>Lees, William ; Busse, Christian E ; Corcoran, Martin ; Ohlin, Mats ; Scheepers, Cathrine ; Matsen, Frederick A ; Yaari, Gur ; Watson, Corey T ; Collins, Andrew ; Shepherd, Adrian J ; AIRR Community ; The AIRR Community</creatorcontrib><description>Abstract High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkz822</identifier><identifier>PMID: 31566225</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Basic Medicine ; Computational Biology - methods ; Database Issue ; Databases, Genetic ; Genomics - methods ; Humans ; Immunologi inom det medicinska området ; Immunology in the medical area ; Medical and Health Sciences ; Medicin och hälsovetenskap ; Medicinska och farmaceutiska grundvetenskaper ; Receptors, Immunologic - genetics ; Software ; Web Browser</subject><ispartof>Nucleic acids research, 2020-01, Vol.48 (D1), p.D964-D970</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c631t-b74d676d5854a74f947c381eb04893702be6a30222d5c15f71e1a64aa4648dfe3</citedby><cites>FETCH-LOGICAL-c631t-b74d676d5854a74f947c381eb04893702be6a30222d5c15f71e1a64aa4648dfe3</cites><orcidid>0000-0001-9834-6840 ; 0000-0001-9311-9884 ; 0000-0001-7553-905X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943078/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943078/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,552,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31566225$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://lup.lub.lu.se/record/5932d5a6-a475-40b9-854d-646ea81f014e$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:143448466$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Lees, William</creatorcontrib><creatorcontrib>Busse, Christian E</creatorcontrib><creatorcontrib>Corcoran, Martin</creatorcontrib><creatorcontrib>Ohlin, Mats</creatorcontrib><creatorcontrib>Scheepers, Cathrine</creatorcontrib><creatorcontrib>Matsen, Frederick A</creatorcontrib><creatorcontrib>Yaari, Gur</creatorcontrib><creatorcontrib>Watson, Corey T</creatorcontrib><creatorcontrib>Collins, Andrew</creatorcontrib><creatorcontrib>Shepherd, Adrian J</creatorcontrib><creatorcontrib>AIRR Community</creatorcontrib><creatorcontrib>The AIRR Community</creatorcontrib><title>OGRDB: a reference database of inferred immune receptor genes</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.</description><subject>Basic Medicine</subject><subject>Computational Biology - methods</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>Genomics - methods</subject><subject>Humans</subject><subject>Immunologi inom det medicinska området</subject><subject>Immunology in the medical area</subject><subject>Medical and Health Sciences</subject><subject>Medicin och hälsovetenskap</subject><subject>Medicinska och farmaceutiska grundvetenskaper</subject><subject>Receptors, Immunologic - genetics</subject><subject>Software</subject><subject>Web Browser</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><sourceid>D8T</sourceid><recordid>eNp9kltrFTEUhYMo9lh98QfIvAgijM1lJ5kIClq1CgcKos8hM7PnOHZuTWYU_fXuw5xW-1AfQsLOt1ZWks3YY8FfCO7UyRDiye7idyHlHbYRysgcnJF32YYrrnPBoThiD1L6zrkAoeE-O1JCGyOl3rBX52ef3719mYUsYoMRhwqzOsyhDAmzscnagaoR66zt-2VAoiqc5jFmOxwwPWT3mtAlfHSYj9nXD--_nH7Mt-dnn07fbPPKKDHnpYXaWFPrQkOw0DiwlSoElhTNKctliSYoLqWsdSV0YwWKYCAEMFDUDapjlq--6SdOS-mn2PYh_vJjaP2hdEEr9GCNFYp4dys_xbH-K7oSClAABRhD2u2t2m6ZaJQ09hrtFAUOxgew2gMvnacL1t6AwVCIhp57H_31akdePdYVDnMM3c1EN3aG9pvfjT-8caC4Lcjg2cEgjpcLptn3baqw68KA45K8lM4BWGEloc9XtIpjSvSh18cI7vet4qlV_NoqBD_5N9g1etUbBDxdgZFu_R-jP4onx4Y</recordid><startdate>20200108</startdate><enddate>20200108</enddate><creator>Lees, William</creator><creator>Busse, Christian E</creator><creator>Corcoran, Martin</creator><creator>Ohlin, Mats</creator><creator>Scheepers, Cathrine</creator><creator>Matsen, Frederick A</creator><creator>Yaari, Gur</creator><creator>Watson, Corey T</creator><creator>Collins, Andrew</creator><creator>Shepherd, Adrian J</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AGCHP</scope><scope>AOWAS</scope><scope>D8T</scope><scope>D95</scope><scope>ZZAVC</scope><orcidid>https://orcid.org/0000-0001-9834-6840</orcidid><orcidid>https://orcid.org/0000-0001-9311-9884</orcidid><orcidid>https://orcid.org/0000-0001-7553-905X</orcidid></search><sort><creationdate>20200108</creationdate><title>OGRDB: a reference database of inferred immune receptor genes</title><author>Lees, William ; Busse, Christian E ; Corcoran, Martin ; Ohlin, Mats ; Scheepers, Cathrine ; Matsen, Frederick A ; Yaari, Gur ; Watson, Corey T ; Collins, Andrew ; Shepherd, Adrian J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c631t-b74d676d5854a74f947c381eb04893702be6a30222d5c15f71e1a64aa4648dfe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Basic Medicine</topic><topic>Computational Biology - methods</topic><topic>Database Issue</topic><topic>Databases, Genetic</topic><topic>Genomics - methods</topic><topic>Humans</topic><topic>Immunologi inom det medicinska området</topic><topic>Immunology in the medical area</topic><topic>Medical and Health Sciences</topic><topic>Medicin och hälsovetenskap</topic><topic>Medicinska och farmaceutiska grundvetenskaper</topic><topic>Receptors, Immunologic - genetics</topic><topic>Software</topic><topic>Web Browser</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lees, William</creatorcontrib><creatorcontrib>Busse, Christian E</creatorcontrib><creatorcontrib>Corcoran, Martin</creatorcontrib><creatorcontrib>Ohlin, Mats</creatorcontrib><creatorcontrib>Scheepers, Cathrine</creatorcontrib><creatorcontrib>Matsen, Frederick A</creatorcontrib><creatorcontrib>Yaari, Gur</creatorcontrib><creatorcontrib>Watson, Corey T</creatorcontrib><creatorcontrib>Collins, Andrew</creatorcontrib><creatorcontrib>Shepherd, Adrian J</creatorcontrib><creatorcontrib>AIRR Community</creatorcontrib><creatorcontrib>The AIRR Community</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SWEPUB Lunds universitet full text</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SWEPUB Lunds universitet</collection><collection>SwePub Articles full text</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lees, William</au><au>Busse, Christian E</au><au>Corcoran, Martin</au><au>Ohlin, Mats</au><au>Scheepers, Cathrine</au><au>Matsen, Frederick A</au><au>Yaari, Gur</au><au>Watson, Corey T</au><au>Collins, Andrew</au><au>Shepherd, Adrian J</au><aucorp>AIRR Community</aucorp><aucorp>The AIRR Community</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>OGRDB: a reference database of inferred immune receptor genes</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2020-01-08</date><risdate>2020</risdate><volume>48</volume><issue>D1</issue><spage>D964</spage><epage>D970</epage><pages>D964-D970</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>Abstract High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31566225</pmid><doi>10.1093/nar/gkz822</doi><orcidid>https://orcid.org/0000-0001-9834-6840</orcidid><orcidid>https://orcid.org/0000-0001-9311-9884</orcidid><orcidid>https://orcid.org/0000-0001-7553-905X</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0305-1048
ispartof Nucleic acids research, 2020-01, Vol.48 (D1), p.D964-D970
issn 0305-1048
1362-4962
1362-4962
language eng
recordid cdi_swepub_primary_oai_swepub_ki_se_476713
source MEDLINE; DOAJ Directory of Open Access Journals; SWEPUB Freely available online; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry
subjects Basic Medicine
Computational Biology - methods
Database Issue
Databases, Genetic
Genomics - methods
Humans
Immunologi inom det medicinska området
Immunology in the medical area
Medical and Health Sciences
Medicin och hälsovetenskap
Medicinska och farmaceutiska grundvetenskaper
Receptors, Immunologic - genetics
Software
Web Browser
title OGRDB: a reference database of inferred immune receptor genes
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-01T19%3A59%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_swepu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=OGRDB:%20a%20reference%20database%20of%20inferred%20immune%20receptor%20genes&rft.jtitle=Nucleic%20acids%20research&rft.au=Lees,%20William&rft.aucorp=AIRR%20Community&rft.date=2020-01-08&rft.volume=48&rft.issue=D1&rft.spage=D964&rft.epage=D970&rft.pages=D964-D970&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gkz822&rft_dat=%3Cproquest_swepu%3E2299447172%3C/proquest_swepu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2299447172&rft_id=info:pmid/31566225&rft_oup_id=10.1093/nar/gkz822&rfr_iscdi=true