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...
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Veröffentlicht in: | Nucleic acids research 2020-01, Vol.48 (D1), p.D964-D970 |
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container_title | Nucleic acids research |
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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 |
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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> |
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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 |
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