Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration
Identifieur interne : 000538 ( Istex/Corpus ); précédent : 000537; suivant : 000539Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration
Auteurs : M. Olivier ; A. Petitjean ; J. Teague ; S. Forbes ; J. K. Dunnick ; J. T. Den Dunnen ; A. Langer D ; J. M. Wilkinson ; M. Vihinen ; R. G. H. Cotton ; P. HainautSource :
- Human Mutation [ 1059-7794 ] ; 2009-03.
English descriptors
Abstract
There are currently less than 40 locus‐specific databases (LSDBs) and one large general database that curate data on somatic mutations in human cancer genes. These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. Hum Mutat 0,1–8, 2008. © 2008 Wiley‐Liss, Inc.
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DOI: 10.1002/humu.20832
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These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. Hum Mutat 0,1–8, 2008. © 2008 Wiley‐Liss, Inc.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>M. Olivier</name><affiliations><json:string>Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France</json:string></affiliations></json:item><json:item><name>A. 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As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. 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These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. 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number="1"></count><count type="tableTotal" number="2"></count><count type="referenceTotal" number="15"></count></countGroup><titleGroup><title type="main" xml:lang="en">Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration<link href="#fn1"></link></title></titleGroup><creators><creator xml:id="au1" creatorRole="author" affiliationRef="#af1" corresponding="yes"><personName><givenNames>M.</givenNames><familyName>Olivier</familyName></personName><contactDetails><email>molivier@iarc.fr</email></contactDetails></creator><creator xml:id="au2" creatorRole="author" affiliationRef="#af1"><personName><givenNames>A.</givenNames><familyName>Petitjean</familyName></personName></creator><creator xml:id="au3" creatorRole="author" affiliationRef="#af2"><personName><givenNames>J.</givenNames><familyName>Teague</familyName></personName></creator><creator xml:id="au4" creatorRole="author" affiliationRef="#af2"><personName><givenNames>S.</givenNames><familyName>Forbes</familyName></personName></creator><creator xml:id="au5" creatorRole="author" affiliationRef="#af3"><personName><givenNames>J.K.</givenNames><familyName>Dunnick</familyName></personName></creator><creator xml:id="au6" creatorRole="author" affiliationRef="#af4"><personName><givenNames>J.T.</givenNames><familyName>den Dunnen</familyName></personName></creator><creator xml:id="au7" creatorRole="author" affiliationRef="#af5"><personName><givenNames>A.</givenNames><familyName>Langerød</familyName></personName></creator><creator xml:id="au8" creatorRole="author" affiliationRef="#af6"><personName><givenNames>J.M.</givenNames><familyName>Wilkinson</familyName></personName></creator><creator xml:id="au9" creatorRole="author" affiliationRef="#af7 #af9"><personName><givenNames>M.</givenNames><familyName>Vihinen</familyName></personName></creator><creator xml:id="au10" creatorRole="author" affiliationRef="#af8"><personName><givenNames>R.G.H.</givenNames><familyName>Cotton</familyName></personName></creator><creator xml:id="au11" creatorRole="author" affiliationRef="#af1"><personName><givenNames>P.</givenNames><familyName>Hainaut</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="af1" countryCode="FR" type="organization"><unparsedAffiliation>Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France</unparsedAffiliation></affiliation><affiliation xml:id="af2" countryCode="GB" type="organization"><unparsedAffiliation>Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</unparsedAffiliation></affiliation><affiliation xml:id="af3" countryCode="US" type="organization"><unparsedAffiliation>Toxicology Operations Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina</unparsedAffiliation></affiliation><affiliation xml:id="af4" countryCode="NL" type="organization"><unparsedAffiliation>Leiden University Medical Center, Leiden, The Netherlands</unparsedAffiliation></affiliation><affiliation xml:id="af5" countryCode="NO" type="organization"><unparsedAffiliation>Department of Genetics, Institute for Cancer Research, Rikshospitalet‐Radiumhospitalet Medical Center, Oslo, Norway</unparsedAffiliation></affiliation><affiliation xml:id="af6" countryCode="GB" type="organization"><unparsedAffiliation>National Cancer Research Institute (NCRI) Cancer Informatics Initiative, London, United Kingdom</unparsedAffiliation></affiliation><affiliation xml:id="af7" countryCode="FI" type="organization"><unparsedAffiliation>Institute of Medical Technology, University of Tampere, Finland</unparsedAffiliation></affiliation><affiliation xml:id="af8" countryCode="FI" type="organization"><unparsedAffiliation>Tampere University Hospital, Tampere, Finland</unparsedAffiliation></affiliation><affiliation xml:id="af9" countryCode="AU" type="organization"><unparsedAffiliation>Genomic Disorders Research Centre, St. Vincent's Hospital Melbourne, Melbourne, Australia</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en" type="author"><keyword xml:id="kwd1">somatic mutation; database; standards</keyword></keywordGroup><fundingInfo><fundingAgency>International Agency for Research on Cancer (IARC);</fundingAgency></fundingInfo><fundingInfo><fundingAgency>European Community (EC) FP6</fundingAgency></fundingInfo><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>There are currently less than 40 locus‐specific databases (LSDBs) and one large general database that curate data on somatic mutations in human cancer genes. These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. Hum Mutat 0,1–8, 2008. © 2008 Wiley‐Liss, Inc.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><p>Communicated by Alastair F. Brown</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration</title></titleInfo><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Olivier</namePart><affiliation>Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France</affiliation><description>Correspondence: International Agency for Research on Cancer, 150 Cours Albert Thomas, Lyon, 69372, France</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="family">Petitjean</namePart><affiliation>Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J.</namePart><namePart type="family">Teague</namePart><affiliation>Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">Forbes</namePart><affiliation>Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J.K.</namePart><namePart type="family">Dunnick</namePart><affiliation>Toxicology Operations Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J.T.</namePart><namePart type="family">den Dunnen</namePart><affiliation>Leiden University Medical Center, Leiden, The Netherlands</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="family">Langerød</namePart><affiliation>Department of Genetics, Institute for Cancer Research, Rikshospitalet‐Radiumhospitalet Medical Center, Oslo, Norway</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J.M.</namePart><namePart type="family">Wilkinson</namePart><affiliation>National Cancer Research Institute (NCRI) Cancer Informatics Initiative, London, United Kingdom</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Vihinen</namePart><affiliation>Institute of Medical Technology, University of Tampere, Finland</affiliation><affiliation>Genomic Disorders Research Centre, St. Vincent's Hospital Melbourne, Melbourne, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R.G.H.</namePart><namePart type="family">Cotton</namePart><affiliation>Tampere University Hospital, Tampere, Finland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P.</namePart><namePart type="family">Hainaut</namePart><affiliation>Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><place><placeTerm type="text">Hoboken</placeTerm></place><dateIssued encoding="w3cdtf">2009-03</dateIssued><dateCaptured encoding="w3cdtf">2008-03-10</dateCaptured><dateValid encoding="w3cdtf">2008-05-01</dateValid><copyrightDate encoding="w3cdtf">2009</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">1</extent><extent unit="tables">2</extent><extent unit="references">15</extent></physicalDescription><abstract lang="en">There are currently less than 40 locus‐specific databases (LSDBs) and one large general database that curate data on somatic mutations in human cancer genes. These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. Hum Mutat 0,1–8, 2008. © 2008 Wiley‐Liss, Inc.</abstract><note type="content">*Communicated by Alastair F. Brown</note><note type="funding">International Agency for Research on Cancer (IARC);</note><note type="funding">European Community (EC) FP6</note><subject lang="en"><genre>keywords</genre><topic>somatic mutation; database; standards</topic></subject><relatedItem type="host"><titleInfo><title>Human Mutation</title></titleInfo><titleInfo type="abbreviated"><title>Hum. Mutat.</title></titleInfo><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>Special Article</topic></subject><identifier type="ISSN">1059-7794</identifier><identifier type="eISSN">1098-1004</identifier><identifier type="DOI">10.1002/(ISSN)1098-1004</identifier><identifier type="PublisherID">HUMU</identifier><part><date>2009</date><detail type="volume"><caption>vol.</caption><number>30</number></detail><detail type="issue"><caption>no.</caption><number>3</number></detail><extent unit="pages"><start>275</start><end>282</end><total>8</total></extent></part></relatedItem><identifier type="istex">2DE84FF813197D14C9BAAE2548E4B68B956C6D42</identifier><identifier type="DOI">10.1002/humu.20832</identifier><identifier type="ArticleID">HUMU20832</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2008 Wiley‐Liss, Inc.</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Wiley Subscription Services, Inc., A Wiley Company</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/2DE84FF813197D14C9BAAE2548E4B68B956C6D42/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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