Diagnostic interpretation of array data using public databases and internet sources
Identifieur interne : 000996 ( Main/Exploration ); précédent : 000995; suivant : 000997Diagnostic interpretation of array data using public databases and internet sources
Auteurs : Nicole De Leeuw [Pays-Bas] ; Trijnie Dijkhuizen [Pays-Bas] ; Jayne Y. Hehir-Kwa [Pays-Bas] ; Nigel P. Carter [Royaume-Uni] ; Lars Feuk [Suède] ; Helen V. Firth [Royaume-Uni] ; Robert M. Kuhn [États-Unis] ; David H. Ledbetter [États-Unis] ; Christa Lese Martin [Géorgie (pays)] ; Conny M. A. Van Ravenswaaij-Arts [Pays-Bas] ; Steven W. Scherer [Canada] ; Soheil Shams [États-Unis] ; Steven Van Vooren [Belgique] ; Rolf Sijmons [Pays-Bas] ; Morris Swertz [Pays-Bas] ; Ros Hastings [Royaume-Uni]Source :
- Human Mutation [ 1059-7794 ] ; 2012-06.
English descriptors
- KwdEn :
Abstract
The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy‐number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires expertise. With our knowledge of the human genome growing rapidly, applications for array testing continuously broadening, and the resolution of CNV detection increasing, this leads to great complexity in interpreting what can be daunting data. Correct CNV interpretation and optimal use of the genotype information provided by single‐nucleotide polymorphism probes on an array depends largely on knowledge present in various resources. In addition to the availability of host laboratories' own datasets and national registries, there are several public databases and Internet resources with genotype and phenotype information that can be used for array data interpretation. With so many resources now available, it is important to know which are fit‐for‐purpose in a diagnostic setting. We summarize the characteristics of the most commonly used Internet databases and resources, and propose a general data interpretation strategy that can be used for comparative hybridization, comparative intensity, and genotype‐based array data. Hum Mutat 33:930–940, 2012. © 2012 Wiley Periodicals, Inc.
Url:
DOI: 10.1002/humu.22049
Affiliations:
- Belgique, Canada, Géorgie (pays), Pays-Bas, Royaume-Uni, Suède, États-Unis
- Angleterre, Californie, East Middle Sweden, Groningue (province), Gueldre, Ontario, Oxfordshire, Pennsylvanie, Svealand
- Groningue, Nimègue, Oxford, Toronto, Uppsala
- Université d'Uppsala, Université de Groningue, Université de Toronto
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Hehir-Kwa</name><affiliation wicri:level="3"><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen</wicri:regionArea><placeName><settlement type="city">Nimègue</settlement><region type="province" nuts="2">Gueldre</region></placeName></affiliation></author><author><name sortKey="Carter, Nigel P" sort="Carter, Nigel P" uniqKey="Carter N" first="Nigel P." last="Carter">Nigel P. Carter</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea><wicri:noRegion>Cambridge</wicri:noRegion></affiliation></author><author><name sortKey="Feuk, Lars" sort="Feuk, Lars" uniqKey="Feuk L" first="Lars" last="Feuk">Lars Feuk</name><affiliation wicri:level="4"><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University</wicri:regionArea><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName><orgName type="university">Université d'Uppsala</orgName></affiliation></author><author><name sortKey="Firth, Helen V" sort="Firth, Helen V" uniqKey="Firth H" first="Helen V." last="Firth">Helen V. Firth</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea><wicri:noRegion>Cambridge</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge</wicri:regionArea><wicri:noRegion>Cambridge</wicri:noRegion></affiliation></author><author><name sortKey="Kuhn, Robert M" sort="Kuhn, Robert M" uniqKey="Kuhn R" first="Robert M." last="Kuhn">Robert M. Kuhn</name><affiliation wicri:level="2"><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Center for Biomolecular Science and Engineering, University of California, Santa Cruz</wicri:cityArea></affiliation></author><author><name sortKey="Ledbetter, David H" sort="Ledbetter, David H" uniqKey="Ledbetter D" first="David H." last="Ledbetter">David H. Ledbetter</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Genomic Medicine Institute, Geisinger Health System, Danville</wicri:cityArea></affiliation></author><author><name sortKey="Martin, Christa Lese" sort="Martin, Christa Lese" uniqKey="Martin C" first="Christa Lese" last="Martin">Christa Lese Martin</name><affiliation wicri:level="1"><country xml:lang="fr">Géorgie (pays)</country><wicri:regionArea>Department of Human Genetics, Emory Genetics Laboratory, Emory University School of Medicine, Atlanta</wicri:regionArea><wicri:noRegion>Atlanta</wicri:noRegion></affiliation></author><author><name sortKey="Van Ravenswaaij Rts, Conny M A" sort="Van Ravenswaaij Rts, Conny M A" uniqKey="Van Ravenswaaij Rts C" first="Conny M. A." last="Van Ravenswaaij-Arts">Conny M. A. Van Ravenswaaij-Arts</name><affiliation wicri:level="4"><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen</wicri:regionArea><placeName><settlement type="city">Groningue</settlement><region nuts="2" type="province">Groningue (province)</region></placeName><orgName type="university">Université de Groningue</orgName></affiliation></author><author><name sortKey="Scherer, Steven W" sort="Scherer, Steven W" uniqKey="Scherer S" first="Steven W." last="Scherer">Steven W. Scherer</name><affiliation wicri:level="4"><country xml:lang="fr">Canada</country><wicri:regionArea>McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Canada</country><wicri:regionArea>The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation></author><author><name sortKey="Shams, Soheil" sort="Shams, Soheil" uniqKey="Shams S" first="Soheil" last="Shams">Soheil Shams</name><affiliation wicri:level="2"><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>BioDiscovery, Inc., El Segundo</wicri:cityArea></affiliation></author><author><name sortKey="Van Vooren, Steven" sort="Van Vooren, Steven" uniqKey="Van Vooren S" first="Steven" last="Van Vooren">Steven Van Vooren</name><affiliation wicri:level="1"><country xml:lang="fr">Belgique</country><wicri:regionArea>Cartagenia, Leuven</wicri:regionArea><wicri:noRegion>Leuven</wicri:noRegion></affiliation></author><author><name sortKey="Sijmons, Rolf" sort="Sijmons, Rolf" uniqKey="Sijmons R" first="Rolf" last="Sijmons">Rolf Sijmons</name><affiliation wicri:level="4"><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen</wicri:regionArea><placeName><settlement type="city">Groningue</settlement><region nuts="2" type="province">Groningue (province)</region></placeName><orgName type="university">Université de Groningue</orgName></affiliation></author><author><name sortKey="Swertz, Morris" sort="Swertz, Morris" uniqKey="Swertz M" first="Morris" last="Swertz">Morris Swertz</name><affiliation wicri:level="4"><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen</wicri:regionArea><placeName><settlement type="city">Groningue</settlement><region nuts="2" type="province">Groningue (province)</region></placeName><orgName type="university">Université de Groningue</orgName></affiliation></author><author><name sortKey="Hastings, Ros" sort="Hastings, Ros" uniqKey="Hastings R" first="Ros" last="Hastings">Ros Hastings</name><affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Cytogenetic European Quality Assessment and United Kingdom National External Quality Assessment Service for Clinical Cytogenetics, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Human Mutation</title><title level="j" type="abbrev">Hum. Mutat.</title><idno type="ISSN">1059-7794</idno><idno type="eISSN">1098-1004</idno><imprint><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2012-06">2012-06</date><biblScope unit="volume">33</biblScope><biblScope unit="issue">6</biblScope><biblScope unit="page" from="930">930</biblScope><biblScope unit="page" to="940">940</biblScope></imprint><idno type="ISSN">1059-7794</idno></series><idno type="istex">48ED99E15E5C0D637F4412A409E02C16FF88D9C5</idno><idno type="DOI">10.1002/humu.22049</idno><idno type="ArticleID">HUMU22049</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1059-7794</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>CNV</term><term>array</term><term>classification</term><term>data interpretation</term><term>database</term><term>diagnostic</term><term>genome wide</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy‐number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires expertise. With our knowledge of the human genome growing rapidly, applications for array testing continuously broadening, and the resolution of CNV detection increasing, this leads to great complexity in interpreting what can be daunting data. Correct CNV interpretation and optimal use of the genotype information provided by single‐nucleotide polymorphism probes on an array depends largely on knowledge present in various resources. In addition to the availability of host laboratories' own datasets and national registries, there are several public databases and Internet resources with genotype and phenotype information that can be used for array data interpretation. With so many resources now available, it is important to know which are fit‐for‐purpose in a diagnostic setting. We summarize the characteristics of the most commonly used Internet databases and resources, and propose a general data interpretation strategy that can be used for comparative hybridization, comparative intensity, and genotype‐based array data. Hum Mutat 33:930–940, 2012. © 2012 Wiley Periodicals, Inc.</div></front></TEI><affiliations><list><country><li>Belgique</li><li>Canada</li><li>Géorgie (pays)</li><li>Pays-Bas</li><li>Royaume-Uni</li><li>Suède</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Californie</li><li>East Middle Sweden</li><li>Groningue (province)</li><li>Gueldre</li><li>Ontario</li><li>Oxfordshire</li><li>Pennsylvanie</li><li>Svealand</li></region><settlement><li>Groningue</li><li>Nimègue</li><li>Oxford</li><li>Toronto</li><li>Uppsala</li></settlement><orgName><li>Université d'Uppsala</li><li>Université de Groningue</li><li>Université de Toronto</li></orgName></list><tree><country name="Pays-Bas"><region name="Gueldre"><name sortKey="De Leeuw, Nicole" sort="De Leeuw, Nicole" uniqKey="De Leeuw N" first="Nicole" last="De Leeuw">Nicole De Leeuw</name></region><name sortKey="Dijkhuizen, Trijnie" sort="Dijkhuizen, Trijnie" uniqKey="Dijkhuizen T" first="Trijnie" last="Dijkhuizen">Trijnie Dijkhuizen</name><name sortKey="Hehir Wa, Jayne Y" sort="Hehir Wa, Jayne Y" uniqKey="Hehir Wa J" first="Jayne Y." last="Hehir-Kwa">Jayne Y. Hehir-Kwa</name><name sortKey="Sijmons, Rolf" sort="Sijmons, Rolf" uniqKey="Sijmons R" first="Rolf" last="Sijmons">Rolf Sijmons</name><name sortKey="Swertz, Morris" sort="Swertz, Morris" uniqKey="Swertz M" first="Morris" last="Swertz">Morris Swertz</name><name sortKey="Van Ravenswaaij Rts, Conny M A" sort="Van Ravenswaaij Rts, Conny M A" uniqKey="Van Ravenswaaij Rts C" first="Conny M. A." last="Van Ravenswaaij-Arts">Conny M. A. Van Ravenswaaij-Arts</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Carter, Nigel P" sort="Carter, Nigel P" uniqKey="Carter N" first="Nigel P." last="Carter">Nigel P. Carter</name></noRegion><name sortKey="Firth, Helen V" sort="Firth, Helen V" uniqKey="Firth H" first="Helen V." last="Firth">Helen V. Firth</name><name sortKey="Firth, Helen V" sort="Firth, Helen V" uniqKey="Firth H" first="Helen V." last="Firth">Helen V. Firth</name><name sortKey="Hastings, Ros" sort="Hastings, Ros" uniqKey="Hastings R" first="Ros" last="Hastings">Ros Hastings</name></country><country name="Suède"><region name="Svealand"><name sortKey="Feuk, Lars" sort="Feuk, Lars" uniqKey="Feuk L" first="Lars" last="Feuk">Lars Feuk</name></region></country><country name="États-Unis"><region name="Californie"><name sortKey="Kuhn, Robert M" sort="Kuhn, Robert M" uniqKey="Kuhn R" first="Robert M." last="Kuhn">Robert M. Kuhn</name></region><name sortKey="Ledbetter, David H" sort="Ledbetter, David H" uniqKey="Ledbetter D" first="David H." last="Ledbetter">David H. Ledbetter</name><name sortKey="Shams, Soheil" sort="Shams, Soheil" uniqKey="Shams S" first="Soheil" last="Shams">Soheil Shams</name></country><country name="Géorgie (pays)"><noRegion><name sortKey="Martin, Christa Lese" sort="Martin, Christa Lese" uniqKey="Martin C" first="Christa Lese" last="Martin">Christa Lese Martin</name></noRegion></country><country name="Canada"><region name="Ontario"><name sortKey="Scherer, Steven W" sort="Scherer, Steven W" uniqKey="Scherer S" first="Steven W." last="Scherer">Steven W. Scherer</name></region><name sortKey="Scherer, Steven W" sort="Scherer, Steven W" uniqKey="Scherer S" first="Steven W." last="Scherer">Steven W. Scherer</name></country><country name="Belgique"><noRegion><name sortKey="Van Vooren, Steven" sort="Van Vooren, Steven" uniqKey="Van Vooren S" first="Steven" last="Van Vooren">Steven Van Vooren</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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