Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.
Identifieur interne : 000C15 ( PubMed/Curation ); précédent : 000C14; suivant : 000C16Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.
Auteurs : D J Vis [Pays-Bas] ; J. Lewin [Canada] ; R G Liao [États-Unis] ; M. Mao [Corée du Sud] ; F. Andre [France] ; R L Ward [Australie] ; F. Calvo [France] ; B T Teh [Singapour] ; A A Camargo [Brésil] ; B M Knoppers [Canada] ; C L Sawyers [États-Unis] ; L F A. Wessels [Pays-Bas] ; M. Lawler [Royaume-Uni] ; L L Siu [Canada] ; E. Voest [Pays-Bas]Source :
- Annals of oncology : official journal of the European Society for Medical Oncology [ 1569-8041 ] ; 2017.
Abstract
While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community.
DOI: 10.1093/annonc/mdx037
PubMed: 28453708
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Lewin</name><affiliation wicri:level="1"><nlm:affiliation>Princess Margaret Cancer Centre, Toronto, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Princess Margaret Cancer Centre, Toronto</wicri:regionArea></affiliation></author><author><name sortKey="Liao, R G" sort="Liao, R G" uniqKey="Liao R" first="R G" last="Liao">R G Liao</name><affiliation wicri:level="1"><nlm:affiliation>Global Alliance for Genomics and Health, Broad Institute, Cambridge, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Global Alliance for Genomics and Health, Broad Institute, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Mao, M" sort="Mao, M" uniqKey="Mao M" first="M" last="Mao">M. Mao</name><affiliation wicri:level="1"><nlm:affiliation>Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, South Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Andre, F" sort="Andre, F" uniqKey="Andre F" first="F" last="Andre">F. Andre</name><affiliation wicri:level="1"><nlm:affiliation>INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif</wicri:regionArea></affiliation></author><author><name sortKey="Ward, R L" sort="Ward, R L" uniqKey="Ward R" first="R L" last="Ward">R L Ward</name><affiliation wicri:level="1"><nlm:affiliation>Research, University of Queensland, Brisbane, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research, University of Queensland, Brisbane</wicri:regionArea></affiliation></author><author><name sortKey="Calvo, F" sort="Calvo, F" uniqKey="Calvo F" first="F" last="Calvo">F. Calvo</name><affiliation wicri:level="1"><nlm:affiliation>Cancer Core Europe, Gustave Roussy, Villejuif, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Cancer Core Europe, Gustave Roussy, Villejuif</wicri:regionArea></affiliation></author><author><name sortKey="Teh, B T" sort="Teh, B T" uniqKey="Teh B" first="B T" last="Teh">B T Teh</name><affiliation wicri:level="1"><nlm:affiliation>National Cancer Centre, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>National Cancer Centre</wicri:regionArea></affiliation></author><author><name sortKey="Camargo, A A" sort="Camargo, A A" uniqKey="Camargo A" first="A A" last="Camargo">A A Camargo</name><affiliation wicri:level="1"><nlm:affiliation>Oncology, Hospital Sírio Libanês, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Oncology, Hospital Sírio Libanês, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Knoppers, B M" sort="Knoppers, B M" uniqKey="Knoppers B" first="B M" last="Knoppers">B M Knoppers</name><affiliation wicri:level="1"><nlm:affiliation>Centre of Genomics and Policy, McGill University, Montreal, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Centre of Genomics and Policy, McGill University, Montreal</wicri:regionArea></affiliation></author><author><name sortKey="Sawyers, C L" sort="Sawyers, C L" uniqKey="Sawyers C" first="C L" last="Sawyers">C L Sawyers</name><affiliation wicri:level="1"><nlm:affiliation>Memorial Sloan Kettering Cancer Centre, New York, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Memorial Sloan Kettering Cancer Centre, New York</wicri:regionArea></affiliation></author><author><name sortKey="Wessels, L F A" sort="Wessels, L F A" uniqKey="Wessels L" first="L F A" last="Wessels">L F A. Wessels</name><affiliation wicri:level="1"><nlm:affiliation>Netherlands Cancer Institute, Amsterdam, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Netherlands Cancer Institute, Amsterdam</wicri:regionArea></affiliation></author><author><name sortKey="Lawler, M" sort="Lawler, M" uniqKey="Lawler M" first="M" last="Lawler">M. Lawler</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast</wicri:regionArea></affiliation></author><author><name sortKey="Siu, L L" sort="Siu, L L" uniqKey="Siu L" first="L L" last="Siu">L L Siu</name><affiliation wicri:level="1"><nlm:affiliation>Princess Margaret Cancer Centre, Toronto, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Princess Margaret Cancer Centre, Toronto</wicri:regionArea></affiliation></author><author><name sortKey="Voest, E" sort="Voest, E" uniqKey="Voest E" first="E" last="Voest">E. Voest</name><affiliation wicri:level="1"><nlm:affiliation>Netherlands Cancer Institute, Amsterdam, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Netherlands Cancer Institute, Amsterdam</wicri:regionArea></affiliation></author></analytic><series><title level="j">Annals of oncology : official journal of the European Society for Medical Oncology</title><idno type="eISSN">1569-8041</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">28453708</PMID><DateCreated><Year>2017</Year><Month>04</Month><Day>28</Day></DateCreated><DateRevised><Year>2017</Year><Month>05</Month><Day>06</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1569-8041</ISSN><JournalIssue CitedMedium="Internet"><Volume>28</Volume><Issue>5</Issue><PubDate><Year>2017</Year><Month>May</Month><Day>01</Day></PubDate></JournalIssue><Title>Annals of oncology : official journal of the European Society for Medical Oncology</Title><ISOAbbreviation>Ann. Oncol.</ISOAbbreviation></Journal><ArticleTitle>Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.</ArticleTitle><Pagination><MedlinePgn>1145-1151</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/annonc/mdx037</ELocationID><Abstract><AbstractText Label="Background" NlmCategory="UNASSIGNED">While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community.</AbstractText><AbstractText Label="Methods" NlmCategory="UNASSIGNED">A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally. Additionally, respondents were asked as to provide the primary intent of their initiative (clinical diagnostic, research or combination).</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (P = 0.03) and whole genome sequencing (P = 0.01) were utilized less frequently in clinical diagnostic than in research initiatives. Procedures to identify cancer-specific variants were heterogeneous, with bioinformatics pipelines employing different mutation calling/variant annotation algorithms. Measurement of treatment efficacy varied amongst initiatives, with time on treatment (57%) and RECIST (53%) being the most common; however, other parameters were also employed. Whilst 72% of initiatives indicated data sharing, its scope varied, with a number of restrictions in place (e.g. transfer of raw data). The largest perceived barriers to data harmonization were the lack of financial support (P < 0.01) and bioinformatics concerns (e.g. lack of interoperability) (P = 0.02). Capturing clinical data was more likely to be perceived as a barrier to data sharing by larger initiatives than by smaller initiatives (P = 0.01).</AbstractText><AbstractText Label="Conclusions" NlmCategory="UNASSIGNED">These results identify the main barriers, as perceived by the cancer sequencing community, to effective sharing of cancer genomic and clinical data. They highlight the need for greater harmonization of technical, ethical and data capture processes in cancer sample sequencing worldwide, in order to support effective and responsible data sharing for the benefit of patients.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vis</LastName><ForeName>D J</ForeName><Initials>DJ</Initials><AffiliationInfo><Affiliation>Netherlands Cancer Institute, Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lewin</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Princess Margaret Cancer Centre, Toronto, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liao</LastName><ForeName>R G</ForeName><Initials>RG</Initials><AffiliationInfo><Affiliation>Global Alliance for Genomics and Health, Broad Institute, Cambridge, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mao</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Andre</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ward</LastName><ForeName>R L</ForeName><Initials>RL</Initials><AffiliationInfo><Affiliation>Research, University of Queensland, Brisbane, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Calvo</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Cancer Core Europe, Gustave Roussy, Villejuif, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Teh</LastName><ForeName>B T</ForeName><Initials>BT</Initials><AffiliationInfo><Affiliation>National Cancer Centre, Singapore.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Camargo</LastName><ForeName>A A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Oncology, Hospital Sírio Libanês, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knoppers</LastName><ForeName>B M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Centre of Genomics and Policy, McGill University, Montreal, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sawyers</LastName><ForeName>C L</ForeName><Initials>CL</Initials><AffiliationInfo><Affiliation>Memorial Sloan Kettering Cancer Centre, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wessels</LastName><ForeName>L F A</ForeName><Initials>LFA</Initials><AffiliationInfo><Affiliation>Netherlands Cancer Institute, Amsterdam, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Bioinformatics & Statistics, Delft University of Technology, Delft, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawler</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Siu</LastName><ForeName>L L</ForeName><Initials>LL</Initials><AffiliationInfo><Affiliation>Princess Margaret Cancer Centre, Toronto, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Voest</LastName><ForeName>E</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Netherlands Cancer Institute, Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><CollectiveName>Clinical Working Group of the Global Alliance for Genomics and Health</CollectiveName></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P30 CA008748</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ann Oncol</MedlineTA><NlmUniqueID>9007735</NlmUniqueID><ISSNLinking>0923-7534</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Cancer Discov. 2015 Nov;5(11):1133-6</RefSource><PMID Version="1">26526696</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Clin Oncol. 2014 Aug 1;32(22):2373-9</RefSource><PMID Version="1">24912897</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>N Engl J Med. 2016 Sep 22;375(12 ):1109-12</RefSource><PMID Version="1">27653561</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Med. 2014 Feb 27;6(2):13</RefSource><PMID Version="1">25031613</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Commun. 2015 Dec 09;6:10001</RefSource><PMID Version="1">26647970</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Clin Oncol. 2016 Mar 1;34(7):756-63</RefSource><PMID Version="1">26755519</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Med. 2016 May 5;22(5):464-71</RefSource><PMID Version="1">27149219</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74</RefSource><PMID Version="1">24217912</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2011 Mar 20;43(4):295-301</RefSource><PMID Version="1">21423179</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Hugo J. 2014 Dec;8(1):3</RefSource><PMID Version="1">27090251</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2014 Apr;46(4):318-9</RefSource><PMID Version="1">24675517</PMID></CommentsCorrections></CommentsCorrectionsList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">cancer</Keyword><Keyword MajorTopicYN="N">data sharing</Keyword><Keyword MajorTopicYN="N">genomics</Keyword><Keyword MajorTopicYN="N">molecular profiling</Keyword><Keyword MajorTopicYN="N">survey</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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