Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape
Identifieur interne : 000148 ( Main/Exploration ); précédent : 000147; suivant : 000149Towards 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 [ 0923-7534 ] ; 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.
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).
Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (
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.
Url:
DOI: 10.1093/annonc/mdx037
PubMed: 28453708
PubMed Central: 5406763
Affiliations:
- Australie, Brésil, Canada, Corée du Sud, France, Pays-Bas, Royaume-Uni, Singapour, États-Unis
- Hollande-Septentrionale, Québec, Région capitale de Séoul, État de New York, État de São Paulo, Île-de-France
- Amsterdam, Montréal, Orsay, São Paulo, Séoul
- Université McGill, Université Paris-Sud
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<author><name sortKey="Calvo, F" sort="Calvo, F" uniqKey="Calvo F" first="F." last="Calvo">F. Calvo</name>
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<country xml:lang="fr">France</country>
<wicri:regionArea>Cancer Core Europe, Gustave Roussy, Villejuif</wicri:regionArea>
<wicri:noRegion>Villejuif</wicri:noRegion>
<wicri:noRegion>Villejuif</wicri:noRegion>
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<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:aff id="mdx037-aff8">National Cancer Centre, Singapore</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea>National Cancer Centre</wicri:regionArea>
</affiliation>
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<author><name sortKey="Camargo, A A" sort="Camargo, A A" uniqKey="Camargo A" first="A. A." last="Camargo">A. A. Camargo</name>
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<author><name sortKey="Knoppers, B M" sort="Knoppers, B M" uniqKey="Knoppers B" first="B. M." last="Knoppers">B. M. Knoppers</name>
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<author><name sortKey="Sawyers, C L" sort="Sawyers, C L" uniqKey="Sawyers C" first="C. L." last="Sawyers">C. L. Sawyers</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Memorial Sloan Kettering Cancer Centre, New York</wicri:regionArea>
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<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Bioinformatics & Statistics, Delft University of Technology, Delft</wicri:regionArea>
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<author><name sortKey="Lawler, M" sort="Lawler, M" uniqKey="Lawler M" first="M." last="Lawler">M. Lawler</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast</wicri:regionArea>
<wicri:noRegion>Belfast</wicri:noRegion>
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<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:aff id="mdx037-aff2">Princess Margaret Cancer Centre, Toronto, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Princess Margaret Cancer Centre, Toronto</wicri:regionArea>
<wicri:noRegion>Toronto</wicri:noRegion>
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<author><name sortKey="Voest, E" sort="Voest, E" uniqKey="Voest E" first="E." last="Voest">E. Voest</name>
<affiliation wicri:level="3"><nlm:aff id="mdx037-aff1">Netherlands Cancer Institute, Amsterdam, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
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<series><title level="j">Annals of Oncology</title>
<idno type="ISSN">0923-7534</idno>
<idno type="eISSN">1569-8041</idno>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Methods</title>
<p>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).</p>
</sec>
<sec><title>Results</title>
<p>Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (<italic>P </italic>
=<italic> </italic>
0.03) and whole genome sequencing (<italic>P = </italic>
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 (<italic>P < </italic>
0.01) and bioinformatics concerns (e.g. lack of interoperability) (<italic>P = </italic>
0.02). Capturing clinical data was more likely to be perceived as a barrier to data sharing by larger initiatives than by smaller initiatives (<italic>P = </italic>
0.01).</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lawler, M" uniqKey="Lawler M">M Lawler</name>
</author>
<author><name sortKey="Siu, Ll" uniqKey="Siu L">LL Siu</name>
</author>
<author><name sortKey="Rehm, Hl" uniqKey="Rehm H">HL Rehm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Siu, Ll" uniqKey="Siu L">LL Siu</name>
</author>
<author><name sortKey="Lawler, M" uniqKey="Lawler M">M Lawler</name>
</author>
<author><name sortKey="Haussler, D" uniqKey="Haussler D">D Haussler</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Schilsky, Rl" uniqKey="Schilsky R">RL Schilsky</name>
</author>
<author><name sortKey="Michels, Dl" uniqKey="Michels D">DL Michels</name>
</author>
<author><name sortKey="Kearbey, Ah" uniqKey="Kearbey A">AH Kearbey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Knoppers, Bm" uniqKey="Knoppers B">BM. Knoppers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Alioto, Ts" uniqKey="Alioto T">TS Alioto</name>
</author>
<author><name sortKey="Buchhalter, I" uniqKey="Buchhalter I">I Buchhalter</name>
</author>
<author><name sortKey="Derdak, S" uniqKey="Derdak S">S Derdak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grossman, Rl" uniqKey="Grossman R">RL Grossman</name>
</author>
<author><name sortKey="Heath, Ap" uniqKey="Heath A">AP Heath</name>
</author>
<author><name sortKey="Ferretti, V" uniqKey="Ferretti V">V Ferretti</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Boutros, Pc" uniqKey="Boutros P">PC Boutros</name>
</author>
<author><name sortKey="Ewing, Ad" uniqKey="Ewing A">AD Ewing</name>
</author>
<author><name sortKey="Ellrott, K" uniqKey="Ellrott K">K Ellrott</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Shah, A" uniqKey="Shah A">A Shah</name>
</author>
<author><name sortKey="Stewart, Ak" uniqKey="Stewart A">AK Stewart</name>
</author>
<author><name sortKey="Kolacevski, A" uniqKey="Kolacevski A">A Kolacevski</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kohler, S" uniqKey="Kohler S">S Köhler</name>
</author>
<author><name sortKey="Doelken, Sc" uniqKey="Doelken S">SC Doelken</name>
</author>
<author><name sortKey="Mungall, Cj" uniqKey="Mungall C">CJ Mungall</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Knoppers, Bm" uniqKey="Knoppers B">BM. Knoppers</name>
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<biblStruct><analytic><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name>
</author>
<author><name sortKey="Borg, J" uniqKey="Borg J">J Borg</name>
</author>
<author><name sortKey="Higgs, Dr" uniqKey="Higgs D">DR Higgs</name>
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</TEI>
<affiliations><list><country><li>Australie</li>
<li>Brésil</li>
<li>Canada</li>
<li>Corée du Sud</li>
<li>France</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
<li>Singapour</li>
<li>États-Unis</li>
</country>
<region><li>Hollande-Septentrionale</li>
<li>Québec</li>
<li>Région capitale de Séoul</li>
<li>État de New York</li>
<li>État de São Paulo</li>
<li>Île-de-France</li>
</region>
<settlement><li>Amsterdam</li>
<li>Montréal</li>
<li>Orsay</li>
<li>São Paulo</li>
<li>Séoul</li>
</settlement>
<orgName><li>Université McGill</li>
<li>Université Paris-Sud</li>
</orgName>
</list>
<tree><country name="Pays-Bas"><region name="Hollande-Septentrionale"><name sortKey="Vis, D J" sort="Vis, D J" uniqKey="Vis D" first="D. J." last="Vis">D. J. Vis</name>
</region>
<name sortKey="Voest, E" sort="Voest, E" uniqKey="Voest E" first="E." last="Voest">E. Voest</name>
<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>
<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>
</country>
<country name="Canada"><noRegion><name sortKey="Lewin, J" sort="Lewin, J" uniqKey="Lewin J" first="J." last="Lewin">J. Lewin</name>
</noRegion>
<name sortKey="Knoppers, B M" sort="Knoppers, B M" uniqKey="Knoppers B" first="B. M." last="Knoppers">B. M. Knoppers</name>
<name sortKey="Siu, L L" sort="Siu, L L" uniqKey="Siu L" first="L. L." last="Siu">L. L. Siu</name>
</country>
<country name="États-Unis"><noRegion><name sortKey="Liao, R G" sort="Liao, R G" uniqKey="Liao R" first="R. G." last="Liao">R. G. Liao</name>
</noRegion>
<name sortKey="Sawyers, C L" sort="Sawyers, C L" uniqKey="Sawyers C" first="C. L." last="Sawyers">C. L. Sawyers</name>
</country>
<country name="Corée du Sud"><region name="Région capitale de Séoul"><name sortKey="Mao, M" sort="Mao, M" uniqKey="Mao M" first="M." last="Mao">M. Mao</name>
</region>
</country>
<country name="France"><region name="Île-de-France"><name sortKey="Andre, F" sort="Andre, F" uniqKey="Andre F" first="F." last="Andre">F. Andre</name>
</region>
<name sortKey="Calvo, F" sort="Calvo, F" uniqKey="Calvo F" first="F." last="Calvo">F. Calvo</name>
</country>
<country name="Australie"><noRegion><name sortKey="Ward, R L" sort="Ward, R L" uniqKey="Ward R" first="R. L." last="Ward">R. L. Ward</name>
</noRegion>
</country>
<country name="Singapour"><noRegion><name sortKey="Teh, B T" sort="Teh, B T" uniqKey="Teh B" first="B. T." last="Teh">B. T. Teh</name>
</noRegion>
</country>
<country name="Brésil"><region name="État de São Paulo"><name sortKey="Camargo, A A" sort="Camargo, A A" uniqKey="Camargo A" first="A. A." last="Camargo">A. A. Camargo</name>
</region>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Lawler, M" sort="Lawler, M" uniqKey="Lawler M" first="M." last="Lawler">M. Lawler</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>
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