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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Identifieur interne : 000B12 ( Main/Exploration ); précédent : 000B11; suivant : 000B13

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Auteurs : Helen Davies [Royaume-Uni] ; Dominik Glodzik [Royaume-Uni] ; Sandro Morganella [Royaume-Uni] ; Lucy R. Yates [Royaume-Uni] ; Johan Staaf [Suède] ; Xueqing Zou [Royaume-Uni] ; Manasa Ramakrishna [Royaume-Uni] ; Sancha Martin [Royaume-Uni] ; Sandrine Boyault [France] ; Anieta M. Sieuwerts [Pays-Bas] ; Peter T. Simpson [Australie] ; Tari A. King [États-Unis] ; Keiran Raine [Royaume-Uni] ; Jorunn E. Eyfjord [Islande] ; Gu Kong [Corée du Sud] ; Ke Borg [Suède] ; Ewan Birney [Royaume-Uni] ; Hendrik G. Stunnenberg [Pays-Bas] ; Marc J. Van De Vijver [Pays-Bas] ; Anne-Lise B Rresen-Dale [Norvège] ; John W M. Martens [Pays-Bas] ; Paul N. Span [Pays-Bas] ; Sunil R. Lakhani [Australie] ; Anne Vincent-Salomon [France] ; Christos Sotiriou [Belgique] ; Andrew Tutt [Royaume-Uni] ; Alastair M. Thompson [États-Unis] ; Steven Van Laere [Belgique] ; Andrea L. Richardson [États-Unis] ; Alain Viari [France] ; Peter J. Campbell [Royaume-Uni] ; Michael R. Stratton [Royaume-Uni] ; Serena Nik-Zainal [Royaume-Uni]

Source :

RBID : pubmed:28288110

Descripteurs français

English descriptors

Abstract

Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.

DOI: 10.1038/nm.4292
PubMed: 28288110


Affiliations:


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Le document en format XML

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<name sortKey="Yates, Lucy R" sort="Yates, Lucy R" uniqKey="Yates L" first="Lucy R" last="Yates">Lucy R. Yates</name>
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<author>
<name sortKey="Zou, Xueqing" sort="Zou, Xueqing" uniqKey="Zou X" first="Xueqing" last="Zou">Xueqing Zou</name>
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<nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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<name sortKey="Ramakrishna, Manasa" sort="Ramakrishna, Manasa" uniqKey="Ramakrishna M" first="Manasa" last="Ramakrishna">Manasa Ramakrishna</name>
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<nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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<name sortKey="Martin, Sancha" sort="Martin, Sancha" uniqKey="Martin S" first="Sancha" last="Martin">Sancha Martin</name>
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<nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton</wicri:regionArea>
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<name sortKey="Boyault, Sandrine" sort="Boyault, Sandrine" uniqKey="Boyault S" first="Sandrine" last="Boyault">Sandrine Boyault</name>
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<nlm:affiliation>Translational Research Lab Department, Centre Léon Bérard, Lyon, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>Translational Research Lab Department, Centre Léon Bérard, Lyon</wicri:regionArea>
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<region type="region">Auvergne-Rhône-Alpes</region>
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</affiliation>
</author>
<author>
<name sortKey="Sieuwerts, Anieta M" sort="Sieuwerts, Anieta M" uniqKey="Sieuwerts A" first="Anieta M" last="Sieuwerts">Anieta M. Sieuwerts</name>
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<nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics, Erasmus University Medical Center, Rotterdam, the Netherlands.</nlm:affiliation>
<country xml:lang="fr" wicri:curation="lc">Pays-Bas</country>
<wicri:regionArea>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics, Erasmus University Medical Center, Rotterdam</wicri:regionArea>
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<name sortKey="Simpson, Peter T" sort="Simpson, Peter T" uniqKey="Simpson P" first="Peter T" last="Simpson">Peter T. Simpson</name>
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<nlm:affiliation>Centre for Clinical Research and School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
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<name sortKey="King, Tari A" sort="King, Tari A" uniqKey="King T" first="Tari A" last="King">Tari A. King</name>
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<nlm:affiliation>Memorial Sloan Kettering Cancer Center, New York, New York, USA.</nlm:affiliation>
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<author>
<name sortKey="Raine, Keiran" sort="Raine, Keiran" uniqKey="Raine K" first="Keiran" last="Raine">Keiran Raine</name>
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<nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton, UK.</nlm:affiliation>
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<name sortKey="Eyfjord, Jorunn E" sort="Eyfjord, Jorunn E" uniqKey="Eyfjord J" first="Jorunn E" last="Eyfjord">Jorunn E. Eyfjord</name>
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<nlm:affiliation>Cancer Research Laboratory, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.</nlm:affiliation>
<country xml:lang="fr">Islande</country>
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<name sortKey="Kong, Gu" sort="Kong, Gu" uniqKey="Kong G" first="Gu" last="Kong">Gu Kong</name>
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<nlm:affiliation>Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea.</nlm:affiliation>
<country xml:lang="fr">Corée du Sud</country>
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<name sortKey="Borg, Ke" sort="Borg, Ke" uniqKey="Borg " first=" Ke" last="Borg"> Ke Borg</name>
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<country xml:lang="fr">Suède</country>
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<name sortKey="Birney, Ewan" sort="Birney, Ewan" uniqKey="Birney E" first="Ewan" last="Birney">Ewan Birney</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton</wicri:regionArea>
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<author>
<name sortKey="Stunnenberg, Hendrik G" sort="Stunnenberg, Hendrik G" uniqKey="Stunnenberg H" first="Hendrik G" last="Stunnenberg">Hendrik G. Stunnenberg</name>
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<nlm:affiliation>Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, the Netherlands.</nlm:affiliation>
<country xml:lang="fr" wicri:curation="lc">Pays-Bas</country>
<wicri:regionArea>Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen</wicri:regionArea>
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<settlement type="city">Nimègue</settlement>
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<name sortKey="Van De Vijver, Marc J" sort="Van De Vijver, Marc J" uniqKey="Van De Vijver M" first="Marc J" last="Van De Vijver">Marc J. Van De Vijver</name>
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<nlm:affiliation>Department of Pathology, Academic Medical Center, Amsterdam, the Netherlands.</nlm:affiliation>
<country xml:lang="fr" wicri:curation="lc">Pays-Bas</country>
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<name sortKey="B Rresen Dale, Anne Lise" sort="B Rresen Dale, Anne Lise" uniqKey="B Rresen Dale A" first="Anne-Lise" last="B Rresen-Dale">Anne-Lise B Rresen-Dale</name>
<affiliation wicri:level="3">
<nlm:affiliation>Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.</nlm:affiliation>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo</wicri:regionArea>
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<settlement type="city">Oslo</settlement>
<region nuts="2">Østlandet</region>
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<name sortKey="Martens, John W M" sort="Martens, John W M" uniqKey="Martens J" first="John W M" last="Martens">John W M. Martens</name>
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<nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics, Erasmus University Medical Center, Rotterdam, the Netherlands.</nlm:affiliation>
<country xml:lang="fr" wicri:curation="lc">Pays-Bas</country>
<wicri:regionArea>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics, Erasmus University Medical Center, Rotterdam</wicri:regionArea>
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<name sortKey="Span, Paul N" sort="Span, Paul N" uniqKey="Span P" first="Paul N" last="Span">Paul N. Span</name>
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<nlm:affiliation>Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands.</nlm:affiliation>
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<name sortKey="Lakhani, Sunil R" sort="Lakhani, Sunil R" uniqKey="Lakhani S" first="Sunil R" last="Lakhani">Sunil R. Lakhani</name>
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<country xml:lang="fr">Australie</country>
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<nlm:affiliation>Department of Pathology, Institut Curie, Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>Department of Pathology, Institut Curie, Paris</wicri:regionArea>
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<region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
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</author>
<author>
<name sortKey="Sotiriou, Christos" sort="Sotiriou, Christos" uniqKey="Sotiriou C" first="Christos" last="Sotiriou">Christos Sotiriou</name>
<affiliation wicri:level="4">
<nlm:affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Brussels, Belgium.</nlm:affiliation>
<country xml:lang="fr">Belgique</country>
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<name sortKey="Tutt, Andrew" sort="Tutt, Andrew" uniqKey="Tutt A" first="Andrew" last="Tutt">Andrew Tutt</name>
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<nlm:affiliation>Breast Cancer Now Research Unit, King's College, London, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
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<name sortKey="Thompson, Alastair M" sort="Thompson, Alastair M" uniqKey="Thompson A" first="Alastair M" last="Thompson">Alastair M. Thompson</name>
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<nlm:affiliation>Department of Breast Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<region type="state">Texas</region>
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<name sortKey="Van Laere, Steven" sort="Van Laere, Steven" uniqKey="Van Laere S" first="Steven" last="Van Laere">Steven Van Laere</name>
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<nlm:affiliation>Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.</nlm:affiliation>
<country xml:lang="fr">Belgique</country>
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<settlement type="city">Anvers</settlement>
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<name sortKey="Richardson, Andrea L" sort="Richardson, Andrea L" uniqKey="Richardson A" first="Andrea L" last="Richardson">Andrea L. Richardson</name>
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<nlm:affiliation>Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<front>
<div type="abstract" xml:lang="en">Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Australie</li>
<li>Belgique</li>
<li>Corée du Sud</li>
<li>France</li>
<li>Islande</li>
<li>Norvège</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
<li>Suède</li>
<li>États-Unis</li>
</country>
<region>
<li>Angleterre</li>
<li>Auvergne-Rhône-Alpes</li>
<li>Grand Londres</li>
<li>Gueldre</li>
<li>Hollande-Méridionale</li>
<li>Hollande-Septentrionale</li>
<li>Massachusetts</li>
<li>Province d'Anvers</li>
<li>Rhône-Alpes</li>
<li>Région capitale de Séoul</li>
<li>Région de Bruxelles-Capitale</li>
<li>Région flamande</li>
<li>Texas</li>
<li>État de New York</li>
<li>Île-de-France</li>
<li>Østlandet</li>
</region>
<settlement>
<li>Amsterdam</li>
<li>Anvers</li>
<li>Bruxelles</li>
<li>Londres</li>
<li>Lyon</li>
<li>Nimègue</li>
<li>Oslo</li>
<li>Paris</li>
<li>Rotterdam</li>
<li>Séoul</li>
</settlement>
<orgName>
<li>Université d'Anvers</li>
<li>Université libre de Bruxelles</li>
</orgName>
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<name sortKey="Davies, Helen" sort="Davies, Helen" uniqKey="Davies H" first="Helen" last="Davies">Helen Davies</name>
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<name sortKey="Birney, Ewan" sort="Birney, Ewan" uniqKey="Birney E" first="Ewan" last="Birney">Ewan Birney</name>
<name sortKey="Campbell, Peter J" sort="Campbell, Peter J" uniqKey="Campbell P" first="Peter J" last="Campbell">Peter J. Campbell</name>
<name sortKey="Glodzik, Dominik" sort="Glodzik, Dominik" uniqKey="Glodzik D" first="Dominik" last="Glodzik">Dominik Glodzik</name>
<name sortKey="Martin, Sancha" sort="Martin, Sancha" uniqKey="Martin S" first="Sancha" last="Martin">Sancha Martin</name>
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<name sortKey="Stratton, Michael R" sort="Stratton, Michael R" uniqKey="Stratton M" first="Michael R" last="Stratton">Michael R. Stratton</name>
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<name sortKey="Yates, Lucy R" sort="Yates, Lucy R" uniqKey="Yates L" first="Lucy R" last="Yates">Lucy R. Yates</name>
<name sortKey="Zou, Xueqing" sort="Zou, Xueqing" uniqKey="Zou X" first="Xueqing" last="Zou">Xueqing Zou</name>
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<name sortKey="Staaf, Johan" sort="Staaf, Johan" uniqKey="Staaf J" first="Johan" last="Staaf">Johan Staaf</name>
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<name sortKey="Borg, Ke" sort="Borg, Ke" uniqKey="Borg " first=" Ke" last="Borg"> Ke Borg</name>
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<region name="Auvergne-Rhône-Alpes">
<name sortKey="Boyault, Sandrine" sort="Boyault, Sandrine" uniqKey="Boyault S" first="Sandrine" last="Boyault">Sandrine Boyault</name>
</region>
<name sortKey="Viari, Alain" sort="Viari, Alain" uniqKey="Viari A" first="Alain" last="Viari">Alain Viari</name>
<name sortKey="Vincent Salomon, Anne" sort="Vincent Salomon, Anne" uniqKey="Vincent Salomon A" first="Anne" last="Vincent-Salomon">Anne Vincent-Salomon</name>
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<country name="Pays-Bas">
<region name="Hollande-Méridionale">
<name sortKey="Sieuwerts, Anieta M" sort="Sieuwerts, Anieta M" uniqKey="Sieuwerts A" first="Anieta M" last="Sieuwerts">Anieta M. Sieuwerts</name>
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<name sortKey="Martens, John W M" sort="Martens, John W M" uniqKey="Martens J" first="John W M" last="Martens">John W M. Martens</name>
<name sortKey="Span, Paul N" sort="Span, Paul N" uniqKey="Span P" first="Paul N" last="Span">Paul N. Span</name>
<name sortKey="Stunnenberg, Hendrik G" sort="Stunnenberg, Hendrik G" uniqKey="Stunnenberg H" first="Hendrik G" last="Stunnenberg">Hendrik G. Stunnenberg</name>
<name sortKey="Van De Vijver, Marc J" sort="Van De Vijver, Marc J" uniqKey="Van De Vijver M" first="Marc J" last="Van De Vijver">Marc J. Van De Vijver</name>
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<country name="Australie">
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<name sortKey="Simpson, Peter T" sort="Simpson, Peter T" uniqKey="Simpson P" first="Peter T" last="Simpson">Peter T. Simpson</name>
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<name sortKey="Lakhani, Sunil R" sort="Lakhani, Sunil R" uniqKey="Lakhani S" first="Sunil R" last="Lakhani">Sunil R. Lakhani</name>
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<country name="États-Unis">
<region name="État de New York">
<name sortKey="King, Tari A" sort="King, Tari A" uniqKey="King T" first="Tari A" last="King">Tari A. King</name>
</region>
<name sortKey="Richardson, Andrea L" sort="Richardson, Andrea L" uniqKey="Richardson A" first="Andrea L" last="Richardson">Andrea L. Richardson</name>
<name sortKey="Thompson, Alastair M" sort="Thompson, Alastair M" uniqKey="Thompson A" first="Alastair M" last="Thompson">Alastair M. Thompson</name>
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<name sortKey="Eyfjord, Jorunn E" sort="Eyfjord, Jorunn E" uniqKey="Eyfjord J" first="Jorunn E" last="Eyfjord">Jorunn E. Eyfjord</name>
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<region name="Région capitale de Séoul">
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<name sortKey="B Rresen Dale, Anne Lise" sort="B Rresen Dale, Anne Lise" uniqKey="B Rresen Dale A" first="Anne-Lise" last="B Rresen-Dale">Anne-Lise B Rresen-Dale</name>
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<name sortKey="Sotiriou, Christos" sort="Sotiriou, Christos" uniqKey="Sotiriou C" first="Christos" last="Sotiriou">Christos Sotiriou</name>
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<name sortKey="Van Laere, Steven" sort="Van Laere, Steven" uniqKey="Van Laere S" first="Steven" last="Van Laere">Steven Van Laere</name>
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</affiliations>
</record>

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