Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Identifieur interne : 001858 ( PubMed/Corpus ); précédent : 001857; suivant : 001859Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Auteurs : Marcel Smid ; F Germán Rodríguez-González ; Anieta M. Sieuwerts ; Roberto Salgado ; Wendy J C. Prager-Van Der Smissen ; Michelle Van Der Vlugt-Daane ; Anne Van Galen ; Serena Nik-Zainal ; Johan Staaf ; Arie B. Brinkman ; Marc J. Van De Vijver ; Andrea L. Richardson ; Aquila Fatima ; Kim Berentsen ; Adam Butler ; Sancha Martin ; Helen R. Davies ; Reno Debets ; Marion E Meijer-Van Gelder ; Carolien H M. Van Deurzen ; Gaëtan Macgrogan ; Gert G G M. Van Den Eynden ; Colin Purdie ; Alastair M. Thompson ; Carlos Caldas ; Paul N. Span ; Peter T. Simpson ; Sunil R. Lakhani ; Steven Van Laere ; Christine Desmedt ; Markus Ringnér ; Stefania Tommasi ; Jorunn Eyford ; Annegien Broeks ; Anne Vincent-Salomon ; P Andrew Futreal ; Stian Knappskog ; Tari King ; Gilles Thomas ; Alain Viari ; Anita Langer D ; Anne-Lise B Rresen-Dale ; Ewan Birney ; Hendrik G. Stunnenberg ; Mike Stratton ; John A. Foekens ; John W M. MartensSource :
- Nature communications [ 2041-1723 ] ; 2016.
Abstract
A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.
DOI: 10.1038/ncomms12910
PubMed: 27666519
Links to Exploration step
pubmed:27666519Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.</title><author><name sortKey="Smid, Marcel" sort="Smid, Marcel" uniqKey="Smid M" first="Marcel" last="Smid">Marcel Smid</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Rodriguez Gonzalez, F German" sort="Rodriguez Gonzalez, F German" uniqKey="Rodriguez Gonzalez F" first="F Germán" last="Rodríguez-González">F Germán Rodríguez-González</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Sieuwerts, Anieta M" sort="Sieuwerts, Anieta M" uniqKey="Sieuwerts A" first="Anieta M" last="Sieuwerts">Anieta M. Sieuwerts</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Salgado, Roberto" sort="Salgado, Roberto" uniqKey="Salgado R" first="Roberto" last="Salgado">Roberto Salgado</name><affiliation><nlm:affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Prager Van Der Smissen, Wendy J C" sort="Prager Van Der Smissen, Wendy J C" uniqKey="Prager Van Der Smissen W" first="Wendy J C" last="Prager-Van Der Smissen">Wendy J C. Prager-Van Der Smissen</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Vlugt Daane, Michelle Van Der" sort="Vlugt Daane, Michelle Van Der" uniqKey="Vlugt Daane M" first="Michelle Van Der" last="Vlugt-Daane">Michelle Van Der Vlugt-Daane</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Van Galen, Anne" sort="Van Galen, Anne" uniqKey="Van Galen A" first="Anne" last="Van Galen">Anne Van Galen</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Nik Zainal, Serena" sort="Nik Zainal, Serena" uniqKey="Nik Zainal S" first="Serena" last="Nik-Zainal">Serena Nik-Zainal</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Staaf, Johan" sort="Staaf, Johan" uniqKey="Staaf J" first="Johan" last="Staaf">Johan Staaf</name><affiliation><nlm:affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Brinkman, Arie B" sort="Brinkman, Arie B" uniqKey="Brinkman A" first="Arie B" last="Brinkman">Arie B. Brinkman</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><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><affiliation><nlm:affiliation>Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Richardson, Andrea L" sort="Richardson, Andrea L" uniqKey="Richardson A" first="Andrea L" last="Richardson">Andrea L. Richardson</name><affiliation><nlm:affiliation>Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Fatima, Aquila" sort="Fatima, Aquila" uniqKey="Fatima A" first="Aquila" last="Fatima">Aquila Fatima</name><affiliation><nlm:affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Berentsen, Kim" sort="Berentsen, Kim" uniqKey="Berentsen K" first="Kim" last="Berentsen">Kim Berentsen</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Butler, Adam" sort="Butler, Adam" uniqKey="Butler A" first="Adam" last="Butler">Adam Butler</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Martin, Sancha" sort="Martin, Sancha" uniqKey="Martin S" first="Sancha" last="Martin">Sancha Martin</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Davies, Helen R" sort="Davies, Helen R" uniqKey="Davies H" first="Helen R" last="Davies">Helen R. Davies</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Debets, Reno" sort="Debets, Reno" uniqKey="Debets R" first="Reno" last="Debets">Reno Debets</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Gelder, Marion E Meijer Van" sort="Gelder, Marion E Meijer Van" uniqKey="Gelder M" first="Marion E Meijer-Van" last="Gelder">Marion E Meijer-Van Gelder</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Van Deurzen, Carolien H M" sort="Van Deurzen, Carolien H M" uniqKey="Van Deurzen C" first="Carolien H M" last="Van Deurzen">Carolien H M. Van Deurzen</name><affiliation><nlm:affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Macgrogan, Gaetan" sort="Macgrogan, Gaetan" uniqKey="Macgrogan G" first="Gaëtan" last="Macgrogan">Gaëtan Macgrogan</name><affiliation><nlm:affiliation>Département de Biopathologie,Institut Bergonié, CS 61283 33076 Bordeaux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Van Den Eynden, Gert G G M" sort="Van Den Eynden, Gert G G M" uniqKey="Van Den Eynden G" first="Gert G G M" last="Van Den Eynden">Gert G G M. Van Den Eynden</name><affiliation><nlm:affiliation>Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Purdie, Colin" sort="Purdie, Colin" uniqKey="Purdie C" first="Colin" last="Purdie">Colin Purdie</name><affiliation><nlm:affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Thompson, Alastair M" sort="Thompson, Alastair M" uniqKey="Thompson A" first="Alastair M" last="Thompson">Alastair M. Thompson</name><affiliation><nlm:affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Caldas, Carlos" sort="Caldas, Carlos" uniqKey="Caldas C" first="Carlos" last="Caldas">Carlos Caldas</name><affiliation><nlm:affiliation>Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Span, Paul N" sort="Span, Paul N" uniqKey="Span P" first="Paul N" last="Span">Paul N. Span</name><affiliation><nlm:affiliation>Department of Radiation Oncology, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Simpson, Peter T" sort="Simpson, Peter T" uniqKey="Simpson P" first="Peter T" last="Simpson">Peter T. Simpson</name><affiliation><nlm:affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Lakhani, Sunil R" sort="Lakhani, Sunil R" uniqKey="Lakhani S" first="Sunil R" last="Lakhani">Sunil R. Lakhani</name><affiliation><nlm:affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Van Laere, Steven" sort="Van Laere, Steven" uniqKey="Van Laere S" first="Steven" last="Van Laere">Steven Van Laere</name><affiliation><nlm:affiliation>Center for Oncological Research, University of Antwerp &GZA Hospitals Sint-Augustinus, 2610 Wilrijk, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Desmedt, Christine" sort="Desmedt, Christine" uniqKey="Desmedt C" first="Christine" last="Desmedt">Christine Desmedt</name><affiliation><nlm:affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Ringner, Markus" sort="Ringner, Markus" uniqKey="Ringner M" first="Markus" last="Ringnér">Markus Ringnér</name><affiliation><nlm:affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Tommasi, Stefania" sort="Tommasi, Stefania" uniqKey="Tommasi S" first="Stefania" last="Tommasi">Stefania Tommasi</name><affiliation><nlm:affiliation>IRCCS Istituto Tumori 'Giovanni Paolo II', 70124 Bari, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Eyford, Jorunn" sort="Eyford, Jorunn" uniqKey="Eyford J" first="Jorunn" last="Eyford">Jorunn Eyford</name><affiliation><nlm:affiliation>Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.</nlm:affiliation></affiliation></author><author><name sortKey="Broeks, Annegien" sort="Broeks, Annegien" uniqKey="Broeks A" first="Annegien" last="Broeks">Annegien Broeks</name><affiliation><nlm:affiliation>The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Vincent Salomon, Anne" sort="Vincent Salomon, Anne" uniqKey="Vincent Salomon A" first="Anne" last="Vincent-Salomon">Anne Vincent-Salomon</name><affiliation><nlm:affiliation>Department of Pathology and INSERM U934, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.</nlm:affiliation></affiliation></author><author><name sortKey="Futreal, P Andrew" sort="Futreal, P Andrew" uniqKey="Futreal P" first="P Andrew" last="Futreal">P Andrew Futreal</name><affiliation><nlm:affiliation>Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Knappskog, Stian" sort="Knappskog, Stian" uniqKey="Knappskog S" first="Stian" last="Knappskog">Stian Knappskog</name><affiliation><nlm:affiliation>Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="King, Tari" sort="King, Tari" uniqKey="King T" first="Tari" last="King">Tari King</name><affiliation><nlm:affiliation>Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Thomas, Gilles" sort="Thomas, Gilles" uniqKey="Thomas G" first="Gilles" last="Thomas">Gilles Thomas</name><affiliation><nlm:affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</nlm:affiliation></affiliation></author><author><name sortKey="Viari, Alain" sort="Viari, Alain" uniqKey="Viari A" first="Alain" last="Viari">Alain Viari</name><affiliation><nlm:affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</nlm:affiliation></affiliation></author><author><name sortKey="Langer D, Anita" sort="Langer D, Anita" uniqKey="Langer D A" first="Anita" last="Langer D">Anita Langer D</name><affiliation><nlm:affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</nlm:affiliation></affiliation></author><author><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><nlm:affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="Birney, Ewan" sort="Birney, Ewan" uniqKey="Birney E" first="Ewan" last="Birney">Ewan Birney</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton CB10 1SD, Cambridgeshire, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Stunnenberg, Hendrik G" sort="Stunnenberg, Hendrik G" uniqKey="Stunnenberg H" first="Hendrik G" last="Stunnenberg">Hendrik G. Stunnenberg</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Stratton, Mike" sort="Stratton, Mike" uniqKey="Stratton M" first="Mike" last="Stratton">Mike Stratton</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Foekens, John A" sort="Foekens, John A" uniqKey="Foekens J" first="John A" last="Foekens">John A. Foekens</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><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><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27666519</idno><idno type="pmid">27666519</idno><idno type="doi">10.1038/ncomms12910</idno><idno type="wicri:Area/PubMed/Corpus">001858</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001858</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.</title><author><name sortKey="Smid, Marcel" sort="Smid, Marcel" uniqKey="Smid M" first="Marcel" last="Smid">Marcel Smid</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Rodriguez Gonzalez, F German" sort="Rodriguez Gonzalez, F German" uniqKey="Rodriguez Gonzalez F" first="F Germán" last="Rodríguez-González">F Germán Rodríguez-González</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Sieuwerts, Anieta M" sort="Sieuwerts, Anieta M" uniqKey="Sieuwerts A" first="Anieta M" last="Sieuwerts">Anieta M. Sieuwerts</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Salgado, Roberto" sort="Salgado, Roberto" uniqKey="Salgado R" first="Roberto" last="Salgado">Roberto Salgado</name><affiliation><nlm:affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Prager Van Der Smissen, Wendy J C" sort="Prager Van Der Smissen, Wendy J C" uniqKey="Prager Van Der Smissen W" first="Wendy J C" last="Prager-Van Der Smissen">Wendy J C. Prager-Van Der Smissen</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Vlugt Daane, Michelle Van Der" sort="Vlugt Daane, Michelle Van Der" uniqKey="Vlugt Daane M" first="Michelle Van Der" last="Vlugt-Daane">Michelle Van Der Vlugt-Daane</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Van Galen, Anne" sort="Van Galen, Anne" uniqKey="Van Galen A" first="Anne" last="Van Galen">Anne Van Galen</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Nik Zainal, Serena" sort="Nik Zainal, Serena" uniqKey="Nik Zainal S" first="Serena" last="Nik-Zainal">Serena Nik-Zainal</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Staaf, Johan" sort="Staaf, Johan" uniqKey="Staaf J" first="Johan" last="Staaf">Johan Staaf</name><affiliation><nlm:affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Brinkman, Arie B" sort="Brinkman, Arie B" uniqKey="Brinkman A" first="Arie B" last="Brinkman">Arie B. Brinkman</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><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><affiliation><nlm:affiliation>Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Richardson, Andrea L" sort="Richardson, Andrea L" uniqKey="Richardson A" first="Andrea L" last="Richardson">Andrea L. Richardson</name><affiliation><nlm:affiliation>Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Fatima, Aquila" sort="Fatima, Aquila" uniqKey="Fatima A" first="Aquila" last="Fatima">Aquila Fatima</name><affiliation><nlm:affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Berentsen, Kim" sort="Berentsen, Kim" uniqKey="Berentsen K" first="Kim" last="Berentsen">Kim Berentsen</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Butler, Adam" sort="Butler, Adam" uniqKey="Butler A" first="Adam" last="Butler">Adam Butler</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Martin, Sancha" sort="Martin, Sancha" uniqKey="Martin S" first="Sancha" last="Martin">Sancha Martin</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Davies, Helen R" sort="Davies, Helen R" uniqKey="Davies H" first="Helen R" last="Davies">Helen R. Davies</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Debets, Reno" sort="Debets, Reno" uniqKey="Debets R" first="Reno" last="Debets">Reno Debets</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Gelder, Marion E Meijer Van" sort="Gelder, Marion E Meijer Van" uniqKey="Gelder M" first="Marion E Meijer-Van" last="Gelder">Marion E Meijer-Van Gelder</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Van Deurzen, Carolien H M" sort="Van Deurzen, Carolien H M" uniqKey="Van Deurzen C" first="Carolien H M" last="Van Deurzen">Carolien H M. Van Deurzen</name><affiliation><nlm:affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Macgrogan, Gaetan" sort="Macgrogan, Gaetan" uniqKey="Macgrogan G" first="Gaëtan" last="Macgrogan">Gaëtan Macgrogan</name><affiliation><nlm:affiliation>Département de Biopathologie,Institut Bergonié, CS 61283 33076 Bordeaux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Van Den Eynden, Gert G G M" sort="Van Den Eynden, Gert G G M" uniqKey="Van Den Eynden G" first="Gert G G M" last="Van Den Eynden">Gert G G M. Van Den Eynden</name><affiliation><nlm:affiliation>Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Purdie, Colin" sort="Purdie, Colin" uniqKey="Purdie C" first="Colin" last="Purdie">Colin Purdie</name><affiliation><nlm:affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Thompson, Alastair M" sort="Thompson, Alastair M" uniqKey="Thompson A" first="Alastair M" last="Thompson">Alastair M. Thompson</name><affiliation><nlm:affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Caldas, Carlos" sort="Caldas, Carlos" uniqKey="Caldas C" first="Carlos" last="Caldas">Carlos Caldas</name><affiliation><nlm:affiliation>Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Span, Paul N" sort="Span, Paul N" uniqKey="Span P" first="Paul N" last="Span">Paul N. Span</name><affiliation><nlm:affiliation>Department of Radiation Oncology, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Simpson, Peter T" sort="Simpson, Peter T" uniqKey="Simpson P" first="Peter T" last="Simpson">Peter T. Simpson</name><affiliation><nlm:affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Lakhani, Sunil R" sort="Lakhani, Sunil R" uniqKey="Lakhani S" first="Sunil R" last="Lakhani">Sunil R. Lakhani</name><affiliation><nlm:affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Van Laere, Steven" sort="Van Laere, Steven" uniqKey="Van Laere S" first="Steven" last="Van Laere">Steven Van Laere</name><affiliation><nlm:affiliation>Center for Oncological Research, University of Antwerp &GZA Hospitals Sint-Augustinus, 2610 Wilrijk, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Desmedt, Christine" sort="Desmedt, Christine" uniqKey="Desmedt C" first="Christine" last="Desmedt">Christine Desmedt</name><affiliation><nlm:affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</nlm:affiliation></affiliation></author><author><name sortKey="Ringner, Markus" sort="Ringner, Markus" uniqKey="Ringner M" first="Markus" last="Ringnér">Markus Ringnér</name><affiliation><nlm:affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</nlm:affiliation></affiliation></author><author><name sortKey="Tommasi, Stefania" sort="Tommasi, Stefania" uniqKey="Tommasi S" first="Stefania" last="Tommasi">Stefania Tommasi</name><affiliation><nlm:affiliation>IRCCS Istituto Tumori 'Giovanni Paolo II', 70124 Bari, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Eyford, Jorunn" sort="Eyford, Jorunn" uniqKey="Eyford J" first="Jorunn" last="Eyford">Jorunn Eyford</name><affiliation><nlm:affiliation>Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.</nlm:affiliation></affiliation></author><author><name sortKey="Broeks, Annegien" sort="Broeks, Annegien" uniqKey="Broeks A" first="Annegien" last="Broeks">Annegien Broeks</name><affiliation><nlm:affiliation>The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Vincent Salomon, Anne" sort="Vincent Salomon, Anne" uniqKey="Vincent Salomon A" first="Anne" last="Vincent-Salomon">Anne Vincent-Salomon</name><affiliation><nlm:affiliation>Department of Pathology and INSERM U934, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.</nlm:affiliation></affiliation></author><author><name sortKey="Futreal, P Andrew" sort="Futreal, P Andrew" uniqKey="Futreal P" first="P Andrew" last="Futreal">P Andrew Futreal</name><affiliation><nlm:affiliation>Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Knappskog, Stian" sort="Knappskog, Stian" uniqKey="Knappskog S" first="Stian" last="Knappskog">Stian Knappskog</name><affiliation><nlm:affiliation>Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="King, Tari" sort="King, Tari" uniqKey="King T" first="Tari" last="King">Tari King</name><affiliation><nlm:affiliation>Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Thomas, Gilles" sort="Thomas, Gilles" uniqKey="Thomas G" first="Gilles" last="Thomas">Gilles Thomas</name><affiliation><nlm:affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</nlm:affiliation></affiliation></author><author><name sortKey="Viari, Alain" sort="Viari, Alain" uniqKey="Viari A" first="Alain" last="Viari">Alain Viari</name><affiliation><nlm:affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</nlm:affiliation></affiliation></author><author><name sortKey="Langer D, Anita" sort="Langer D, Anita" uniqKey="Langer D A" first="Anita" last="Langer D">Anita Langer D</name><affiliation><nlm:affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</nlm:affiliation></affiliation></author><author><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><nlm:affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</nlm:affiliation></affiliation></author><author><name sortKey="Birney, Ewan" sort="Birney, Ewan" uniqKey="Birney E" first="Ewan" last="Birney">Ewan Birney</name><affiliation><nlm:affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton CB10 1SD, Cambridgeshire, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Stunnenberg, Hendrik G" sort="Stunnenberg, Hendrik G" uniqKey="Stunnenberg H" first="Hendrik G" last="Stunnenberg">Hendrik G. Stunnenberg</name><affiliation><nlm:affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</nlm:affiliation></affiliation></author><author><name sortKey="Stratton, Mike" sort="Stratton, Mike" uniqKey="Stratton M" first="Mike" last="Stratton">Mike Stratton</name><affiliation><nlm:affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Foekens, John A" sort="Foekens, John A" uniqKey="Foekens J" first="John A" last="Foekens">John A. Foekens</name><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author><author><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><affiliation><nlm:affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nature communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">27666519</PMID><DateCreated><Year>2016</Year><Month>09</Month><Day>26</Day></DateCreated><DateRevised><Year>2017</Year><Month>09</Month><Day>22</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2041-1723</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><PubDate><Year>2016</Year><Month>Sep</Month><Day>26</Day></PubDate></JournalIssue><Title>Nature communications</Title><ISOAbbreviation>Nat Commun</ISOAbbreviation></Journal><ArticleTitle>Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.</ArticleTitle><Pagination><MedlinePgn>12910</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/ncomms12910</ELocationID><Abstract><AbstractText>A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Smid</LastName><ForeName>Marcel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rodríguez-González</LastName><ForeName>F Germán</ForeName><Initials>FG</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sieuwerts</LastName><ForeName>Anieta M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salgado</LastName><ForeName>Roberto</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Prager-Van der Smissen</LastName><ForeName>Wendy J C</ForeName><Initials>WJ</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vlugt-Daane</LastName><ForeName>Michelle van der</ForeName><Initials>MV</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Galen</LastName><ForeName>Anne</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nik-Zainal</LastName><ForeName>Serena</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Staaf</LastName><ForeName>Johan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brinkman</LastName><ForeName>Arie B</ForeName><Initials>AB</Initials><AffiliationInfo><Affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van de Vijver</LastName><ForeName>Marc J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Richardson</LastName><ForeName>Andrea L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fatima</LastName><ForeName>Aquila</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berentsen</LastName><ForeName>Kim</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Butler</LastName><ForeName>Adam</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Sancha</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Davies</LastName><ForeName>Helen R</ForeName><Initials>HR</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Debets</LastName><ForeName>Reno</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gelder</LastName><ForeName>Marion E Meijer-Van</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van Deurzen</LastName><ForeName>Carolien H M</ForeName><Initials>CH</Initials><AffiliationInfo><Affiliation>Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>MacGrogan</LastName><ForeName>Gaëtan</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Département de Biopathologie,Institut Bergonié, CS 61283 33076 Bordeaux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van den Eynden</LastName><ForeName>Gert G G M</ForeName><Initials>GG</Initials><AffiliationInfo><Affiliation>Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Molecular Immunology Unit, Jules Bordet Institute, B-1000 Brussels, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Purdie</LastName><ForeName>Colin</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thompson</LastName><ForeName>Alastair M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Caldas</LastName><ForeName>Carlos</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Span</LastName><ForeName>Paul N</ForeName><Initials>PN</Initials><AffiliationInfo><Affiliation>Department of Radiation Oncology, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Laboratory Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Simpson</LastName><ForeName>Peter T</ForeName><Initials>PT</Initials><AffiliationInfo><Affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lakhani</LastName><ForeName>Sunil R</ForeName><Initials>SR</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-1879-2555</Identifier><AffiliationInfo><Affiliation>The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane 4029, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van Laere</LastName><ForeName>Steven</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Center for Oncological Research, University of Antwerp &GZA Hospitals Sint-Augustinus, 2610 Wilrijk, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Desmedt</LastName><ForeName>Christine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ringnér</LastName><ForeName>Markus</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tommasi</LastName><ForeName>Stefania</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IRCCS Istituto Tumori 'Giovanni Paolo II', 70124 Bari, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eyford</LastName><ForeName>Jorunn</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Broeks</LastName><ForeName>Annegien</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vincent-Salomon</LastName><ForeName>Anne</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Pathology and INSERM U934, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Futreal</LastName><ForeName>P Andrew</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knappskog</LastName><ForeName>Stian</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>King</LastName><ForeName>Tari</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thomas</LastName><ForeName>Gilles</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Viari</LastName><ForeName>Alain</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Av. de l'Europe, 38330 Montbonnot-Saint Martin, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Langerød</LastName><ForeName>Anita</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Børresen-Dale</LastName><ForeName>Anne-Lise</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Birney</LastName><ForeName>Ewan</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton CB10 1SD, Cambridgeshire, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stunnenberg</LastName><ForeName>Hendrik G</ForeName><Initials>HG</Initials><AffiliationInfo><Affiliation>Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stratton</LastName><ForeName>Mike</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Foekens</LastName><ForeName>John A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martens</LastName><ForeName>John W M</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>322737</GrantID><Agency>European Research Council</Agency><Country>International</Country></Grant><Grant><GrantID>9675</GrantID><Agency>Cancer Research UK</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>P30 CA008748</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P50 CA168504</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>09</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nat Commun</MedlineTA><NlmUniqueID>101528555</NlmUniqueID><ISSNLinking>2041-1723</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>BMC Cancer. 2007 Sep 25;7:182</RefSource><PMID Version="1">17894856</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W509-12</RefSource><PMID Version="1">18463140</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2010 Jan 14;463(7278):191-6</RefSource><PMID Version="1">20016485</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2000 Jan 1;28(1):27-30</RefSource><PMID Version="1">10592173</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Lancet. 2011 Nov 19;378(9805):1812-23</RefSource><PMID Version="1">22098854</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8</RefSource><PMID Version="1">9843981</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):E1754-62</RefSource><PMID Version="1">25831525</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2015 Apr 3;348(6230):124-8</RefSource><PMID Version="1">25765070</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Mol Biol. 1982 May 5;157(1):105-32</RefSource><PMID Version="1">7108955</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Int J Cancer. 2010 Jul 15;127(2):355-60</RefSource><PMID Version="1">19904758</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2000 Aug 17;406(6797):747-52</RefSource><PMID Version="1">10963602</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Oncogene. 2004 Oct 7;23(46):7669-78</RefSource><PMID Version="1">15361840</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2009 Nov 30;10:394</RefSource><PMID Version="1">19948066</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Natl Cancer Inst. 2014 Dec 04;107(1):357</RefSource><PMID Version="1">25479802</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Cancer. 2015 Nov 09;15:877</RefSource><PMID Version="1">26553136</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Biostatistics. 2010 Apr;11(2):242-53</RefSource><PMID Version="1">20097884</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cancer Res. 2008 May 1;68(9):3108-14</RefSource><PMID Version="1">18451135</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Hum Pathol. 2015 Feb;46(2):182-90</RefSource><PMID Version="1">25522926</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Biol. 2015 Aug 08;16:160</RefSource><PMID Version="1">26253137</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Am J Surg Pathol. 2007 Jan;31(1):121-8</RefSource><PMID Version="1">17197928</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2004 Jan 1;20(1):93-9</RefSource><PMID Version="1">14693814</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>EMBO J. 1995 Dec 15;14(24):6107-15</RefSource><PMID Version="1">8557030</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Oncogene. 1996 Nov 7;13(9):1919-25</RefSource><PMID Version="1">8934538</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Biostatistics. 2007 Jan;8(1):118-27</RefSource><PMID Version="1">16632515</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Clin Cancer Res. 2006 Feb 15;12(4):1157-67</RefSource><PMID Version="1">16489069</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2013 Aug 22;500(7463):415-21</RefSource><PMID Version="1">23945592</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cell. 2012 May 25;149(5):979-93</RefSource><PMID Version="1">22608084</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Endocr Relat Cancer. 2000 Sep;7(3):143-64</RefSource><PMID Version="1">11021963</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 Apr 18;486(7403):346-52</RefSource><PMID Version="1">22522925</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 Oct 4;490(7418):61-70</RefSource><PMID Version="1">23000897</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 May 16;486(7403):400-4</RefSource><PMID Version="1">22722201</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 Jun 20;486(7403):405-9</RefSource><PMID Version="1">22722202</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2015 Apr 3;348(6230):69-74</RefSource><PMID Version="1">25838375</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2016 May 02;534(7605):47-54</RefSource><PMID Version="1">27135926</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Breast Cancer Res Treat. 2014 Jul;146(1):211-20</RefSource><PMID Version="1">24839032</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cancer Res. 2009 Jan 15;69(2):663-71</RefSource><PMID Version="1">19147582</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>N Engl J Med. 2014 Dec 4;371(23 ):2189-99</RefSource><PMID Version="1">25409260</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Carcinogenesis. 2012 Nov;33(11):2007-17</RefSource><PMID Version="1">22822097</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Breast Cancer Res Treat. 2012 Jun;133(2):583-94</RefSource><PMID Version="1">22002566</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Breast Cancer Res. 2007;9(3):R30</RefSource><PMID Version="1">17504517</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74</RefSource><PMID Version="1">11553815</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cancer Res. 1992 Mar 1;52(5):1107-13</RefSource><PMID Version="1">1737370</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Protein Sci. 2003 May;12(5):1007-17</RefSource><PMID Version="1">12717023</PMID></CommentsCorrections></CommentsCorrectionsList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>03</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>08</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>9</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>9</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27666519</ArticleId><ArticleId IdType="pii">ncomms12910</ArticleId><ArticleId IdType="doi">10.1038/ncomms12910</ArticleId><ArticleId IdType="pmc">PMC5052682</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001858 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001858 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Asie
|area= AustralieFrV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:27666519
|texte= Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:27666519" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a AustralieFrV1
| This area was generated with Dilib version V0.6.33. |  |