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Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.

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Title: Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Authors: Chong C; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Müller M; Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland., Pak H; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Harnett D; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany., Huber F; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Grun D; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland., Leleu M; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland., Auger A; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Arnaud M; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Stevenson BJ; Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland., Michaux J; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Bilic I; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany., Hirsekorn A; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany., Calviello L; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany., Simó-Riudalbas L; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland., Planet E; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland., Lubiński J; Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland.; International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland., Bryśkiewicz M; Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Rybacka 1, 70-204, Szczecin, Poland.; International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland., Wiznerowicz M; International Institute for Molecular Oncology, Jakuba Krauthofera 23, 60-203, Poznań, Poland.; Poznan University of Medical Sciences, Fredry 10, 61-701, Poznań, Poland., Xenarios I; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Genome Center Health 2030, Chemin de Mines 9, 1202, Genève, Switzerland.; Department of Training and Research, CHUV/UNIL Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland., Zhang L; Center for Research on Reproduction and Women's Health, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA, 19104, USA.; Department of Obstetrics and Gynecology, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA., Trono D; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland., Harari A; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Ohler U; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.; Departments of Biology and Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany., Coukos G; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland., Bassani-Sternberg M; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland. michal.bassani@chuv.ch.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland. michal.bassani@chuv.ch.
Source: Nature communications [Nat Commun] 2020 Mar 10; Vol. 11 (1), pp. 1293. Date of Electronic Publication: 2020 Mar 10.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Database: MEDLINE Ultimate
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  Data: <searchLink fieldCode="AU" term="%22Chong+C%22">Chong C</searchLink>; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Müller+M%22">Müller M</searchLink>; Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Pak+H%22">Pak H</searchLink>; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Harnett+D%22">Harnett D</searchLink>; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.<br /><searchLink fieldCode="AU" term="%22Huber+F%22">Huber F</searchLink>; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Grun+D%22">Grun D</searchLink>; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Leleu+M%22">Leleu M</searchLink>; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Auger+A%22">Auger A</searchLink>; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Arnaud+M%22">Arnaud M</searchLink>; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Stevenson+BJ%22">Stevenson BJ</searchLink>; Vital IT, Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Michaux+J%22">Michaux J</searchLink>; Ludwig Institute for Cancer Research, University of Lausanne, Agora Center, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Bilic+I%22">Bilic I</searchLink>; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.<br /><searchLink fieldCode="AU" term="%22Hirsekorn+A%22">Hirsekorn A</searchLink>; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.<br /><searchLink fieldCode="AU" term="%22Calviello+L%22">Calviello L</searchLink>; Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.<br /><searchLink fieldCode="AU" term="%22Simó-Riudalbas+L%22">Simó-Riudalbas L</searchLink>; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Planet+E%22">Planet E</searchLink>; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, 1015, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Lubiński+J%22">Lubiński J</searchLink>; Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. 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