Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Autor: Sieberts, Solveig K., Zhu, Fan, García-García, Javier, Stahl, Eli, Pratap, Abhishek, Pandey, Gaurav, Pappas, Dimitrios, Aguilar, Daniel, Anton, Bernat, Bonet, Jaume, Eksi, Ridvan, Fornés, Oriol, Guney, Emre, Li, Hongdong, Marín, Manuel Alejandro, Panwar, Bharat, Planas-Iglesias, Joan, Poglayen, Daniel, Cui, Jing, Falcao, Andre O., Suver, Christine, Hoff, Bruce, Balagurusamy, Venkat S. K., Dillenberger, Donna, Neto, Elias Chaibub, Norman, Thea, Aittokallio, Tero, Ammad-ud-din, Muhammad, Azencott, Chloe-Agathe, Bellón, Víctor, Boeva, Valentina, Bunte, Kerstin, Chheda, Himanshu, Cheng, Lu, Corander, Jukka, Dumontier, Michel, Goldenberg, Anna, Gopalacharyulu, Peddinti, Hajiloo, Mohsen, Hidru, Daniel, Jaiswal, Alok, Kaski, Samuel, Khalfaoui, Beyrem, Khan, Suleiman Ali, Kramer, Eric R., Marttinen, Pekka, Mezlini, Aziz M., Molparia, Bhuvan, Pirinen, Matti, Saarela, Janna, Samwald, Matthias, Stoven, Véronique, Tang, Hao, Tang, Jing, Torkamani, Ali, Vert, Jean-Phillipe, Wang, Bo, Wang, Tao, Wennerberg, Krister, Wineinger, Nathan E., Xiao, Guanghua, Xie, Yang, Yeung, Rae, Zhan, Xiaowei, Zhao, Cheng, Calaza, Manuel, Elmarakeby, Haitham, Heath, Lenwood S., Long, Quan, Moore, Jonathan D., Opiyo, Stephen Obol, Savage, Richard S., Zhu, Jun, Greenberg, Jeff, Kremer, Joel, Michaud, Kaleb, Barton, Anne, Coenen, Marieke, Mariette, Xavier, Miceli, Corinne, Shadick, Nancy, Weinblatt, Michael, de Vries, Niek, Tak, Paul P., Gerlag, Danielle, Huizinga, Tom W. J., Kurreeman, Fina, Allaart, Cornelia F., Louis Bridges Jr., S., Criswell, Lindsey, Moreland, Larry, Klareskog, Lars, Saevarsdottir, Saedis, Padyukov, Leonid, Gregersen, Peter K., Friend, Stephen, Plenge, Robert, Stolovitzky, Gustavo, Oliva, Baldo, Guan, Yuanfang, Mangravite, Lara M., Bridges, S. Louis
Přispěvatelé: Intelligent Systems, Institute for Molecular Medicine Finland, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Jukka Corander / Principal Investigator, Department of Computer Science, Janna Saarela / Principal Investigator, Krister Wennerberg / Principal Investigator, Biostatistics Helsinki, Statistical and population genetics, AII - Amsterdam institute for Infection and Immunity, Clinical Immunology and Rheumatology, Zhejiang University, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), DYNBIO LEGOS, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut d'Ecologia Aquàtica, Universitat de Girona (UdG), Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), China Agricultural University (CAU), Computational Intelligence Research Group (CA3), Centre of Technology and Systems (CTS), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Bioinformatique (CBIO), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Hefei University of Technology (HFUT), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Service de génétique [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Technical Research Centre of Finland, VTT Technical Research Centre of Finland (VTT), U.S. Food and Drug Administration (FDA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Profium Oy [Helsinki], Chinese Academy of Agricultural Sciences (CAAS), Business School [Hohai University], Hohai University, Institute of Industrial Economics [Hohai University], State Key Laboratory of Medical Genetics of China, Hunan Medical College, State Key Laboratory of Advanced Special Steel, Shanghai University, Quantitative Biomedical Research Center (QBRC), University of Texas Southwestern Medical Center [Dallas], Harold C. Simmons Comprehensive Cancer Center [Dallas, TX, États-Unis], Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique (LHEEA), École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), China National Research Center of Intelligent Equipment for Agriculture [Beijing] (NRCIEA), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Tongji University, Laboratory for Measles and Rubella, Laboratoire National de Santé [Luxembourg] (LNS), Department of Human Genetics, Radboud University Medical Center [Nijmegen], INSERM U1012, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), School of biosciences and biotechnology, University of Camerino, Università degli Studi di Camerino = University of Camerino (UNICAM), Division of Rheumatology, Immunology and Allergy and Partners Asthma Center, Brigham and Women's Hospital [Boston], Department of Health Education and Promotion, Maastricht University [Maastricht], University of Amsterdam [Amsterdam] (UvA), Department of rheumatology, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Rheumatology Unit, Department of Medicine, University of California [San Francisco] (UC San Francisco), University of California (UC), Rheumatology Unit, Karolinska Institutet [Stockholm], Merck & Co. Inc, Structural Bioinformatics Group (GRIB), Barcelona Research Park of Biomedicine (PRBB), Universitat Pompeu Fabra [Barcelona] (UPF), Capital Normal University [Beijing], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), MINES ParisTech - École nationale supérieure des mines de Paris, California Institute of Technology (CALTECH)-NASA, Department of Mechanical and Aerospace Engineering [Davis], University of California-University of California, Università degli Studi di Camerino (UNICAM), University of California [San Francisco] (UCSF), University of California, Sage Bionetworks, University of Michigan, Ann Arbor, Pompeu Fabra University, Icahn School of Medicine at Mount Sinai, Corrona LLC, Northeastern University, Harvard University, University of Lisbon, IBM, INSERM U900, University of Helsinki, University of Toronto, Scripps Research Institute, Medical University of Vienna, University of Texas at Dallas, New York University, Albany Medical College, Arthritis Research Center Foundation, Radboud University Nijmegen, INSERM U1184, University of Amsterdam, Glaxo Smith Kline, Leiden University, University of Alabama at Birmingham, University of California San Francisco, University of Pittsburgh, Karolinska Institutet, North Shore-Long Island Jewish Health System, Merck, Aalto-yliopisto, Aalto University
Jazyk: angličtina
Rok vydání: 2016
Předmět:
Male
0301 basic medicine
General Physics and Astronomy
Arthritis
Genome-wide association study
Bioinformatics
DISEASE
Arthritis
Rheumatoid
Cohort Studies
Missing heritability problem
MISSING HERITABILITY
Medicine
Certolizumab pegol
RISK
Multidisciplinary
Antibodies
Monoclonal
Middle Aged
Prognosis
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
3. Good health
STACKED GENERALIZATION
Treatment Outcome
Antirheumatic Agents
Crowdsourcing
Biomarker (medicine)
Female
Erratum
medicine.drug
Adult
Science
Context (language use)
Antibodies
Monoclonal
Humanized
Polymorphism
Single Nucleotide
Article
General Biochemistry
Genetics and Molecular Biology
03 medical and health sciences
INFLIXIMAB
Journal Article
Humans
SNP
Genetic Predisposition to Disease
GENOME-WIDE ASSOCIATION
METAANALYSIS
Aged
ta113
Tumor Necrosis Factor-alpha
business.industry
NETWORK INFERENCE
COMPLEX TRAITS
Artritis reumatoide -- Tractament
CLINICAL-RESPONSE
General Chemistry
113 Computer and information sciences
medicine.disease
Infliximab
030104 developmental biology
3121 General medicine
internal medicine and other clinical medicine
Certolizumab Pegol
business
RC
Zdroj: Nature Communications, 7:12460 (2016). Nature Publishing Group
Recercat. Dipósit de la Recerca de Catalunya
instname
Nature communications, 7. Nature Publishing Group
Nature Communications
Nature Communications, 2016, 7, pp.12460. ⟨10.1038/ncomms12460⟩
Nature Communications, 7:12460. Nature Publishing Group
Nature Communications, Nature Publishing Group, 2016, 7, pp.12460. ⟨10.1038/ncomms12460⟩
Nature Communications, Vol 7, Iss 1, Pp 1-10 (2016)
Nature Communications, 7
Sieberts, S K, Zhu, F, García-García, J, Stahl, E, Pratap, A, Pandey, G, Pappas, D, Aguilar, D, Anton, B, Bonet, J, Eksi, R, Fornés, O, Guney, E, Li, H, Marín, M A, Panwar, B, Planas-Iglesias, J, Poglayen, D, Cui, J, Falcao, A O, Suver, C, Hoff, B, Balagurusamy, V S K, Dillenberger, D, Neto, E C, Norman, T, Aittokallio, T, Ammad-Ud-Din, M, Azencott, C A, Bellón, V, Boeva, V, Bunte, K, Chheda, H, Cheng, L, Corander, J, Dumontier, M, Goldenberg, A, Gopalacharyulu, P, Hajiloo, M, Hidru, D, Jaiswal, A, Kaski, S, Khalfaoui, B, Khan, S A, Kramer, E R, Marttinen, P, Mezlini, A M, Molparia, B, Pirinen, M, Saarela, J, Samwald, M, Stoven, V, Tang, H, Tang, J, Torkamani, A, Vert, J P, Wang, B, Wang, T, Wennerberg, K, Wineinger, N E, Xiao, G, Xie, Y, Yeung, R, Zhan, X, Zhao, C, Greenberg, J, Kremer, J, Michaud, K, Barton, A, Coenen, M, Mariette, X, Miceli, C, Shadick, N, Weinblatt, M, De Vries, N, Tak, P P, Gerlag, D, Huizinga, T W J, Kurreeman, F, Allaart, C F, Louis Bridges, S, Criswell, L, Moreland, L, Klareskog, L, Saevarsdottir, S, Padyukov, L, Gregersen, P K, Friend, S, Plenge, R, Stolovitzky, G, Oliva, B, Guan, Y & Mangravite, L M 2016, ' Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis ', Nature Communications, vol. 7, 12460 . https://doi.org/10.1038/ncomms12460
ISSN: 2041-1723
Popis: Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h2=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.
Rheumatoid arthritis patients respond differently to anti-TNF treatment. Using community-based challenge, the authors show that currently available data does not reveal meaningful genetic predictors of response to anti-TNF therapy, thus confirming clinical observations.
Databáze: OpenAIRE
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