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A Deep Learning Framework for Predicting Response to Therapy in Cancer

Sakellaropoulos, Theodore
Author Sakellaropoulos, Theodore Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
Vougas, Konstantinos
Author Vougas, Konstantinos Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece. Electronic address: kvougas@bioacademy.gr
Narang, Sonali
Author Narang, Sonali Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
Koinis, Filippos
Author Koinis, Filippos Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
Kotsinas, Athanassios
Author Kotsinas, Athanassios Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
Polyzos, Alexander
Author Polyzos, Alexander Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
Moss, Tyler J
Author Moss, Tyler J Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
Piha-Paul, Sarina
Author Piha-Paul, Sarina Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
Zhou, Hua
Author Zhou, Hua Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
Kardala, Eleni
Author Kardala, Eleni Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
Damianidou, Eleni
Author Damianidou, Eleni Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
Alexopoulos, Leonidas G
Author Alexopoulos, Leonidas G School of Mechanical Engineering, National Technical University of Athens, Zografou 15780, Greece
Aifantis, Iannis
Author Aifantis, Iannis Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
Townsend, Paul A
Author Townsend, Paul A Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK
Panayiotidis, Mihalis I
Author Panayiotidis, Mihalis I Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Department of Electron Microscopy & Molecular Pathology, Cyprus Institute of Neurology & Genetics, Nicosia, 2371, Cyprus
Sfikakis, Petros
Author Sfikakis, Petros 1st Department of Propaedeutic Internal Medicine, Medical School, Laikon Hospital, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
Bartek, Jiri
Author Bartek, Jiri Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, Copenhagen 2100, Denmark; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Hněvotínská, Olomouc 1333/5 779 00, Czech Republic; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-171 77, Sweden
Fitzgerald, Rebecca C
Author Fitzgerald, Rebecca C Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
Thanos, Dimitris
Author Thanos, Dimitris Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece
Mills Shaw, Kenna R
Author Mills Shaw, Kenna R Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
Petty, Russell
Author Petty, Russell Division of Molecular and Clinical Medicine, Ninewells Hospital and School of Medicine, University of Dundee, Dundee DD1 9SY, UK
Tsirigos, Aristotelis
Author Tsirigos, Aristotelis Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA. Electronic address: aristotelis.tsirigos@nyulangone.org
Gorgoulis, Vassilis G
Author Gorgoulis, Vassilis G Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece; Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK; 1st Department of Propaedeutic Internal Medicine, Medical School, Laikon Hospital, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece. Electronic address: vgorg@med.uoa.gr

Cell reports. 2019 Dec 10 ; 29 (11) : 3367-3373.e4.

Cell Rep
ISSN 2211-1247
Source

Language English Country United States Media print

Document type Journal Article, Research Support, Non-U.S. Gov't

Persistent link https://www.medvik.cz/link/pmid31825821

Grant support
15874 Cancer Research UK - United Kingdom
MC_PC_14112 Medical Research Council - United Kingdom
MC_UU_12022/2 Medical Research Council - United Kingdom

PubMed 31825821
DOI 10.1016/j.celrep.2019.11.017
PII: S2211-1247(19)31488-3
Knihovny.cz E-resources

Keywords
DNN, deep neural networks, drug response prediction, machine learning, precision medicine,
MeSH
Survival Analysis MeSH
Drug Resistance, Neoplasm * MeSH
Deep Learning * MeSH
Precision Medicine methods MeSH
Humans MeSH
Cell Line, Tumor MeSH
Neoplasms drug therapy genetics metabolism MeSH
Check Tag
Humans MeSH
Publication type
Journal Article MeSH
Research Support, Non-U.S. Gov't MeSH

A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed their performance on multiple clinical cohorts. We demonstrate that deep neural networks outperform the current state in machine learning frameworks. We provide a proof of concept for the use of deep neural network-based frameworks to aid precision oncology strategies.

1st Department of Propaedeutic Internal Medicine Medical School Laikon Hospital National and Kapodistrian University of Athens 75 Mikras Asias Str Athens 11527 Greece; Center for New Biotechnologies and Precision Medicine Medical School National and Kapodistrian University of Athens 75 Mikras Asias Str Athens 11527 Greece

Applied Bioinformatics Laboratories NYU School of Medicine New York NY 10016 USA

Biomedical Research Foundation of the Academy of Athens 4 Soranou Ephessiou Str Athens 11527 Greece

Biomedical Research Foundation of the Academy of Athens 4 Soranou Ephessiou Str Athens 11527 Greece; Molecular Carcinogenesis Group Department of Histology and Embryology School of Medicine National and Kapodistrian University of Athens 75 Mikras Asias Str Athens 11527 Greece; Division of Cancer Sciences Faculty of Biology Medicine and Health Manchester Academic Health Science Centre Manchester Cancer Research Centre NIHR Manchester Biomedical Research Centre University of Manchester Manchester M20 4GJ UK; 1st Department of Propaedeutic Internal Medicine Medical School Laikon Hospital National and Kapodistrian University of Athens 75 Mikras Asias Str Athens 11527 Greece

Department of Applied Sciences Northumbria University Newcastle upon Tyne NE1 8ST UK; Department of Electron Microscopy and Molecular Pathology Cyprus Institute of Neurology and Genetics Nicosia 2371 Cyprus

Department of Investigational Cancer Therapeutics The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd Houston TX 77030 USA

Department of Pathology NYU School of Medicine New York NY 10016 USA; Laura and Isaac Perlmutter Cancer Center NYU School of Medicine New York NY 10016 USA

Department of Pathology NYU School of Medicine New York NY 10016 USA; Laura and Isaac Perlmutter Cancer Center NYU School of Medicine New York NY 10016 USA; Applied Bioinformatics Laboratories NYU School of Medicine New York NY 10016 USA

Division of Cancer Sciences Faculty of Biology Medicine and Health Manchester Academic Health Science Centre Manchester Cancer Research Centre NIHR Manchester Biomedical Research Centre University of Manchester Manchester M20 4GJ UK

Division of Molecular and Clinical Medicine Ninewells Hospital and School of Medicine University of Dundee Dundee DD1 9SY UK

Genome Integrity Unit Danish Cancer Society Research Centre Strandboulevarden 49 Copenhagen 2100 Denmark; Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University Hněvotínská Olomouc 1333 5 779 00 Czech Republic; Science for Life Laboratory Division of Genome Biology Department of Medical Biochemistry and Biophysics Karolinska Institute Stockholm SE 171 77 Sweden

Medical Research Council Cancer Unit Hutchison Medical Research Council Research Centre University of Cambridge Cambridge CB2 0XZ UK