A Deep Learning Framework for Predicting Response to Therapy in Cancer

被引：158

作者：

Sakellaropoulos, Theodore ^{[1
,2
]}

Vougas, Konstantinos ^{[3
,4
]}

Narang, Sonali ^{[1
,2
]}

Koinis, Filippos ^{[4
]}

Kotsinas, Athanassios ^{[4
]}

Polyzos, Alexander ^{[5
]}

Moss, Tyler J. ^{[6
]}

Piha-Paul, Sarina ^{[7
]}

Zhou, Hua ^{[8
]}

Kardala, Eleni ^{[4
]}

Damianidou, Eleni ^{[4
]}

Alexopoulos, Leonidas G. ^{[9
]}

Aifantis, Iannis ^{[1
,2
]}

Townsend, Paul A. ^{[10
]}

Panayiotidis, Mihalis I. ^{[11
,12
]}

Sfikakis, Petros ^{[13
,14
]}

Bartek, Jiri ^{[15
,16
,17
]}

Fitzgerald, Rebecca C. ^{[18
]}

Thanos, Dimitris ^{[3
]}

Shaw, Kenna R. Mills ^{[6
]}

Petty, Russell ^{[19
,20
]}

Tsirigos, Aristotelis ^{[1
,2
,8
]}

Gorgoulis, Vassilis G. ^{[3
,4
,10
,13
]}

机构：

[1] NYU, Sch Med, Dept Pathol, New York, NY 10016 USA

[2] NYU, Sch Med, Laura & Isaac Perlmutter Canc Ctr, New York, NY 10016 USA

[3] Acad Athens, Biomed Res Fdn, 4 Soranou Ephessiou Str, Athens 11527, Greece

[4] Natl & Kapodistrian Univ Athens, Sch Med, Dept Histol & Embryol, Mol Carcinogenesis Grp, 75 Mikras Asias Str, Athens 11527, Greece

[5] Weill Cornell Med, Sandra & Edward Meyer Canc Ctr, Sanford I Weill Dept Med, New York, NY 10021 USA

[6] Univ Texas MD Anderson Canc Ctr, Sheikh Khalifa Bin Zayed al Nahyan Inst Personali, 1515 Holcombe Blvd, Houston, TX 77030 USA

[7] Univ Texas MD Anderson Canc Ctr, Dept Invest Canc Therapeut, 1515 Holcombe Blvd, Houston, TX 77030 USA

[8] NYU, Sch Med, Appl Bioinformat Labs, New York, NY 10016 USA

[9] Natl Tech Univ Athens, Sch Mech Engn, Zografos 15780, Greece

[10] Univ Manchester, NIHR Manchester Biomed Res Ctr, Manchester Canc Res Ctr,Div Canc Sci, Fac Biol Med & Hlth,Manchester Acad Hlth Sci Ctr, Manchester M20 4GJ, Lancs, England

[11] Northumbria Univ, Dept Appl Sci, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England

[12] Cyprus Inst Neurol & Genet, Dept Electron Microscopy & Mol Pathol, CY-2371 Nicosia, Cyprus

[13] Natl & Kapodistrian Univ Athens, Laikon Hosp, Med Sch, Dept Propaedeut Internal Med 1, 75 Mikras Asias Str, Athens 11527, Greece

[14] Natl & Kapodistrian Univ Athens, Med Sch, Ctr New Biotechnol & Precis Med, 75 Mikras Asias Str, Athens 11527, Greece

[15] Danish Canc Soc Res Ctr, Genome Integr Unit, Strandboulevarden 49, DK-2100 Copenhagen, Denmark

[16] Palacky Univ, Fac Med & Dent, Inst Mol & Translat Med, Olomouc 77900, Czech Republic

[17] Karolinska Inst, Dept Med Biochem & Biophys, Div Genome Biol, Sci Life Lab, SE-17177 Stockholm, Sweden

[18] Univ Cambridge, Med Res Council, Canc Unit, Res Ctr, Cambridge CB20XZ, England

[19] Univ Dundee, Ninewells Hosp, Div Mol & Clin Med, Dundee DD1 9SY, Scotland

[20] Univ Dundee, Sch Med, Dundee DD1 9SY, Scotland

来源：

CELL REPORTS | 2019年 / 29卷 / 11期

基金：

英国医学研究理事会;

关键词：

DRUG-SENSITIVITY; NEURAL-NETWORKS; CHEMORESISTANCE; RESISTANCE;

D O I：

10.1016/j.celrep.2019.11.017

中图分类号：

Q2 [细胞生物学];

学科分类号：

071013 [干细胞生物学];

摘要：

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.

引用

页码：3367 / +

页数：11

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