Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

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Menden , M P , Wang , D , Mason , M J , Szalai , B , Bulusu , K C , Guan , Y , Yu , T , Kang , J , Jeon , M , Wolfinger , R , Nguyen , T , Zaslavskiy , M , Abante , J , Abecassis , B S , Aben , N , Aghamirzaie , D , Aittokallio , T , Akhtari , F S , Al-lazikani , B , Alam , T , Allam , A , Allen , C , de Almeida , M P , Altarawy , D , Alves , V , Amadoz , A , Anchang , B , Antolin , A A , Ash , J R , Aznar , V R , Ba-alawi , W , Bagheri , M , Bajic , V , Ball , G , Ballester , P J , Baptista , D , Bare , C , Bateson , M , Bender , A , Bertrand , D , Wijayawardena , B , Boroevich , K A , Bosdriesz , E , Bougouffa , S , Bounova , G , Brouwer , T , Bryant , B , Calaza , M , Calderone , A , Calza , S , Capuzzi , S , Carbonell-Caballero , J , Carlin , D , Carter , H , Castagnoli , L , Celebi , R , Cesareni , G , Chang , H , Chen , G , Chen , H , Chen , H , Cheng , L , Chernomoretz , A , Chicco , D , Cho , K-H , Cho , S , Choi , D , Choi , J , Choi , K , Choi , M , Cock , M D , Coker , E , Cortes-Ciriano , I , Cserzö , M , Cubuk , C , Curtis , C , Daele , D V , Dang , C C , Dijkstra , T , Dopazo , J , Draghici , S , Drosou , A , Dumontier , M , Ehrhart , F , Eid , F-E , ElHefnawi , M , Elmarakeby , H , van Engelen , B , Engin , H B , de Esch , I , Evelo , C , Falcao , A O , Farag , S , Fernandez-Lozano , C , Fisch , K , Flobak , A , Fornari , C , Foroushani , A B K , Fotso , D C , Fourches , D , Friend , S , Frigessi , A , Gao , F , Gao , X , Gerold , J M , Gestraud , P , Ghosh , S , Gillberg , J , Godoy-Lorite , A , Godynyuk , L , Godzik , A , Goldenberg , A , Gomez-Cabrero , D , Gonen , M , de Graaf , C , Gray , H , Grechkin , M , Guimera , R , Guney , E , Haibe-Kains , B , Han , Y , Hase , T , He , D , He , L , Heath , L S , Hellton , K H , Helmer-Citterich , M , Hidalgo , M R , Hidru , D , Hill , S M , Hochreiter , S , Hong , S , Hovig , E , Hsueh , Y-C , Hu , Z , Huang , J K , Huang , R S , Hunyady , L , Hwang , J , Hwang , T H , Hwang , W , Hwang , Y , Isayev , O , Don’t Walk , O B , Jack , J , Jahandideh , S , Ji , J , Jo , Y , Kamola , P J , Kanev , G K , Karacosta , L , Karimi , M , Kaski , S , Kazanov , M , Khamis , A M , Khan , S A , Kiani , N A , Kim , A , Kim , J , Kim , J , Kim , K , Kim , K , Kim , S , Kim , Y , Kim , Y , Kirk , P D W , Kitano , H , Klambauer , G , Knowles , D , Ko , M , Kohn-Luque , A , Kooistra , A J , Kuenemann , M A , Kuiper , M , Kurz , C , Kwon , M , van Laarhoven , T , Laegreid , A , Lederer , S , Lee , H , Lee , J , Lee , Y W , Lepp_aho , E , Lewis , R , Li , J , Li , L , Liley , J , Lim , W K , Lin , C , Liu , Y , Lopez , Y , Low , J , Lysenko , A , Machado , D , Madhukar , N , Maeyer , D D , Malpartida , A B , Mamitsuka , H , Marabita , F , Marchal , K , Marttinen , P , Mason , D , Mazaheri , A , Mehmood , A , Mehreen , A , Michaut , M , Miller , R A , Mitsopoulos , C , Modos , D , Moerbeke , M V , Moo , K , Motsinger-Reif , A , Movva , R , Muraru , S , Muratov , E , Mushthofa , M , Nagarajan , N , Nakken , S , Nath , A , Neuvial , P , Newton , R , Ning , Z , Niz , C D , Oliva , B , Olsen , C , Palmeri , A , Panesar , B , Papadopoulos , S , Park , J , Park , S , Park , S , Pawitan , Y , Peluso , D , Pendyala , S , Peng , J , Perfetto , L , Pirro , S , Plevritis , S , Politi , R , Poon , H , Porta , E , Prellner , I , Preuer , K , Pujana , M A , Ramnarine , R , Reid , J E , Reyal , F , Richardson , S , Ricketts , C , Rieswijk , L , Rocha , M , Rodriguez-Gonzalvez , C , Roell , K , Rotroff , D , de Ruiter , J R , Rukawa , P , Sadacca , B , Safikhani , Z , Safitri , F , Sales-Pardo , M , Sauer , S , Schlichting , M , Seoane , J A , Serra , J , Shang , M-M , Sharma , A , Sharma , H , Shen , Y , Shiga , M , Shin , M , Shkedy , Z , Shopsowitz , K , Sinai , S , Skola , D , Smirnov , P , Soerensen , I F , Soerensen , P , Song , J-H , Song , S O , Soufan , O , Spitzmueller , A , Steipe , B , Suphavilai , C , Tamayo , S P , Tamborero , D , Tang , J , Tanoli , Z-R , Tarres-Deulofeu , M , Tegner , J , Thommesen , L , Tonekaboni , S A M , Tran , H , Troyer , E D , Truong , A , Tsunoda , T , Turu , G , Tzeng , G-Y , Verbeke , L , Videla , S & Consortium , A-S D C DREAM 2019 , ' Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen ' , Nature Communications , vol. 10 , no. 1 , 2674 . https://doi.org/10.1038/s41467-019-09799-2

Title: Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Author: Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Aznar, Victoria Romeo; Ba-alawi, Wail; Bagheri, Moeen; Bajic, Vladimir; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang-Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; Cock, Martine De; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzö, Miklós; Cubuk, Cankut; Curtis, Christina; Daele, Dries Van; Dang, Cuong C.; Dijkstra, Tjeerd; Dopazo, Joaquin; Draghici, Sorin; Drosou, Anastasios; Dumontier, Michel; Ehrhart, Friederike; Eid, Fatma-Elzahraa; ElHefnawi, Mahmoud; Elmarakeby, Haitham; van Engelen, Bo; Engin, Hatice Billur; de Esch, Iwan; Evelo, Chris; Falcao, Andre O.; Farag, Sherif; Fernandez-Lozano, Carlos; Fisch, Kathleen; Flobak, Asmund; Fornari, Chiara; Foroushani, Amir B. K.; Fotso, Donatien Chedom; Fourches, Denis; Friend, Stephen; Frigessi, Arnoldo; Gao, Feng; Gao, Xiaoting; Gerold, Jeffrey M.; Gestraud, Pierre; Ghosh, Samik; Gillberg, Jussi; Godoy-Lorite, Antonia; Godynyuk, Lizzy; Godzik, Adam; Goldenberg, Anna; Gomez-Cabrero, David; Gonen, Mehmet; de Graaf, Chris; Gray, Harry; Grechkin, Maxim; Guimera, Roger; Guney, Emre; Haibe-Kains, Benjamin; Han, Younghyun; Hase, Takeshi; He, Di; He, Liye; Heath, Lenwood S.; Hellton, Kristoffer H.; Helmer-Citterich, Manuela; Hidalgo, Marta R.; Hidru, Daniel; Hill, Steven M.; Hochreiter, Sepp; Hong, Seungpyo; Hovig, Eivind; Hsueh, Ya-Chih; Hu, Zhiyuan; Huang, Justin K.; Huang, R. Stephanie; Hunyady, László; Hwang, Jinseub; Hwang, Tae Hyun; Hwang, Woochang; Hwang, Yongdeuk; Isayev, Olexandr; Don’t Walk, Oliver Bear; Jack, John; Jahandideh, Samad; Ji, Jiadong; Jo, Yousang; Kamola, Piotr J.; Kanev, Georgi K.; Karacosta, Loukia; Karimi, Mostafa; Kaski, Samuel; Kazanov, Marat; Khamis, Abdullah M.; Khan, Suleiman Ali; Kiani, Narsis A.; Kim, Allen; Kim, Jinhan; Kim, Juntae; Kim, Kiseong; Kim, Kyung; Kim, Sunkyu; Kim, Yongsoo; Kim, Yunseong; Kirk, Paul D. W.; Kitano, Hiroaki; Klambauer, Gunter; Knowles, David; Ko, Melissa; Kohn-Luque, Alvaro; Kooistra, Albert J.; Kuenemann, Melaine A.; Kuiper, Martin; Kurz, Christoph; Kwon, Mijin; van Laarhoven, Twan; Laegreid, Astrid; Lederer, Simone; Lee, Heewon; Lee, Jeon; Lee, Yun Woo; Lepp_aho, Eemeli; Lewis, Richard; Li, Jing; Li, Lang; Liley, James; Lim, Weng Khong; Lin, Chieh; Liu, Yiyi; Lopez, Yosvany; Low, Joshua; Lysenko, Artem; Machado, Daniel; Madhukar, Neel; Maeyer, Dries De; Malpartida, Ana Belen; Mamitsuka, Hiroshi; Marabita, Francesco; Marchal, Kathleen; Marttinen, Pekka; Mason, Daniel; Mazaheri, Alireza; Mehmood, Arfa; Mehreen, Ali; Michaut, Magali; Miller, Ryan A.; Mitsopoulos, Costas; Modos, Dezso; Moerbeke, Marijke Van; Moo, Keagan; Motsinger-Reif, Alison; Movva, Rajiv; Muraru, Sebastian; Muratov, Eugene; Mushthofa, Mushthofa; Nagarajan, Niranjan; Nakken, Sigve; Nath, Aritro; Neuvial, Pierre; Newton, Richard; Ning, Zheng; Niz, Carlos De; Oliva, Baldo; Olsen, Catharina; Palmeri, Antonio; Panesar, Bhawan; Papadopoulos, Stavros; Park, Jaesub; Park, Seonyeong; Park, Sungjoon; Pawitan, Yudi; Peluso, Daniele; Pendyala, Sriram; Peng, Jian; Perfetto, Livia; Pirro, Stefano; Plevritis, Sylvia; Politi, Regina; Poon, Hoifung; Porta, Eduard; Prellner, Isak; Preuer, Kristina; Pujana, Miguel Angel; Ramnarine, Ricardo; Reid, John E.; Reyal, Fabien; Richardson, Sylvia; Ricketts, Camir; Rieswijk, Linda; Rocha, Miguel; Rodriguez-Gonzalvez, Carmen; Roell, Kyle; Rotroff, Daniel; de Ruiter, Julian R.; Rukawa, Ploy; Sadacca, Benjamin; Safikhani, Zhaleh; Safitri, Fita; Sales-Pardo, Marta; Sauer, Sebastian; Schlichting, Moritz; Seoane, Jose A.; Serra, Jordi; Shang, Ming-Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je-Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia-ur-Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong; Troyer, Ewoud De; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gábor; Tzeng, Guang-Yo; Verbeke, Lieven; Videla, Santiago; Consortium, AstraZeneca-Sanger Drug Combination DREAM
Contributor: University of Helsinki, Tero Aittokallio / Principal Investigator
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Aalto University
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Case Western University
University of Helsinki, Karolinska institute
University of Helsinki, Aalto University
University of Helsinki, Institute for Molecular Medicine Finland
Date: 2019-06-17
Language: eng
Number of pages: 17
Belongs to series: Nature Communications
ISSN: 2041-1723
URI: http://hdl.handle.net/10138/308081
Abstract: The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
Subject: ANDROGEN RECEPTOR
BREAST-CANCER
CELL
GENE
INHIBITION
LANDSCAPE
MUTATIONS
PATHWAY
RESISTANCE
RESOURCE
317 Pharmacy
3122 Cancers
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