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

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Menden, MP (author)

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

Article/chapterEnglish2019

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2019-06-17
Springer Science and Business Media LLC,2019

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LIBRIS-ID:oai:prod.swepub.kib.ki.se:141113030
http://kipublications.ki.se/Default.aspx?queryparsed=id:141113030URI
https://doi.org/10.1038/s41467-019-09799-2DOI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype

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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.

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Wang, D (author)
Mason, MJ (author)
Szalai, B (author)
Bulusu, KC (author)
Guan, YF (author)
Yu, T (author)
Kang, J (author)
Jeon, M (author)
Wolfinger, R (author)
Nguyen, T (author)
Zaslavskiy, M (author)
Jang, IS (author)
Ghazoui, Z (author)
Ahsen, ME (author)
Vogel, R (author)
Neto, EC (author)
Norman, T (author)
Tang, EKY (author)
Garnett, MJ (author)
Di Veroli, GY (author)
Fawell, S (author)
Stolovitzky, G (author)
Guinney, J (author)
Dry, JR (author)
Saez-Rodriguez, J (author)
Abante, J (author)
Abecassis, BS (author)
Aben, N (author)
Aghamirzaie, D (author)
Aittokallio, T (author)
Akhtari, FS (author)
Al-lazikani, B (author)
Alam, T (author)
Allam, A (author)
Allen, C (author)
de Almeida, MP (author)
Altarawy, D (author)
Alves, V (author)
Amadoz, A (author)
Anchang, B (author)
Antolin, AA (author)
Ash, JR (author)
Aznar, VR (author)
Ba-alawi, W (author)
Bagheri, M (author)
Bajic, V (author)
Ball, G (author)
Ballester, PJ (author)
Baptista, D (author)
Bare, C (author)
Bateson, M (author)
Bender, A (author)
Bertrand, D (author)
Wijayawardena, B (author)
Boroevich, KA (author)
Bosdriesz, E (author)
Bougouffa, S (author)
Bounova, G (author)
Brouwer, T (author)
Bryant, B (author)
Calaza, M (author)
Calderone, A (author)
Calza, S (author)
Capuzzi, S (author)
Carbonell-Caballero, J (author)
Carlin, D (author)
Carter, H (author)
Castagnoli, L (author)
Celebi, R (author)
Cesareni, G (author)
Chang, H (author)
Chen, GC (author)
Chen, HR (author)
Chen, HY (author)
Cheng, LJ (author)
Chernomoretz, A (author)
Chicco, D (author)
Cho, KH (author)
Cho, S (author)
Choi, D (author)
Choi, J (author)
Choi, K (author)
Choi, M (author)
De Cock, M (author)
Coker, E (author)
Cortes-Ciriano, I (author)
Cserzo, M (author)
Cubuk, C (author)
Curtis, C (author)
Van Daele, D (author)
Dang, CC (author)
Dijkstra, T (author)
Dopazo, J (author)
Draghici, S (author)
Drosou, A (author)
Dumontier, M (author)
Ehrhart, F (author)
Eid, FE (author)
ElHefnawi, M (author)
Elmarakeby, H (author)
van Engelen, B (author)
Engin, HB (author)
de Esch, I (author)
Evelo, C (author)
Falcao, AO (author)
Farag, S (author)
Fernandez-Lozano, C (author)
Fisch, K (author)
Flobak, A (author)
Fornari, C (author)
Foroushani, ABK (author)
Fotso, DC (author)
Fourches, D (author)
Friend, S (author)
Frigessi, A (author)
Gao, F (author)
Gao, XT (author)
Gerold, JM (author)
Gestraud, P (author)
Ghosh, S (author)
Gillberg, J (author)
Godoy-Lorite, A (author)
Godynyuk, L (author)
Godzik, A (author)
Goldenberg, A (author)
Gomez-Cabrero, DKarolinska Institutet (author)
Gonen, M (author)
de Graaf, C (author)
Gray, H (author)
Grechkin, M (author)
Guimera, R (author)
Guney, E (author)
Haibe-Kains, B (author)
Han, Y (author)
Hase, T (author)
He, D (author)
He, LY (author)
Heath, LS (author)
Hellton, KH (author)
Helmer-Citterich, M (author)
Hidalgo, MR (author)
Hidru, D (author)
Hill, SM (author)
Hochreiter, S (author)
Hong, S (author)
Hovig, E (author)
Hsueh, YC (author)
Hu, ZY (author)
Huang, JK (author)
Huang, RS (author)
Hunyady, L (author)
Hwang, J (author)
Hwang, TH (author)
Hwang, W (author)
Hwang, Y (author)
Isayev, O (author)
Walk, OBD (author)
Jack, J (author)
Jahandideh, S (author)
Ji, JD (author)
Jo, Y (author)
Kamola, PJ (author)
Kanev, GK (author)
Karacosta, L (author)
Karimi, M (author)
Kaski, S (author)
Kazanov, M (author)
Khamis, AM (author)
Khan, SA (author)
Kiani, NAKarolinska Institutet (author)
Kim, A (author)
Kim, J (author)
Kim, J (author)
Kim, K (author)
Kim, K (author)
Kim, S (author)
Kim, Y (author)
Kim, Y (author)
Kirk, PDW (author)
Kitano, H (author)
Klambauer, G (author)
Knowles, D (author)
Ko, M (author)
Kohn-Luque, A (author)
Kooistra, AJ (author)
Kuenemann, MA (author)
Kuiper, M (author)
Kurz, C (author)
Kwon, M (author)
van Laarhoven, T (author)
Laegreid, A (author)
Lederer, S (author)
Lee, H (author)
Lee, J (author)
Lee, YW (author)
Leppaho, E (author)
Lewis, R (author)
Li, J (author)
Li, L (author)
Liley, J (author)
Lim, WK (author)
Lin, C (author)
Liu, YY (author)
Lopez, Y (author)
Low, J (author)
Lysenko, A (author)
Machado, D (author)
Madhukar, N (author)
De Maeyer, D (author)
Malpartida, AB (author)
Mamitsuka, H (author)
Marabita, FKarolinska Institutet (author)
Marchal, K (author)
Marttinen, P (author)
Mason, D (author)
Mazaheri, A (author)
Mehmood, A (author)
Mehreen, A (author)
Michaut, M (author)
Miller, RA (author)
Mitsopoulos, C (author)
Modos, D (author)
Van Moerbeke, M (author)
Moo, K (author)
Motsinger-Reif, A (author)
Movva, R (author)
Muraru, S (author)
Muratov, E (author)
Mushthofa, M (author)
Nagarajan, N (author)
Nakken, S (author)
Nath, A (author)
Neuvial, P (author)
Newton, R (author)
Ning, Z (author)
De Niz, C (author)
Oliva, B (author)
Olsen, C (author)
Palmeri, A (author)
Panesar, B (author)
Papadopoulos, S (author)
Park, J (author)
Park, S (author)
Park, S (author)
Pawitan, Y (author)
Peluso, D (author)
Pendyala, S (author)
Peng, J (author)
Perfetto, L (author)
Pirro, S (author)
Plevritis, S (author)
Politi, R (author)
Poon, H (author)
Porta, E (author)
Prellner, I (author)
Preuer, K (author)
Pujana, MA (author)
Ramnarine, R (author)
Reid, JE (author)
Reyal, F (author)
Richardson, S (author)
Ricketts, C (author)
Rieswijk, L (author)
Rocha, M (author)
Rodriguez-Gonzalvez, C (author)
Roell, K (author)
Rotroff, D (author)
de Ruiter, JR (author)
Rukawa, P (author)
Sadacca, B (author)
Safikhani, Z (author)
Safitri, F (author)
Sales-Pardo, M (author)
Sauer, S (author)
Schlichting, M (author)
Seoane, JA (author)
Serra, J (author)
Shang, MMKarolinska Institutet (author)
Sharma, A (author)
Sharma, H (author)
Shen, Y (author)
Shiga, M (author)
Shin, M (author)
Shkedy, Z (author)
Shopsowitz, K (author)
Sinai, S (author)
Skola, D (author)
Smirnov, P (author)
Soerensen, IF (author)
Soerensen, P (author)
Song, JH (author)
Song, SO (author)
Soufan, O (author)
Spitzmueller, A (author)
Steipe, B (author)
Suphavilai, C (author)
Tamayo, SP (author)
Tamborero, DKarolinska Institutet (author)
Tang, J (author)
Tanoli, ZUR (author)
Tarres-Deulofeu, M (author)
Tegner, JKarolinska Institutet (author)
Thommesen, L (author)
Tonekaboni, SAM (author)
Tran, H (author)
De Troyer, E (author)
Truong, A (author)
Tsunoda, T (author)
Turu, G (author)
Tzeng, GY (author)
Verbeke, L (author)
Videla, S (author)
Vis, D (author)
Voronkov, A (author)
Votis, K (author)
Wang, A (author)
Wang, HQH (author)
Wang, PW (author)
Wang, S (author)
Wang, W (author)
Wang, XC (author)
Wang, X (author)
Wennerberg, K (author)
Wernisch, L (author)
Wessels, L (author)
van Westen, GJP (author)
Westerman, BA (author)
White, SR (author)
Willighagen, E (author)
Wurdinger, T (author)
Xie, L (author)
Xie, SL (author)
Xu, H (author)
Yadav, B (author)
Yau, C (author)
Yeerna, H (author)
Yin, JW (author)
Yu, M (author)
Yu, M (author)
Yun, SJ (author)
Zakharov, A (author)
Zamichos, A (author)
Zanin, M (author)
Zeng, L (author)
Zenil, H (author)
Zhang, F (author)
Zhang, PY (author)
Zhang, W (author)
Zhao, HY (author)
Zhao, L (author)
Zheng, WJ (author)
Zoufir, A (author)
Zucknick, M (author)
Karolinska Institutet (creator_code:org_t)

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In:Nature communications: Springer Science and Business Media LLC10:1, s. 2674-2041-1723

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By the author/editor: Menden, MP; Wang, D; Mason, MJ; Szalai, B; Bulusu, KC; Guan, YF; show more...; Yu, T; Kang, J; Jeon, M; Wolfinger, R; Nguyen, T; Zaslavskiy, M; Jang, IS; Ghazoui, Z; Ahsen, ME; Vogel, R; Neto, EC; Norman, T; Tang, EKY; Garnett, MJ; Di Veroli, GY; Fawell, S; Stolovitzky, G; Guinney, J; Dry, JR; Saez-Rodriguez, ...; Abante, J; Abecassis, BS; Aben, N; Aghamirzaie, D; Aittokallio, T; Akhtari, FS; Al-lazikani, B; Alam, T; Allam, A; Allen, C; de Almeida, MP; Altarawy, D; Alves, V; Amadoz, A; Anchang, B; Antolin, AA; Ash, JR; Aznar, VR; Ba-alawi, W; Bagheri, M; Bajic, V; Ball, G; Ballester, PJ; Baptista, D; Bare, C; Bateson, M; Bender, A; Bertrand, D; Wijayawardena, B; Boroevich, KA; Bosdriesz, E; Bougouffa, S; Bounova, G; Brouwer, T; Bryant, B; Calaza, M; Calderone, A; Calza, S; Capuzzi, S; Carbonell-Caball ...; Carlin, D; Carter, H; Castagnoli, L; Celebi, R; Cesareni, G; Chang, H; Chen, GC; Chen, HR; Chen, HY; Cheng, LJ; Chernomoretz, A; Chicco, D; Cho, KH; Cho, S; Choi, D; Choi, J; Choi, K; Choi, M; De Cock, M; Coker, E; Cortes-Ciriano, ...; Cserzo, M; Cubuk, C; Curtis, C; Van Daele, D; Dang, CC; Dijkstra, T; Dopazo, J; Draghici, S; Drosou, A; Dumontier, M; Ehrhart, F; Eid, FE; ElHefnawi, M; Elmarakeby, H; van Engelen, B; Engin, HB; de Esch, I; Evelo, C; Falcao, AO; Farag, S; Fernandez-Lozano ...; Fisch, K; Flobak, A; Fornari, C; Foroushani, ABK; Fotso, DC; Fourches, D; Friend, S; Frigessi, A; Gao, F; Gao, XT; Gerold, JM; 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, LY; Heath, LS; Hellton, KH; Helmer-Citterich ...; Hidalgo, MR; Hidru, D; Hill, SM; Hochreiter, S; Hong, S; Hovig, E; Hsueh, YC; Hu, ZY; Huang, JK; Huang, RS; Hunyady, L; Hwang, J; Hwang, TH; Hwang, W; Hwang, Y; Isayev, O; Walk, OBD; Jack, J; Jahandideh, S; Ji, JD; Jo, Y; Kamola, PJ; Kanev, GK; Karacosta, L; Karimi, M; Kaski, S; Kazanov, M; Khamis, AM; Khan, SA; Kiani, NA; Kim, A; Kim, J; Kim, K; Kim, S; Kim, Y; Kirk, PDW; Kitano, H; Klambauer, G; Knowles, D; Ko, M; Kohn-Luque, A; Kooistra, AJ; Kuenemann, MA; Kuiper, M; Kurz, C; Kwon, M; van Laarhoven, T; Laegreid, A; Lederer, S; Lee, H; Lee, J; Lee, YW; Leppaho, E; Lewis, R; Li, J; Li, L; Liley, J; Lim, WK; Lin, C; Liu, YY; Lopez, Y; Low, J; Lysenko, A; Machado, D; Madhukar, N; De Maeyer, D; Malpartida, AB; Mamitsuka, H; Marabita, F; Marchal, K; Marttinen, P; Mason, D; Mazaheri, A; Mehmood, A; Mehreen, A; Michaut, M; Miller, RA; Mitsopoulos, C; Modos, D; Van Moerbeke, M; Moo, K; Motsinger-Reif, ...; Movva, R; Muraru, S; Muratov, E; Mushthofa, M; Nagarajan, N; Nakken, S; Nath, A; Neuvial, P; Newton, R; Ning, Z; De Niz, C; Oliva, B; Olsen, C; Palmeri, A; Panesar, B; Papadopoulos, S; Park, J; 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, MA; Ramnarine, R; Reid, JE; Reyal, F; Richardson, S; Ricketts, C; Rieswijk, L; Rocha, M; Rodriguez-Gonzal ...; Roell, K; Rotroff, D; de Ruiter, JR; Rukawa, P; Sadacca, B; Safikhani, Z; Safitri, F; Sales-Pardo, M; Sauer, S; Schlichting, M; Seoane, JA; Serra, J; Shang, MM; Sharma, A; Sharma, H; Shen, Y; Shiga, M; Shin, M; Shkedy, Z; Shopsowitz, K; Sinai, S; Skola, D; Smirnov, P; Soerensen, IF; Soerensen, P; Song, JH; Song, SO; Soufan, O; Spitzmueller, A; Steipe, B; Suphavilai, C; Tamayo, SP; Tamborero, D; Tang, J; Tanoli, ZUR; Tarres-Deulofeu, ...; Tegner, J; Thommesen, L; Tonekaboni, SAM; Tran, H; De Troyer, E; Truong, A; Tsunoda, T; Turu, G; Tzeng, GY; Verbeke, L; Videla, S; Vis, D; Voronkov, A; Votis, K; Wang, A; Wang, HQH; Wang, PW; Wang, S; Wang, W; Wang, XC; Wang, X; Wennerberg, K; Wernisch, L; Wessels, L; van Westen, GJP; Westerman, BA; White, SR; Willighagen, E; Wurdinger, T; Xie, L; Xie, SL; Xu, H; Yadav, B; Yau, C; Yeerna, H; Yin, JW; Yu, M; Yun, SJ; Zakharov, A; Zamichos, A; Zanin, M; Zeng, L; Zenil, H; Zhang, F; Zhang, PY; Zhang, W; Zhao, HY; Zhao, L; Zheng, WJ; Zoufir, A; Zucknick, M; show less...

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