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

Autor: Menden M, Wang D, Mason M, Szalai B, Bulusu K, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang I, Ghazoui Z, Ahsen M, Vogel R, Neto E, Norman T, Tang E, Garnett M, Di Veroli G, Fawell S, Stolovitzky G, Guinney J, Dry J, Saez-Rodriguez J, Abante J, Abecassis B, Aben N, Aghamirzaie D, Aittokallio T, Akhtari F, Al-lazikani B, Alam T, Allam A, Allen C, de Almeida M, Altarawy D, Alves V, Amadoz A, Anchang B, Antolin A, Ash J, Aznar V, Ba-alawi W, Bagheri M, Bajic V, Ball G, Ballester P, Baptista D, Bare C, Bateson M, Bender A, Bertrand D, Wijayawardena B, Boroevich K, 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, Cheng L, Chernomoretz A, Chicco D, Cho K, Cho S, Choi D, Choi J, Choi K, Choi M, De Cock M, Coker E, Cortes-Ciriano I, Cserzo M, Cubuk C, Curtis C, Van Daele D, Dang C, Dijkstra T, Dopazo J, Draghici S, Drosou A, Dumontier M, Ehrhart F, Eid F, ElHefnawi M, Elmarakeby H, van Engelen B, Engin H, de Esch I, Evelo C, Falcao A, Farag S, Fernandez-Lozano C, Fisch K, Flobak A, Fornari C, Foroushani A, Fotso D, Fourches D, Friend S, Frigessi A, Gao F, Gao X, Gerold J, 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, Hellton K, Helmer-Citterich M, Hidalgo M, Hidru D, Hill S, Hochreiter S, Hong S, Hovig E, Hsueh Y, Hu Z, Huang J, Huang R, Hunyady L, Hwang J, Hwang T, Hwang W, Hwang Y, Isayev O, Walk O, Jack J, Jahandideh S, Ji J, Jo Y, Kamola P, Kanev G, Karacosta L, Karimi M, Kaski S, Kazanov M, Khamis A, Khan S, Kiani N, Kim A, Kim J, Kim K, Kim S, Kim Y, Kirk P, Kitano H, Klambauer G, Knowles D, Ko M, Kohn-Luque A, Kooistra A, Kuenemann M, Kuiper M, Kurz C, Kwon M, van Laarhoven T, Laegreid A, Lederer S, Lee H, Lee J, Lee Y, Leppaho E, Lewis R, Li J, Li L, Liley J, Lim W, Lin C, Liu Y, Lopez Y, Low J, Lysenko A, Machado D, Madhukar N, De Maeyer D, Malpartida A, Mamitsuka H, Marabita F, Marchal K, Marttinen P, Mason D, Mazaheri A, Mehmood A, Mehreen A, Michaut M, Miller R, Mitsopoulos C, Modos D, Van Moerbeke M, 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, 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 M, Ramnarine R, Reid J, Reyal F, Richardson S, Ricketts C, Rieswijk L, Rocha M, Rodriguez-Gonzalvez C, Roell K, Rotroff D, de Ruiter J, Rukawa P, Sadacca B, Safikhani Z, Safitri F, Sales-Pardo M, Sauer S, Schlichting M, Seoane J, Serra J, Shang M, Sharma A, Sharma H, Shen Y, Shiga M, Shin M, Shkedy Z, Shopsowitz K, Sinai S, Skola D, Smirnov P, Soerensen I, Soerensen P, Song J, Song S, Soufan O, Spitzmueller A, Steipe B, Suphavilai C, Tamayo S, Tamborero D, Tang J, Tanoli Z, Tarres-Deulofeu M, Tegner J, Thommesen L, Tonekaboni S, Tran H, De Troyer E, Truong A, Tsunoda T, Turu G, Tzeng G, Verbeke L, Videla S, Vis D, Voronkov A, Votis K, Wang A, Wang H, Wang P, Wang S, Wang W, Wang X, Wennerberg K, Wernisch L, Wessels L, van Westen G, Westerman B, White S, Willighagen E, Wurdinger T, Xie L, Xie S, Xu H, Yadav B, Yau C, Yeerna H, Yin J, Yu M, Yun S, Zakharov A, Zamichos A, Zanin M, Zeng L, Zenil H, Zhang F, Zhang P, Zhang W, Zhao H, Zhao L, Zheng W, Zoufir A, Zucknick M, AstraZeneca-Sanger Drug Combinatio

Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-17 (2019)
Nature Communications
Nature Communications, 10, 2674
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Nature Communications, 10, pp. 1-17
Nature Communications 10, 2674 (2019). doi:10.1038/s41467-019-09799-2
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Nature communications, 10 (1
AstraZeneca-Sanger Drug Combination DREAM Consortium 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
Nature Communications, 10:2674. Nature Publishing Group
NATURE COMMUNICATIONS
Nature Communications, 10, 1-17
Nature communications, vol 10, iss 1
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, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang, I S, Ghazoui, Z, Ahsen, M E, Vogel, R, Neto, E C, Norman, T, Tang, E K Y, Garnett, M J, Veroli, G Y D, Fawell, S, Stolovitzky, G, Guinney, J, Dry, J R & Saez-Rodriguez, J 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
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Nature Communications, 10(1):2674. Nature Publishing Group
Recercat. Dipósit de la Recerca de Catalunya

PubMed: 31209238
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 a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1827ac4799243e82b5025526f2e5a77a
http://link.springer.com/article/10.1038/s41467-019-09799-2

Identifying individual risk rare variants using protein structure guided local tests (POINT)

Autor: Kuenemann, M.A., Wu, M.C., Buse, J.B., Rotroff, D.M., Chang, S.-M., West, R.M., Tzeng, J.-Y., Lu, W., Fourches, D., Wagner, M.J., Motsinger-Reif, A.A.

Rare variants are of increasing interest to genetic association studies because of their etiological contributions to human complex diseases. Due to the rarity of the mutant events, rare variants are routinely analyzed on an aggregate level. While ag

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::76e665c43e77962a87c041dc0ee4516c

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia

Autor: Legge, S. E., Hamshere, M. L., Ripke, S., Pardinas, A. F., Goldstein, J. I., Rees, E., Richards, A. L., Leonenko, G., Jorskog, L. F., Jarskog, L. F., Hilliard, C., Alfirevic, A., Duncan, L., Fourches, D., Huang, H., Lek, M., Neale, B. M., Shianna, K., Szatkiewicz, J. P., Tropsha, A., van den Oord, E. J. C. G., Cascorbi, I., Dettling, M., Gazit, E., Goff, D. C., Holden, A. L., Kelly, D. L., Malhotra, A. K, Nielsen, J., Pirmohamed, M., Rujescu, D., Werge, T., Levy, D. L., Josiassen, R. C., Kennedy, J. L., Lieberman, J. A., Daly, M. J., Sullivan, P. F., Chambert, K. D., Collier, D. A., Genovese, G., Giegling, I., Holmans, P., Jonasdottir, A., Kirov, G., McCarroll, S. A., MacCabe, J. H., Mantripragada, K, Moran, J. L., Stefansson, H., Owen, M. J., O'Donovan, M. C., Walters, J.T. R, Clozapine-Induced Agranulocytosis Consortium

Publikováno v: Molecular Psychiatry
Legge, S E, Hamshere, M L, Ripke, S, Pardinas, A F, Goldstein, J I, Rees, E, Richards, A L, Leonenko, G, Jorskog, L F, Chambert, K D, Collier, D A, Genovese, G, Giegling, I, Holmans, P, Jonasdottir, A, Kirov, G, McCarroll, S A, MacCabe, J H, Mantripragada, K, Moran, J L, Neale, B M, Stefansson, H, Rujescu, D, Daly, M J, Sullivan, P F, Owen, M J, O'Donovan, M C, Walters, J T R 2016, ' Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia ', Molecular Psychiatry, vol. 22, pp. 1502–1508 . https://doi.org/10.1038/mp.2016.97
Legge, S E, Hamshere, M L, Ripke, S, Pardinas, A F, Goldstein, J I, Rees, E, Richards, A L, Leonenko, G, Jorskog, L F, Chambert, K D, Collier, D A, Genovese, G, Giegling, I, Holmans, P, Jonasdottir, A, Kirov, G, McCarroll, S A, MacCabe, J H, Mantripragada, K, Moran, J L, Neale, B M, Stefansson, H, Rujescu, D, Daly, M J, Sullivan, P F, Owen, M J, O'Donovan, M C, Walters, J T R 2018, ' Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia ', Molecular Psychiatry, vol. 23, no. 1, pp. 162-163 . https://doi.org/10.1038/mp.2017.214

The antipsychotic clozapine is uniquely effective in the management of schizophrenia; however, its use is limited by its potential to induce agranulocytosis. The causes of this, and of its precursor neutropenia, are largely unknown, although genetic

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::54d65254bff1e0d97dcd2fc74aa0a836

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