Community assessment of cancer drug combination screens identifies strategies for synergy prediction

Menden, M. P.; Wang, D.; Guan, Y.; Mason, M.; Szalai, B.; Bulusu, K. C.; Yu, T.; Kang, J.; Jeon, M.; Wolfinger, R.; Nguyen, T.; Zaslavskiy, M.; AstraZeneca-Sanger Drug Combination DREAM Consorti,; Jang, I. S.; Ghazoui, Z.; Ahsen, M. E.; Vogel, R.; Chaibub Neto, E.; Norman, T.; Tang, E. K.; Garnett, M. J.; Di Veroli, G.; Fawell, S.; Stolovitzky, G.; Guinney, J.; Dry, J. R.; Saez-Rodriguez, J.

doi:10.1101/200451

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bioRxiv · 10.1101/200451

Community assessment of cancer drug combination screens identifies strategies for synergy prediction

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Abstract

The effectiveness of most cancer targeted therapies is short lived since tumors evolve and develop resistance. Combinations of drugs offer the potential to overcome resistance, however the number of possible combinations is vast necessitating data-driven approaches to find optimal treatments tailored to a patients tumor. AstraZeneca carried out 11,576 experiments on 910 drug combinations across 85 cancer cell lines, recapitulating in vivo response profiles. These data, the largest openly available screen, were hosted by DREAM alongside deep molecular characterization from the Sanger Institute for a Challenge to computationally predict synergistic drug pairs and associated biomarkers. 160 teams participated to provide the most comprehensive methodological development and subsequent benchmarking to date. Winning methods incorporated prior knowledge of putative drug target interactions. For >60% of drug combinations synergy was reproducibly predicted with an accuracy matching biological replicate experiments, however 20% of drug combinations were poorly predicted by all methods. Genomic rationale for synergy predictions were identified, including antagonism unique to combined PIK3CB/D inhibition with the ADAM17 inhibitor where synergy is seen with other PI3K pathway inhibitors. All data, methods and code are freely available as a resource to the community.

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Menden, M. P., Wang, D., Guan, Y., Mason, M., Szalai, B., Bulusu, K. C., Yu, T., Kang, J., Jeon, M., Wolfinger, R., Nguyen, T., Zaslavskiy, M., AstraZeneca-Sanger Drug Combination DREAM Consorti,, Jang, I. S., Ghazoui, Z., Ahsen, M. E., Vogel, R., Chaibub Neto, E., Norman, T., Tang, E. K., Garnett, M. J., Di Veroli, G., Fawell, S., Stolovitzky, G., Guinney, J., Dry, J. R., Saez-Rodriguez, J.. 2017-10-09. Community assessment of cancer drug combination screens identifies strategies for synergy prediction. https://doi.org/10.1101/200451

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