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

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  • dc.contributor.author Menden, Michael P.
  • dc.contributor.author AstraZeneca-Sanger Drug Combination DREAM Consortium
  • dc.contributor.author Saez-Rodriguez, Julio
  • dc.date.accessioned 2019-09-05T15:58:12Z
  • dc.date.available 2019-09-05T15:58:12Z
  • dc.date.issued 2019
  • dc.description.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.
  • dc.description.sponsorship We thank the Genomics of Drug Sensitivity in Cancer and COSMIC teams at the Wellcome Trust Sanger Institute for help with the preparation of the molecular data, Denes Turei for help with Omnipath, and Katjusa Koler for help with matching drug names across combination screens. We thank AstraZeneca for funding and provision of data to the DREAM Consortium to run the challenge, and funding from the European Union Horizon 2020 research (under grant agreement No 668858 PrECISE to J.S.R.), the Joint Research Center for Computational Biomedicine (which is partially funded by Bayer AG) to J.S.R., National Institute for Health Research (NIHR) Sheffield Biomedical Research Center, Premium Postdoctoral Fellowship Program of the Hungarian Academy of Sciences. M.G lab is supported by Wellcome Trust (102696 and 206194).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC1, Guan Y et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun. 2019;10(1):2674. DOI: 10.1038/s41467-019-09799-2
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-019-09799-2
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/42248
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nature Communications. 2019;10(1):2674
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/668858
  • dc.rights © The Author(s) 2019. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Cancer
  • dc.subject.keyword High-throughput screening
  • dc.subject.keyword Machine learning
  • dc.subject.keyword Statistical methods
  • dc.subject.keyword Systems biology
  • dc.title Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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