Assessment of pharmacogenomic agreement

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Assessment of pharmacogenomic agreement

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Title: Assessment of pharmacogenomic agreement
Author: Safikhani, Zhaleh; El-Hachem, Nehme; Quevedo, Rene; Smirnov, Petr; Goldenberg, Anna; Juul Birkbak, Nicolai; Mason, Christopher; Hatzis, Christos; Shi, Leming; Aerts, Hugo JWL; Quackenbush, John; Haibe-Kains, Benjamin

Note: Order does not necessarily reflect citation order of authors.

Citation: Safikhani, Z., N. El-Hachem, R. Quevedo, P. Smirnov, A. Goldenberg, N. Juul Birkbak, C. Mason, et al. 2016. “Assessment of pharmacogenomic agreement.” F1000Research 5 (1): 825. doi:10.12688/f1000research.8705.1. http://dx.doi.org/10.12688/f1000research.8705.1.
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Abstract: In 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), were inconsistent. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response, seemingly contradicting our previous findings. Reanalyzing the authors’ published methods and results, we found that their analysis failed to account for variability in the genomic data and more importantly compared different drug sensitivity measures from each study, which substantially deviate from our more stringent consistency assessment. Our comparison of the most updated genomic and pharmacological data from the GDSC and CCLE confirms our published findings that the measures of drug response reported by these two groups are not consistent. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings.
Published Version: doi:10.12688/f1000research.8705.1
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926729/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:27822178
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