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bioRxiv · 10.1101/048470

Assessment of pharmacogenomic agreement

Zhaleh Safikhani·Nehme El-Hachem·Rene Quevedo·Petr Smirnov·Anna Goldenberg·Nicolai Juul Birkbak·Christopher E Mason·Christos Hatzis·Leming Shi·Hugo JWL Aerts·John Quackenbush·Benjamin Haibe-Kains
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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 Cancer1 (GDSC) and Cancer Cell Line Encyclopedia2 (CCLE), were inconsistent3. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response4, seemingly contradicting our previous findings3. 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 consistent5. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings.

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Zhaleh Safikhani, Nehme El-Hachem, Rene Quevedo, Petr Smirnov, Anna Goldenberg, Nicolai Juul Birkbak, Christopher E Mason, Christos Hatzis, Leming Shi, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains. 2016-04-13. Assessment of pharmacogenomic agreement. https://doi.org/10.1101/048470

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