RT Journal Article
SR Electronic
T1 Assessment of pharmacogenomic agreement
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 048470
DO 10.1101/048470
A1 Zhaleh Safikhani
A1 Nehme El-Hachem
A1 Rene Quevedo
A1 Petr Smirnov
A1 Anna Goldenberg
A1 Nicolai Juul Birkbak
A1 Christopher E. Mason
A1 Christos Hatzis
A1 Leming Shi
A1 Hugo JWL Aerts
A1 John Quackenbush
A1 Benjamin Haibe-Kains
YR 2016
UL http://biorxiv.org/content/early/2016/04/13/048470.abstract
AB 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.