PT - JOURNAL ARTICLE AU - Zhaleh Safikhani AU - Kelsie L. Thu AU - Jennifer Silvester AU - Petr Smirnov AU - Mathieu Lupien AU - Tak W. Mak AU - David Cescon AU - Benjamin Haibe-Kains TI - Gene isoforms as expression-based biomarkers predictive of drug response <em>in vitro</em> AID - 10.1101/160937 DP - 2017 Jan 01 TA - bioRxiv PG - 160937 4099 - http://biorxiv.org/content/early/2017/07/08/160937.short 4100 - http://biorxiv.org/content/early/2017/07/08/160937.full AB - Background One of the main challenges in precision medicine is the identification of molecular features associated to drug response to provide clinicians with tools to select the best therapy for each individual cancer patient. The recent adoption of next-generation sequencing technologies enables accurate profiling of not only gene expression but also alternatively-spliced transcripts in large-scale pharmacogenomic studies. Given that altered mRNA splicing has been shown to be prominent in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery.Methods To address the lack of reproducibility of drug sensitivity measurements across studies, we developed a meta-analytical framework combining the pharmacological data generated within the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC). Predictive models are fitted with CCLE RNA-seq data as predictor variables, controlled for tissue type, and combined GDSC and CCLE drug sensitivity values as dependent variables.Results We first validated the biomarkers identified from GDSC and CCLE using an existing pharmacogenomic dataset of 70 breast cancer cell lines. We further selected four drugs with the most promising biomarkers to test whether their predictive value is robust to change in pharmacological assay. We successfully validated 10 isoform-based biomarkers predictive of drug response in breast cancer, including TGFA-001 for the MEK tyrosine kinase inhibitor (TKI) AZD6244, DUOX-001 for the EGFR inhibitor erlotinib, and CPEB4-001 transcript expression associated with lack of sensitivity to paclitaxel.Conclusion The results of our meta-analysis of pharmacogenomic data suggest that isoforms represent a rich resource for biomarkers predictive of response to chemo- and targeted therapies. Our study also showed that the validation rate for this type of biomarkers is low (&lt;50%) for most drugs, supporting the requirements for independent datasets to identify reproducible predictors of response to anticancer drugs.