Prostate cancer (PC) is the most common cancer and the third leading cause of cancer death in men worldwide. Despite its high incidence and mortality, the likelihood of a cure is low for late-stages of PC. There is an unmet need for more effective agents for treating PC. Here, we present a drug repositioning system, GenoPredict, for finding new drug candidates for treating PC. GenoPredict leverages upon a large amount of disease genomics data and a large-scale drug treatment knowledge base (TreatKB) that we recently constructed. We constructed a genetic disease network (GDN) that comprised of 882 nodes and 200,758 edges. We applied a network-based ranking algorithm to find diseases from GDN that are genetically related to PC. We developed a drug prioritization algorithm to reposition drugs from PC-related diseases to treat PC. When evaluated in a \emph{de-novo} prediction setting using 27 FDA-approved PC drugs, GenoPredict found 25 of 27 FDA-approved PC drugs and ranked them highly (recall: 0.925, mean ranking: 27.3%, median ranking: 15.6%). When compared to PREDICT, a comprehensive drug repositioning systems, in novel predictions, GenoPredict performed better than PREDICT across two evaluation datasets. GenoPredict achieved a mean average precision (MAP) of 0.447 when evaluated with 172 PC drugs extracted from 172,888 clinical trial reports, representing a 164.5% improvement as compared to a MAP of 0.169 for PREDICT. When evaluated with 72 PC drugs extracted from 43,811 ongoing clinical trial reports, GenoPredict achieved a MAP of 0.278, representing a 231.1% improvement as compared to a MAP of 0.084 for PREDICT. The data is publicly available at: http://nlp.case.edu/public/data/PC_GenoPredict and http://nlp.case.edu/public/data/treatKB.

Learning Objective 1: To develop data-driven drug repostioning approach to identify drug candidates for prostate cancer.


Rong Xu (Presenter)
Case Western Reserve University

QuanQiu Wang, ThinTek Inc

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