The optimal design of clinical trials with potential biomarker effects: A novel computational approach

As a future trend of healthcare, personalized medicine tailors medical treatments to individual patients. It requires to identify a subset of patients with the best response to treatment. The subset can be defined by a biomarker (eg, expression of a gene) and its cutoff value. Topics on subset identification have received massive attention. There are over two million hits by keyword searches on Google Scholar. However, designing clinical trials that utilize the discovered uncertain subsets/biomarkers is not trivial and rarely discussed in the literature. This leads to a gap between research results and real-world drug development. To fill in this gap, we formulate the problem of clinical trial design into an optimization problem involving high-dimensional integration, and propose a novel computational solution based on Monte Carlo and smoothing methods. Our method utilizes the modern techniques of general purpose computing on graphics processing units for large-scale parallel computing. Compared to a published method in three-dimensional problems, our approach is more accurate and 133 times faster. This advantage increases when dimensionality increases. Our method is scalable to higher dimensional problems since the precision bound of our estimated study power is a finite number not affected by dimensionality. To design clinical trials incorporating the potential biomarkers, users can use our software "DesignCTPB". This software can be found on Github and will be available as an R package on CRAN. Although our research is motivated by the design of clinical trials, the method can be used widely to solve other optimization problems involving high-dimensional integration.