Abstract 828: gDR suite: an integrative solution for handling cell line drug response data

Abstract

Abstract Assessing the response of cancer cell lines to drugs and treatments that affect their growth is the cornerstone of drug discovery and development. On one hand, large screens are performed across many lines and drugs in a semi-automated manner. On the other hand, small-scale studies, for example focused on factors that contribute to sensitivity and resistance, are generally performed in labs with limited automation. Data from these complementary approaches are rarely handled in the same manner: commercial software are available for the former case, whereas experimentalists in the latter case often handle files manually and process data in spreadsheets. Here we propose a suite of computational tools that enable the processing, archiving, and visualization of drug response data from any experiment, thus ensuring reproducibility and implementation of the FAIR principles. The core of the gDR suite is a database designed to host drug response data from large screens, single-agent treatments, combination experiments, as well as data from complex experimental designs including ligand co-treatments or shRNA. Experimentalists can upload metadata files along with unprocessed output files from plate readers in an interactive web application built with R Shiny. Data normalization and quality control are performed by the software before the data is stored in the database. Data from commercial software or other databases can also be easily pushed into the database through a REST API. To fetch the processed data, we developed an R package as well as another R shiny-based web application. Both tools allow users to efficiently search the database, easily plot the data from the selected experiments, and perform basic analyses. Overall, the gDR suite is a modular software that provides an end-to-end solution for managing drug response data. At the conference, we will describe our implementation and demonstrate how to use the gDR suite. We hope that this tool will facilitate the handling of drug response data and thus contribute to the quality of published data. In addition, we hope that the community will contribute to the gDR suite by adding new functionalities for either importing, plotting, or analyzing the data. Citation Format: Marc Hafner, Arkadiusz Gladki, Jane Li, Eva Lin, Aaron Lun, Scott Martin, Natalia Potocka, Dariusz Scigocki, Steffan Vartanian, Jan Vogel, Allison Vuong. gDR suite: an integrative solution for handling cell line drug response data [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 828.