Breeze: an integrated quality control and data analysis application for high-throughput drug screening

Abstract

Summary High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results. Availability and implementation The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0. Contact swapnil.potdar@helsinki.fi Supplementary information Supplementary data are available at Bioinformatics online.

High NRF2 Levels Correlate with Poor Prognosis in Colorectal Cancer Patients and with Sensitivity to the Kinase Inhibitor AT9283 In Vitro

“…Drug sensitivity and resistance testing (DSRT) [ 44 ] was performed on DLD1 NRF2 wild-type (WT) and GOF cell lines in collaboration with The FIMM High-Throughput Biomedicine Unit at the University of Helsinki (Helsinki, Finland). The compound library included 528 substances consisting of conventional chemotherapeutics and a broad range of targeted oncology compounds.…”

Identification of novel regulators of STAT3 activity

“…DSS, a quantitative drug sensitivity score, which is based on the area under the dose response curve, was used to measure drug efficacies [21,23]. The DSS values were calculated in the Breeze web-based application [24].…”

STRN-ALK rearranged pediatric malignant peritoneal mesothelioma – Functional testing of 527 cancer drugs in patient-derived cancer cells

“…Quantitative dose response curves for each drug were generated as previously described [15] . The drug efficacy was quantified with a modified area-under-the-curve measurement called drug sensitivity score (DSS), calculated and visualized as previously described [ 16 , 17 ]. For measuring the drug responses for ALK inhibitors in 3D culture conditions, the assay was carried out similarly, except PDCs or Mixed culture were seeded on ultra-low attachment 384-well round bottom cell culture plates (Corning) pre-plated with drugs in nine increasing concentrations.…”