Swapnil Potdar1, Aleksandr Ianevski1,2, John-Patrick Mpindi1, Dmitrii Bychkov1, Clément Fiere1, Philipp Ianevski1, Bhagwan Yadav1, Krister Wennerberg1,3, Tero Aittokallio1,2,4, Olli Kallioniemi1,5, Jani Saarela1, Päivi Östling1,5. 1. Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland. 2. Department of Computer Science, Helsinki Institute for Information Technology (HIIT), Aalto University, FI-02150 Espoo, Finland. 3. Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen N, Denmark. 4. Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland. 5. Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden.
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.
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.
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