Real time PCR - European Pharmaceutical Review

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HIGH CONTENT SCREENING ISSUE 2009 Open source data management in High Content Screening technology Karol Kozak, Head of Data Handling Facility, Dr Gabor Csucs, Head of the High-thorughput/high-content screening facility, LMC-RISC, ETH Zurich, Switzerland and Andrzej Firkowski, Professor of Chemical Technology at the Technical University of Radom, Director of the Faculty of Materials Science and Technology and a member of the Advisory Board, Noster-IT, Dresden, Germany Screening for biological or chemical compounds with a favourable biological effect is at the core of the modern drug discovery process. High Content Screening (HCS) is increasingly used for the automated evaluation of spatio-temporally resolved multiple biochemical and morphological parameters in cellular systems. HCS data include comprehensive information about the bioactive molecules, the targeted genes, and images as well as their extracted data matrices after acquisition. This paper will describe an open-source data management solution for integrating, sharing, analysis and processing HCS data using a distributed service-oriented architecture. Fluorescent microscopy has enabled multifaceted insights into the detail and complexity of cellular structures and their functions for well over two decades. As an essential prerequisite for a systematic phenotypical analysis of gene functions in cells at a genome-wide scale, the throughput of microscopy had to be improved through automation. HCS is defined as multiplexed functional screening based on imaging multiple targets in the physiologic context of intact cells by extraction of multicolour fluorescence information. Simultaneous staining in three or four colours allows the extraction of various parameters from each cell quantitatively as well as qualitatively such as intensity, size, distance or distribution (spatial resolution). The parameters might be referenced to each other, for example the use of nuclei staining to normalise other signals against cell number, or particular parameters might verify or exclude each other. An essential factor in the success of high content screening projects is the existence of algorithms and software that can reliably and automatically extract information from the masses of captured images. Typically, nuclei are identified and masked first. Then, areas around the nuclei are determined or the cell boundaries are searched to mask the cell shape. For popular HCS assays at the sub-cellular level such as cell cycle analysis (mitotic index), cytotoxicity, apoptosis, micronuclei detection, receptor internalisation, protein translocation (membrane to cytosol, cytosol to nucleus, and vice versa), co-localisation, cytoskeletal arrangements, or morphological analysis at the cellular level such as neurite outgrowth, cell spreading, cell motility, colony formation, or tube formation, ready-to-use scripts are available and need only some fineadjustment for the particular cell line and/or conditions of the assay. Presently available analysis methodologies for large-scale RNAi (siRNA) data sets typically rely on ranking data and are based on single image descriptor (feature) or significance value 1,10,12 . However, identifying patterns of image descriptors and grouping genes into classes based on multiparamteric 16 www.europeanpharmaceuticalreview.com
© 2008 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. What does Productivity mean to you For many, choosing better leads, eliminating problem compounds early, understanding disease targets better or predicting human toxicity is the route to discovery productivity. Did you know, the Thermo Scientific Cellomics high content screening (HCS) platform is addressing these issues in laboratories around the world, every day Did you also know that based on an analysis of the literature, users of our platform generate 5 <strong>time</strong>s the number of peer reviewed publications compared to all the other HCS platforms put together. Learn more about how we can redefine your HCS productivity and take advantage of our special offer to receive either one HCS Reagent Kit or one Redistribution CryoRedi 2-pack, at half price, visit www.thermo.com/hcs Our complete HCS solution. Flexible, modular instrumentation Powerful, easy to use image analysis software Open standards data management HCS Reagent Kits and Redistribution cell lines Moving science forward
Page 1 and 2: TECHNOLOGY / KNOWLEDGE / INNOVATION
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