The analysis of DNA damage is also discussed as a tool for forensics. Bioimage informatics is a branch of bioinformatics that deals with informatics tools to support the analysis and numerical description of images in biological and biomedical studies. One goal is to develop a tailor-made therapy for each patient, which can be based on the automated processing of large image data sets and the classification of defined biomarker image patterns ( 14). Precision medicine uses biomarkers to stratify patients. The quantification of foci is considered as a tool for precision medicine. They are accompanied by the phosphorylation of the histone 2AX (H2AX), which can be detected as discrete spots, the so-called γH2AX focal points (foci), using immunofluorescence detection methods (e.g., fluorescence microscopy) ( 2, 11- 13). The detection and assessment of DNA damage like DNA double-strand breaks (DSBs) are of interest in clinical diagnostics, cancer research, radiation therapy, chemotherapy, forensics and life sciences ( 6- 10). Cells counteract DNA damage events by various repair mechanisms like non-homologous end joining (NHEJ), homologous recombination (HR) ( 2), mismatch repair and base or nucleotide excision repair ( 3- 5). DNA damage response (DDR) mechanisms signal the presence of DNA damage and exert their repair by often redundant pathways. ĭeoxyribonucleic acid (DNA) is exposed to several endogenous as well as exogenous factors that can profoundly change and damage its structure and function ( 1). Received: 01 March 2018 Accepted: 22 April 2019 Published. Keywords: Bioimage informatics DNA damage response (DDR) double-strand break (DSB) immunofluorescence microscopy open source software Programming languages, like Python, are discussed briefly. Software packages like CellProfiler and Icy enable to gain high-content information about DSB biomarkers. This review gives an overview of open source image processing software packages, including graphical user interfaces (GUIs) such as CellProfiler, Icy and ImageJ/Fiji. There are numerous software solutions for the analysis of foci. This includes, for example, pre-processing, transformation and presentation of the data in a less complex structure for further data analysis. This requires software tools that are suitable for the analysis of large complex data sets, even for users with limited experience in digital image processing. The quantification and characterization of foci ideally uses large cell numbers to achieve statistical validity. The correlation between the number of foci and the number of DSBs makes them a useful tool for quantification of DNA damage in precision medicine, forensics and cancer research. DSB biomarkers, like phosphorylated histone 2AX (γH2AX) and p53-binding protein 1 (53BP1), are detectable by immunofluorescence as either foci or distinct patterns in the vicinity of DSBs. DSBs initiate repair mechanisms by recruiting sensor proteins and mediators.
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