DNA repair is one of the most critical cellular functions, and deficiencies in repair have been related to increased susceptibility to genetic disease, chromosomal abnormalities, and cancer. Custom cDNA microarrays that contain genes involved in various DNA repair pathways as well as genes involved stress/damage response, cell cycle control and various repair-related functions have been developed to investigate cellular response to low dose ionizing radiation. Our approach to microarray analyses incorporates several features designed to improve and optimize the information content from all genes on smaller arrays. For image capture we take advantage of a adaptable wide field fluorescence imaging system, which allows us to image multiple dyes in the same hybridization, including DAPI to locate the spotted DNA. Image processing and analysis software were validated using ground-truth dilution studies. We have also conducted validation studies that demonstrate our ability to detect transcript ratio differences of less than 2 fold with strong signal specificity and sensitivity. These methodologies have been applied to biological samples to investigate baseline differences among normal tissue, and to investigate the effects of ionizing radiation on various cell lines and tissues.
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