Contour Area Filtering of Restriction Landmark Genomic Scanning 2-Dimensional Electrophoresis Profiles

Restriction Landmark Genome Scanning (RLGS) is a 2-dimensional gel electrophoresis technique for detecting DNA molecular changes that occur within restriction fragments. A typical RLGS profile consists of an electrophoretogram or a phosphor image of approximately 2500 spots. The profiles are quantitative with spot intensities reflective of the copy number of the DNA fragment resulting in a variety of spot intensities, particularly when applied to cancer genomes. The background intensity can vary widely across the image caused both by variation in spot density and by the physical laboratory process of creating a gel. We describe an algorithm based on contour areas for distinguishing between background and foreground in an RLGS profile. We present experimental results which show that contour area filtering is a quick, efficient method for separating background from foreground with extremely high accuracy.