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Computer methods for visualization chromosome-specific DNA sequences in FISH images

A great number of interspersed repetitive sequences in chromosomes make it difficult to identify chromosomal material via fluorescence in situ hybridization (FISH). The traditional approach to solve this problem is chromosome in situ suppression hybridization (CISS-hybridization). Unfortunately, it is impossible to be performed or fails with chromosomes of many eukaryote species. The aim of this study was to consider the image enhance procedure [1] and the in silico method of chromosome specific signal visualization (method VISSIS) [2] as alternatives to CISS-hybridization. The effectiveness of approaches for identification of specific signals was estimated by signal-to-background ratio (SNR). The computer methods were applied to images of human chromosomes, obtained with FISH of the whole chromosome painting DNA probes. Results showed that effectiveness of image processing methods depends on ratio of short and line interspersed elements (SINEs/LINEs) in DNA probes. The closer chromosomes in ratio of SINEs/LINEs, the higher specific signal intensities and signal-to-background ratios could be achieved. This suggests that computer methods can be efficient only with application of DNA probes derived from chromosomes characterized with similar ratio of SINE and LINE contents.