A subtractive suppression hybridization (SSH) assay and uses thereof are described. In particular, methods of identifying and isolating nucleic acid sequences, which are unique for a certain cell, tissue or organism are provided, wherein said unique nucleid acid sequences are related to for example diseases genes. More specifically, SSH assays for unique genomic DNA sequences and improved SSH assays that are combined with 2D gel electrophoresis techniques are provided. The presented methods are particular useful for the identification of genes involved in the development of various diseases, including cancer, hypertension and diabetes as well as for monitoring animals and food, for example for infection agents and other contaminants.