Use of NotI microarrays in analysis of epigenetic and structural changes in epithelial tumor genomes by the example of human chromosome 3

A new comparative genome hybridization technology using NotI microarrays is described (Karolinska Institute International Patent WO02/086163). The method is based on comparative genome hybridization of NotI-enriched probes from tumor and normal genomic DNA with radically new NotI microarrays. A total of 181 NotI-binding loci of human chromosome 3 were assayed in 200 human malignant tissue samples from various organs: kidney, lung, breast, ovary, cervix, and prostate. The most significant portion (above 30%) of aberrations (deletions and methylation) were detected in NotI sites located in the MINT24, BHLHB2, RPL15, RARbeta1, ITGA9, RBSP3, VHL , and ZIC4 genes. This indicates that they may be associated with cancer development. Methylation of these genomic loci was confirmed by methylation-specific PCR and bisulfite sequencing. The results confirm that the proposed method can contribute to cancer genomics.