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.