Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes

Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of Nod clone microarrays and genomic subtraction, because Not! recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to Nod flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Nod-CODE procedure can be used to prepare Nod representations (NRs) containing 0.1-0.5% of the total DNA. The NRs contain, on average, 10-fold less repetitive sequences than the whole human genome and can be used as probes for hybridization to Nod microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Nod microarrays offer a powerful tool with which to study carcinogenesis.