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

  1. Author:
    Li, J. F.
    Protopopov, A.
    Wang, F. L.
    Senchenko, V.
    Petushkov, V.
    Vorontsova, O.
    Petrenko, L.
    Zabarovska, V.
    Muravenko, O.
    Braga, E.
    Kisselev, L.
    Lerman, M. I.
    Kashuba, V.
    Klein, G.
    Ernberg, I.
    Wahlestedt, C.
    Zabarovsky, E. R.

  2. Author Address

    Karolinska Inst, Ctr Microbiol & Tumor Biol, S-17177 Stockholm, Sweden Karolinska Inst, Ctr Microbiol & Tumor Biol, S-17177 Stockholm, Sweden Karolinska Inst, Ctr Genomics & Bioinformat, S-17177 Stockholm, Sweden NCI, Immunobiol Lab, Frederick, MD 21702 USA State Res Ctr VNII Genet, Moscow 113545, Russia Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 117984, Russia Russian Acad Sci, Ctr Bioengn, Moscow 117984, Russia Zabarovsky ER Karolinska Inst, Ctr Microbiol & Tumor Biol, S-17177 Stockholm, Sweden
    1. Year: 2002
  2. Journal: Proceedings of the National Academy of Sciences of the United States of America
    1. 99
    2. 16
    3. Pages: 10724-10729
  4. Type of Article: Article
  1. Abstract:

    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.

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