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

Jingfeng Li, Alexei Protopopov, Fuli Wang, Vera Senchenko, Valentin Petushkov, Olga Vorontsova, Lev Petrenko, Veronika Zabarovska, Olga Muravenko, Eleonora Braga, Lev Kisselev, Michael I. Lerman, Vladimir Kashuba, George Klein, Ingemar Ernberg, Claes R Wahlestedt, Eugene R. Zabarovsky

Research output: Contribution to journalArticle

51 Citations (Scopus)

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 Notl clone microarrays and genomic subtraction, because Notl 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 Notl flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Notl-CODE procedure can be used to prepare Notl 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 Notl microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Notl microarrays offer a powerful tool with which to study carcinogenesis.

Original languageEnglish
Pages (from-to)10724-10729
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume99
Issue number16
DOIs
StatePublished - Aug 1 2002
Externally publishedYes

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Methylation
CpG Islands
Genome
Organism Cloning
Carcinogenesis
Nucleic Acid Repetitive Sequences
Neoplasm Genes
Human Genome
Clone Cells
DNA
Genes

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes. / Li, Jingfeng; Protopopov, Alexei; Wang, Fuli; Senchenko, Vera; Petushkov, Valentin; Vorontsova, Olga; Petrenko, Lev; Zabarovska, Veronika; Muravenko, Olga; Braga, Eleonora; Kisselev, Lev; Lerman, Michael I.; Kashuba, Vladimir; Klein, George; Ernberg, Ingemar; Wahlestedt, Claes R; Zabarovsky, Eugene R.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 16, 01.08.2002, p. 10724-10729.

Research output: Contribution to journalArticle

Li, J, Protopopov, A, Wang, F, Senchenko, V, Petushkov, V, Vorontsova, O, Petrenko, L, Zabarovska, V, Muravenko, O, Braga, E, Kisselev, L, Lerman, MI, Kashuba, V, Klein, G, Ernberg, I, Wahlestedt, CR & Zabarovsky, ER 2002, 'Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes', Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 16, pp. 10724-10729. https://doi.org/10.1073/pnas.132271699
Li, Jingfeng ; Protopopov, Alexei ; Wang, Fuli ; Senchenko, Vera ; Petushkov, Valentin ; Vorontsova, Olga ; Petrenko, Lev ; Zabarovska, Veronika ; Muravenko, Olga ; Braga, Eleonora ; Kisselev, Lev ; Lerman, Michael I. ; Kashuba, Vladimir ; Klein, George ; Ernberg, Ingemar ; Wahlestedt, Claes R ; Zabarovsky, Eugene R. / Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes. In: Proceedings of the National Academy of Sciences of the United States of America. 2002 ; Vol. 99, No. 16. pp. 10724-10729.
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AU - Vorontsova, Olga

AU - Petrenko, Lev

AU - Zabarovska, Veronika

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AU - Braga, Eleonora

AU - Kisselev, Lev

AU - Lerman, Michael I.

AU - Kashuba, Vladimir

AU - Klein, George

AU - Ernberg, Ingemar

AU - Wahlestedt, Claes R

AU - Zabarovsky, Eugene R.

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N2 - Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of Notl clone microarrays and genomic subtraction, because Notl 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 Notl flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Notl-CODE procedure can be used to prepare Notl 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 Notl microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Notl microarrays offer a powerful tool with which to study carcinogenesis.

AB - Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of Notl clone microarrays and genomic subtraction, because Notl 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 Notl flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Notl-CODE procedure can be used to prepare Notl 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 Notl microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Notl microarrays offer a powerful tool with which to study carcinogenesis.

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