title: NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes.
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 NotI clone microarrays and genomic subtraction, because NotI 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 NotI flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A NotI-CODE procedure can be used to prepare NotI 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 NotI microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. NotI microarrays offer a powerful tool with which to study carcinogenesis.
authors.affiliation: Microbiology and Tumor Biology Center, Karolinska Institute, 171 77 Stockholm, Sweden.
authors.forename: Jingfeng
authors.initials: J
authors.lastname: Li
authors.forename: Alexei
authors.initials: A
authors.lastname: Protopopov
authors.forename: Fuli
authors.initials: F
authors.lastname: Wang
authors.forename: Vera
authors.initials: V
authors.lastname: Senchenko
authors.forename: Valentin
authors.initials: V
authors.lastname: Petushkov
authors.forename: Olga
authors.initials: O
authors.lastname: Vorontsova
authors.forename: Lev
authors.initials: L
authors.lastname: Petrenko
authors.forename: Veronika
authors.initials: V
authors.lastname: Zabarovska
authors.forename: Olga
authors.initials: O
authors.lastname: Muravenko
authors.forename: Eleonora
authors.initials: E
authors.lastname: Braga
authors.forename: Lev
authors.initials: L
authors.lastname: Kisselev
authors.forename: Michael I
authors.initials: MI
authors.lastname: Lerman
authors.forename: Vladimir
authors.initials: V
authors.lastname: Kashuba
authors.forename: George
authors.initials: G
authors.lastname: Klein
authors.forename: Ingemar
authors.initials: I
authors.lastname: Ernberg
authors.forename: Claes
authors.initials: C
authors.lastname: Wahlestedt
authors.forename: Eugene R
authors.initials: ER
authors.lastname: Zabarovsky
mesh_terms: D000818:Animals; D002292:Carcinoma, Renal Cell / Q000235:genetics*; D018288:Carcinoma, Small Cell / Q000235:genetics*; D002872:Chromosome Deletion; D002893:Chromosomes, Human, Pair 3; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000032:analysis*; D015252:Deoxyribonucleases, Type II Site-Specific; D018628:Gene Dosage; D005820:Genetic Testing; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics*; D008175:Lung Neoplasms / Q000235:genetics*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D004273:DNA, Neoplasm; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases