Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on microarray-CGH

Seung Hui Kang, Chan Hee Park, Hei Cheul Jeung, Ki Yeol Kim, Sun Young Rha, Hyun Cheol Chung

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

In array-CGH, various factors may act as variables influencing the result of experiments. Among them, Cot-1 DNA, which has been used as a repetitive sequence-blocking agent, may become an artifact-inducing factor in BAC array-CGH. To identify the effect of Cot-1 DNA on Microarray-CGH experiments, Cot-1 DNA was labeled directly and Microarray-CGH experiments were performed. The results confirmed that probes which hybridized more completely with Cot-1 DNA had a higher sequence similarity to the Alu element. Further, in the sex-mismatched Microarray-CGH experiments, the variation and intensity in the fluorescent signal were reduced in the high intensity probe group in which probes were better hybridized with C ot-1 DNA. Otherwise, those of the low intensity probe group showed no alterations regardless of Cot-1 DNA. These results confirmed by in silico methods that Cot-1 DNA could block repetitive sequences in gDNA and probes. In addition, it was confirmed biologically that the blocking effect of Cot-1 DNA could be presented via its repetitive sequences, especially Alu elements. Thus, in contrast to BAC-array CGH, the use of C ot-1 DNA is advantageous in controlling experimental variation in Microarray-CGH.

Original languageEnglish
Pages (from-to)901-908
Number of pages8
JournalInternational journal of molecular medicine
Volume19
Issue number6
Publication statusPublished - 2007 Jun 1

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Oligonucleotide Array Sequence Analysis
Computer Simulation
DNA
Nucleic Acid Repetitive Sequences
Alu Elements
Artifacts

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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title = "Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on microarray-CGH",
abstract = "In array-CGH, various factors may act as variables influencing the result of experiments. Among them, Cot-1 DNA, which has been used as a repetitive sequence-blocking agent, may become an artifact-inducing factor in BAC array-CGH. To identify the effect of Cot-1 DNA on Microarray-CGH experiments, Cot-1 DNA was labeled directly and Microarray-CGH experiments were performed. The results confirmed that probes which hybridized more completely with Cot-1 DNA had a higher sequence similarity to the Alu element. Further, in the sex-mismatched Microarray-CGH experiments, the variation and intensity in the fluorescent signal were reduced in the high intensity probe group in which probes were better hybridized with C ot-1 DNA. Otherwise, those of the low intensity probe group showed no alterations regardless of Cot-1 DNA. These results confirmed by in silico methods that Cot-1 DNA could block repetitive sequences in gDNA and probes. In addition, it was confirmed biologically that the blocking effect of Cot-1 DNA could be presented via its repetitive sequences, especially Alu elements. Thus, in contrast to BAC-array CGH, the use of C ot-1 DNA is advantageous in controlling experimental variation in Microarray-CGH.",
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Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on microarray-CGH. / Kang, Seung Hui; Park, Chan Hee; Jeung, Hei Cheul; Kim, Ki Yeol; Rha, Sun Young; Chung, Hyun Cheol.

In: International journal of molecular medicine, Vol. 19, No. 6, 01.06.2007, p. 901-908.

Research output: Contribution to journalArticle

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AU - Chung, Hyun Cheol

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