Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH.
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 Cot-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 Cot-1 DNA is advantageous in controlling experimental variation in Microarray-CGH.
Kang
Seung-Hui
SH
Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul 120-752, Korea.
Park
Chan Hee
CH
Jeung
Hei Cheul
HC
Kim
Ki-Yeol
KY
Rha
Sun Young
SY
Chung
Hyun Cheol
HC
D000465:Algorithms; D020087:Alu Elements; D001483:Base Sequence; D004247:DNA / Q000494:pharmacology*; D015342:DNA Probes / Q000737:chemistry; D005260:Female; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000187:drug effects* / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012815:Signal Processing, Computer-Assisted
D015342:DNA Probes; D004247:DNA