Algorithms ; Alu Elements ; Base Sequence ; DNA/pharmacology* ; DNA Probes/chemistry ; Female ; Humans ; Male ; Molecular Sequence Data ; Nucleic Acid Hybridization/drug effects* ; Nucleic Acid Hybridization/methods* ; Oligonucleotide Array Sequence Analysis/methods* ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Signal Processing, Computer-Assisted
Keywords
Cot-1 DNA ; Microarray-CGH ; sequence similarity ; Alu repetitive elements
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 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.