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Optimization of DOP-PCR amplification of DNA for high-resolution comparative genomic hybridization analysis
J Larsen1, A M Ottesen, C Lundsteen
1Finsen Laboratory, Finsen Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark. jacob.larsen@finsenlab.dk
Background:
Whole-genome amplification of minute samples of DNA for the use in comparative genomic hybridization (CGH) analysis has found widespread use, but the method has not been well validated.
Methods:
Four protocols for degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and fluorescence labeling were applied to test DNA from normal and K-562 cells. The DNA products were used for CGH analysis.
Results:
The DOP-PCR-amplified DNA from each protocol produced hybridizations with different qualities. These could be seen primarily as differences in background staining and signal-to-noise ratios, but also as characteristic deviations of normal/normal hybridizations. One DOP-PCR-protocol was further investigated. We observed concordance between CGH results using unamplified and DOP-PCR-amplified DNA. An example of an analysis of an invasive carcinoma of the breast supports the practical value of this approach.
Conclusions:
DOP-PCR-amplified DNA is applicable for high- resolution CGH, the results being similar to those of CGH using unamplified DNA.