Optimization of DOP-PCR amplification of DNA for high-resolution comparative genomic hybridization analysis.
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.
Larsen
J
J
Finsen Laboratory, Finsen Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark. jacob.larsen@finsenlab.dk
Ottesen
A M
AM
Lundsteen
C
C
Leffers
H
H
Larsen
J K
JK
D001943:Breast Neoplasms / Q000235:genetics; D017931:DNA Primers / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis; D006801:Humans; D007951:Leukemia, Myeloid / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques / Q000379:methods / Q000592:standards*; D009693:Nucleic Acid Hybridization / Q000235:genetics / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D014407:Tumor Cells, Cultured
D017931:DNA Primers; D004273:DNA, Neoplasm