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GenomiPhi amplification of FFPE tissue DNA for array CGH

tuting approximately 2600 human BAC clones at 1-Mb resolution. A section of hybridization images from the BAC arrays is shown in Figure 4. The signal intensities from array features were quantitated to compare hybridization performance. The scatter plots of mean intensities from DOP-PCR and GenomiPhi amplifications showed hybridization characteristics to be similar between the two methods (Fig 5). Microarray hybridization data for mean intensities and background was compared between GenomiPhi and DOP-PCR to assess amplification performance between the two techniques. The results are summarized in Table 2.



amplifications. Right: Hybridization image from GenomiPhi amplifications. DOP-PCR and GenomiPhi amplifications showed hybridization characteristics to be similar between the two methods (Fig 5). Microarray hybridization data for mean intensities and background was compared between GenomiPhi and DOP-PCR to assess amplification performance between the two techniques. The results are summarized in Table 2.

The total signal from the arrays (5200 features, in duplicate) was similar between the two amplification methods. With GenomiPhi amplification products, nearly equivalent signal was seen from both the Cy3 and Cy5 dyes, indicating that DNA amplified with the Phi29 enzyme can be efficiently labeled and hybridized with both dyes. The mean signal intensities from DOP-PCR and GenomiPhi amplified samples were similar, with values averaged from both the Cy3 and Cy5 dyes of 315 and 381, respectively. The averaged signal-to-background ratios from DOP-PCR and GenomiPhi amplified DNA were 4.92 and 5.02, respectively. The BAC array hybridization results demonstrate that FFPE samples can be amplified with the GenomiPhi kit for array CGH profiling. Hybridization data from the low-density Constitutional Chip™ 1.0 BAC array (Spectral Genomics) w
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