Because identical FFPE samples were amplified and labeled with Cy3 and Cy5 dyes, the log2 ratios from GenomiPhi amplified samples clustered close to the baseline level, i.e. 0 (data not shown). While no DNA copy-number changes were measured, previous data published using Phi29-based amplification has shown that GenomiPhi DNA Amplification Kit is highly sensitive in detecting monosomy and trisomy in array CGH (6, 7).
Our results showed that GenomiPhi DNA Amplification Kit can be used to amplify DNA extracted from FFPE tissue. Phi29-based whole-genome amplification, with its high processivity and strand-displacement activity, proved to be a robust method for amplifying DNA extracted from FFPE templates. The amplification yield from the GenomiPhi kit was higher than that from the DOP-PCR method. We also showed that FFPE tissues can be subjected to CGH analysis using samples amplified with GenomiPhi DNA Amplification Kit. Spectral Genomics human BAC arrays were successfully used to test the feasibility of array CGH using the GenomiPhi method. Comparison of hybridization results showed mean signal intensities and signal-to-background ratios of GenomiPhi amplified samples to be similar to those of DOP-PCR. Because GenomiPhi DNA Amplification Kit can amplify DNA from small quantities of template, this method can be used to study copy-number changes in FFPE samples on BAC CGH arrays.
Low yield from DNA extraction from FFPE tissue.
Use FFPE slides with at least 20 µm of tissue for DNA extraction. Complete the extraction method without a purification step because increased manipulation of the genomic DNA can result in loss of overall yield.