0.5 microgram of digested and purified DNA were labeled by a random primer reaction, using Bioprime DNA Labeling System and either Cy3-dCTP or Cy5-dCTP.
Data preprosessing included filtering of weak and bad spots, lowess normalization, and exclusion of clones showing a SD > 0.2
Image analysis was performed with GenePix 6.0 image analysis software
Tumor biopsies were taken at the time of diagnosis
Scanning was performed with an Agilent scanner at 100 pmt
Genomic DNA was isolated according to a standard protocol, including proteinase K, phenol, chloroform, and isoamylalcohol
The labeled tumor and normal DNA was co-hybridized to the array slides for 42 to 46 hours, using an automated hybridization station.
Commercially available genomic DNA (Promega, Madison, WI) was used.
Normal female DNA was used