After centrifugation, primary cells in pleural effusions or ascites were cultured in -MEM (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Equitech-Bio, Ingram, TX, USA). Surgically resected tumors were cut into small pieces. These pieces were plated on culture dishes and gently overlaid with culture medium. Primary outgrowth cells were cultured in -MEM–10% FBS. Adherent cells were expanded by several passages for several weeks or months.
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. Genomic DNA from peripheral blood was isolated with a QIAamp DNA Blood Mini Kit (Qiagen).
Label
Biotin
Label protocol
As per manufacturer (Affymetrix)
Hybridization protocol
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description
Hybridized to 250K_Sty
Data processing
The probe intensities at each locus were determined in the Affymetrix GeneChip Operating System GCOS software, and genotype calls were generated using the Affymetrix Genotyping Console GTC Software (Version 3.0.2). Primary data analysis was performed using GTC software, and further statistical studies were analyzed using the CNAG (Copy Number Analyzer for Affymetrix GeneChip Mapping arrays) software, version 2.0 (Genome Laboratory, The University of Tokyo, http://www.genome.umin.jp) for Mapping 500K set. For SNP6.0 array, genotype calls were generated using the Affymetrix Genotyping Console GTC Software (Version 3.0.2) using birdseed version 2 algorithm with other 100 files. Call (SNP call): AA, AB, BB, and NoCall; Log2Ratio: copy number log2 ratio between the test and reference samples of zero; LOH: posibility of loss of heterozygosity (bigger number means higher posibility of LOH for CNAG, but Genotyping Console gave 1 with posibility of LOH)
