Array comparative genomic hybridization analysis of metastatic lung tumors

Comparative genomic hybridization analysis for detection of recurring gene copy number variation (CNV) among a set of lung cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled Agilent characterized normal human reference DNA Twenty-seven de-identified, fresh-frozen surgically resected lung metastatic brain tumors were analyzed. The work was approved by the Wayne State University Institutional Review Board. Genomic DNA was isolated using the EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD). A Trinean DropSense96 Spectrophotometer (PerkinElmer, Waltham, MA) and TapeStation (Agilent, Santa Clara, CA) were used to measure DNA quantity and quality. aCGH analysis employed the Agilent SureScan platform and SurePrint G3 Cancer CGH+SNP (4x180K) microarrays following manufacturer’s recommendations. Agilent’s characterized normal human DNA (male or female, used according to patient gender) was the reference sample. Tumor sample DNA was labeled with Cy5 and normal reference DNA was labeled with Cy3. Probe fluorescence intensity data was extracted from scanned microarray images using Agilent Cytogenomics software. GC Correction, Diploid Peak Centralization (normalization) and Aberration Detection Method 2 (quality control) algorithms were also applied using this software. Aggregate data (all 27 samples) were analyzed using Nexus Copy Number software (Biodiscovery, El Segundo, CA).