Comparative genomic hybridization of normal karyotype lung tumors from heavy smokers using Affymetrix SNP arrays

Whole genome analysis on normal karyotype lung tumors from heavy smokers.
Our study regarded a population of 5203 heavy smokers volunteers, enrolled in a screening program set up at the European Institute of Oncology. Each volunteer yearly undergoes low dose CT-scan. At the end of the second year, among 89 screening-identified patients with lung cancers, 57 cases with clinical localized lung malignancy were evaluated for the present analysis. These, together with 21 other asymptomatic patients (pilot population), carrying non-screening detected lung cancers, but with same characteristics of the screened population (asymptomatic, smokers, older than 50, with an occasionally detected localized cancer), constituted our study population (78 cases). At the time of surgical resection, a portion of the tumoral tissue was collected, snap-frozen and stored at -80 C, for the subsequent tumor cellularity evaluation and DNA extraction. Tumor cellularity was determined by analyzing ematossilin-eosin stained sections of the tumor samples. The evaluation was carried out by a pathologist of the Molecular Pathology Unit, at the IFOM-IEO campus. Only NK samples with an evaluated tumor cellularity of at least 70% were used for the high-resolution genomic analysis: this allowed us to restrict normal cells contamination of the tumor genome pattern in our analysis. A genomic macroscopic analysis was carried out in order to identify tumors harboring a normal karyotype, which were then subjected to a high-resolution genomic analysis, through the Affymetrix SNPs technology.