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Chromosome abnormalities often correlate with molecular abnormalities and provide a starting point for gene discovery and characterization in the context of a specific disorder. In cancer biology, chromosomal abnormalities carry diagnosis, prognostic, and predictive value of response to treatment. Recently, methodologies such as array comparative genomic hybridization and oligonucleotide microarrays allow discovery of regions of frequent alterations with high resolution. Genomic gain at chromosome 3q location has been recognized as one the most prevalent and significant alterations in lung cancer. Emerging data suggests that regions of amplification have profound effect on tumor development and house candidate biomarkers of disease progression, response to therapy and prognosis. This review examines how genome-wide analysis of lung cancer lead to the evaluation of a specific genomic alteration on chromosome 3q, the study of candidate driver genes and their potential clinical implications.