In our study we observed that 1) absolute copy number of 3q chromosomal region may harbour false positive interpretation of 3q amplification in squamous cell carcinoma; 3) correction for chromosome 3 is important to identify true 3q amplification; 4) we propose to consider a case “amplified for chromosome 3q” when scoring ≥8 fluorescent signals; 5) false versus true 3q chromosomal amplification in squamous cell lung carcinoma merit consideration at light of emerging trials involving anti-PI3CA and SOX-2 targeted drugs. The gene discussed is SOX2; the disease is squamous cell lung carcinoma.