NanoString nCounter assay DNA was extracted from two sections of 10-μm-thick FFPE tissue samples after deparaffinization with xylene and using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's instructions. After extraction, the quality and quantity of genomic DNA were analyzed using a NanoDrop 8000 UV–Vis spectrometer (Thermo Scientific Inc.). For copy number variation (CNV) detection, among the genes that showed gain in SqCC in a previous study, 37 were located at 3q26-28.
