Du J, et al. - In this analysis, 13 benign notochordal cell tumour (BNCT) cases were investigated to study the clinicopathological and molecular features and their differential diagnosis of chordoma. In three cases, the genome-wide copy number imbalances were performed using the Oncoscan CNV array and fluorescence in situ hybridisation (FISH) detection of epidermal growth factor receptor (EGFR)/chromosome 7 enumeration probe (CEP7), LSI1p36/1q21, LSI19p13/19q13, CEP3/CEP12 and Telvysion 6 P was performed in 13 cases. The absence of extracellular matrix and eosinophil cells and the presence of vacuoles in most tumour cells was the important histological character for differential diagnosis with chordoma. Unlike chordoma, chromosome gain or normal copy number was more common, whereas chromosome loss was rare in BNCTs. This can be a differential diagnostic clue for chordoma and can be an important feature of notochordal cell tumours progression.