Purpose: The purpose of this study was to evaluate a polymorphism frequency between oral squamous cell carcinoma (OSCC) patients and healthy volunteers.

Materials and methods: 54 Japanese OSCC patients and 60 Japanese healthy volunteers were included in the present study. To select regions with copy number variations, we used tumor DNA from 20 OSCC patients for comprehensive genome-wide variability analysis using array-based CGH (Agilent Human Genome CGH Microarray 44B). The frequency difference of selected gene polymorphisms was verified between 54 tumor DNA and 60 healthy volunteers’ normal DNA using real-time quantitative PCR.

Results: We found a frequent deletion at chromosome 3q26.1 in OSCC patients by array-based CGH. It was a genetic deletion polymorphism with a gene frequency of 0.293–0.368 in healthy volunteers ( n = 60) and that of 0.129–0.195 in OSCC patients ( n = 54). Detail analysis around the polymorphic region indicated that breaking point of the deletion existed around the polymorphic region.

Conclusions: Significant association of gene frequency for the deletion polymorphism between healthy volunteers and OSCC patients suggested possibility of involvement of genetic factors related to this polymorphism in the occurrence of OSCC. At the moment no gene is suggested to be present within 3606 kbp region around this polymorphic region. Although occurrence of the OSCC cannot be explained by single-gene model, we believe that it is of value to include examination of this polymorphism to search for risk factors of OSCC.

Conflict of interest: None declared.