Use of single nucleotide polykorphism arrays to identify a novel region of loss on chromosome 6q in squamous cell carcinomas of the oral cavity

Background. A subset of patients with oral cavity squamous cell carcinoma (SCC), often of young age yet lacking a history of carcinogen exposure, has been identified, with no clear etiology for tumor development. Methods. To identify somatic genetic alterations unique to this patient population, we performed a high throughput single nucleotide polymorphism (SNP) analysis, quantitative PCR of the E6 and E7 regions of human papillomavirus (HPV) 16, sequencing of the IVSF-4+ locus of the FANC-C gene, and microsatellite analysis for 18 nonsmoking patients, age 23 to 57 years (median age, 39 years). We compared these results with oral SCC from 17 patients 47 to 81 (median, 64) years of age with significant tobacco exposure (>40 pack-years) to identify unique genetic alterations for each group. Results. SNP analysis demonstrated variable rates of allelic imbalance (Al) and no significant difference in terms of Al patterns between the two groups. However, we found an elevated rate of Al in chromosomal arms 6q (47% [17 of 36]) by performing microsatellite analysis of both groups. Only one tumor demonstrated the presence of HPV 16, and none of the tumors demonstrated mutations in the IVSF-4+ region of FANC-C. Conclusions. Despite variable marker density, SNP array analysis is an emerging technique for genome-wide assessment and is a useful tool for discovery of novel sites of allelic loss in oral SCC, including a novel region of allelic loss on chromosome 6q.