Genome-wide Loss of Heterozygosity Analysis in Head and Neck Squamous Cell Carcinomas

Identifying the tumor suppressor gene (TSG) loci by genomic studies is an important step to uncover the molecular mechanisms involved in HNSCC pathogenesis. We therefore performed comprehensive analyses on loss of heterozygosity (LOH) using a genome-wide panel of 191 microsatellite markers in 22 HNSCC samples. We found 53 markers with significantly high LOH (>30%) on 21 chromosomal arms, the highest values of those were observed on 3p, 9p, 13q, 15q, and 17p, corresponding to D3S2432 (67%), D9S921- D9S925 (67%) and GATA62F03 (86%), D13S1493 (60%), D15S211 (62%) and D17S1353 (88%), respectively. Fifteen hot spots of LOH were defined in 13 chromosomal arms reported previously in HNSCCs. Furthermore, we identified 5 novel hot spots of LOH on 3 chromosomal arms in HNSCC at 2q33 (D2S1384), 2q37 (D2S125), 8q12-13 (D8S1136), 8q24 (D8S1128) and 15q21 (D15S211). In conclusion, our comprehensive allelotype analyses have unveiled and confirmed a total of 20 possible TSG loci that could be involved in the development of HNSCC. These results provide useful clues for identification of putative TSGs involved in HNSCC by fine mapping of the suspected regions.