The purpose of this study was to perform a whole-genome analysis of loss of heterozygosity (LOH) in tongue squamous cell carcinoma (SCC) using the Affymetrix 10K SNP Mapping Array. In the gene which had been identified by whole-genome analysis of LOH, we analyzed allelic imbalance to identify the role of the gene. We applied whole-genome analysis of LOH in the specimens from the 5 cases of tongue SCC using this array. In the chromosomal region which had been identified by whole-genome analysis of LOH, we reconfirmed the existence of LOH in 30 cases using microsatellite markers. The expression levels of the mRNA in the region were examined in 15 cases and in 5 tongue SCC-derived cell lines by real-time quantitative RT-PCR analysis. LOH was observed in all of the 5 cases in the 1q31.1 region. Only 3 microsatellite markers (D1S1189, D1S2151, and D1S2595) existed in the 1q31.1 region. A high frequency of LOH was found at the D1S1189 locus in 18/30 (60%), D1S2151 locus in 16/30 (53%) and D1S2595 locus in 21/30 (70%). Only the Family with sequence similarity 5, member C (FAM5C) gene was located in the 1q31.1 region. There was statistically significant difference in the FAM5C mRNA expression levels between tongue SCC and normal tissues. All tongue SCC-derived cell lines decreased FAM5C mRNA expression compared with normal oral keratinocytes (NOKs). We conclude that FAM5C may be a novel tumor suppressor gene (TSG) in tongue SCC.

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