Genetic alterations in oral squamous cell carcinoma progression detected by combining array-based comparative genomic hybridization and multiplex ligation-dependent probe amplification

Background. Oral squamous cell carcinoma (OSCC), the most common malignancy of the oral cavity, has been shown to occur via a multistep process driven by the accumulation of carcinogen-induced genetic changes. Study design. Array-based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) were conducted to screen human genomewide alterations on fresh tissues of the cancer area, the dysplastic transitional area, and the resection margin (normal) free of tumor; these samples were obtained from 7 OSCC patients. Results. The highest amplification frequencies (100%, 7/7) were detected in FAM5B, TIPARP, PIK3CA, NLGN1, FGF10, HDAC9, GRM3, DDEF1, EDNRB, CHRDL1, and HTR2C, and the highest deletion frequencies in THRAP3, CTTNBP2NL, GATAD2B, REL, CKAP2L, RHOA, EIF4E3, PDLIM5, FBXO3, NEUROD4, and ABCA5 in the OSCC. In the dysplasia, amplification (100%, 7/7) was detected in RNF36 and deletion in CKAP2L and TCF8. We could detect large differences with MLPA in the number of alterations between the cancer or dysplasia versus the normal area with P values of <.001. Conclusion. These findings indicate that these DNA copy number changes on each chromosome in the 3 categories may be associated with OSCC tumorigenesis and/or progression. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2011;111:594-607)