A functional single nucleotide polymorphism site detected in nasopharyngeal carcinoma-associated transforming gene Tx.

Tx is a transforming gene cloned from a nasopharyngeal carcinoma (NPC) cell line CNE2. Sequence analysis revealed that Tx encoded an aberrant immunoglobulin kappa light chain, which is abnormally expressed in epithelial tumor cells and plays an important role in nasopharyngeal carcinogenesis. Bioinformatic analysis confirmed the presence of a single nucleotide polymorphism (SNP) site in the Tx gene as matched to the Cancer Genome Anatomy Project SNP clusters database, which predicted 8 candidate SNP sites. Distribution of the confirmed SNP site in the genomes of healthy individuals and NPC patients was analyzed by denaturing high performance liquid chromatography. Heteroduplex genotype (GC/CG) occurred in NPC patients with a frequency significantly higher (52.44%) than that detected in healthy individuals (33.75%). In contrast, homoduplex genotype (GG) was less frequent in NPC patients (31.70%) than in normal individuals (56.25%), suggesting that heteroduplex genotype of Tx gene might be a risk factor for NPC.