| Nasopharyngeal carcinoma (NPC) is a rare tumor in most parts of the world but occurs at relatively high incidence among people of southern China. The epidemiologic investigation indicates that NPC is a multi-gene hereditary disease, which relates to race and familial traits, as well as concerns with oncogenes and/or suppressor genes. The etiology studies demonstrate that environment factors and the infection of Epstein-Barr virus as well as genetic alterations play a very important role in NPC developing. Up till now there hasn't been identified own gene of NPC but some related genes.Single nucleotide polymorphism (SNP) is a useful genetic marker because of its high density and hereditary stability and the capacity for highly automated analysis. SNP is thought to be a powerful tool for finding the contributions of individual genes to complex, multigene diseases. Actually, genetic variations underline differences in our susceptibility to, or protection from, all kinds of disease. Knowledge of genetic variations also affects patient treatment to some degree.Using bioinformatics means, 7 genes were picked out to be studied , including the tumour suppressor gene candidates, such as YH1, NPCR and NAG22, EBV receptor CR2 which can guide EBV into lymphocytes, TSG101 which is a suppressor gene and multi-organ metabolic enzyme at the same time, as well as CYP2E1 and GSTm1 which are very important phase I (oxidation) and II (conjugation) metabolic enzymes.In order to gain SNP from these genes, 27 samples and 5 pools, which originated from the Han nationality and minority of Chinese, were examined by sequence and 102 SNP loci were discovered. There are 46 and 9 SNP in 5'Flank and 5'UTR, respectively; only 14 SNP in coding region are discovered. In 3TJTR and 3'Flank, there are 11 and 14 SNP, respectively. 73 in 102 SNP haven't been reported. 7 in 14 cSNP have moderate or high frequency (the rare allele frequency is from 7.4% to 32.7%), only 2 loci have no changes among amino acids, the rest 5 in 14 SNP have lower frequency (the rare allele gene frequency is just 1.9%), onlylof them has no change.87 loci of 102 SNP, which allele frequencies exceed 0.01, were analyzed by linkage disequilibrium (LD), the results showed that 83 pairs locus presented highly linkage disequilibrium each other, 21 pairs in CR2, 21 pairs in YH1, 1 pair in NAG22, 9 pairs in TSG101, 29 pairs in NPCR, 13 pairs in GSTml and 12 pairs in CYP2E1, respectively.In the present study, we investigated the correlation between the polymorphism of the 7 genes and NPC on a total of 238 patients and 286 controls. The PCR-RFLP and tetra-Primer ARMS-PCR analysis were used to evaluate 12 polymorphisms in the coding region of 6 genes, htSNP derived from results by calculating haplotype was also applied to estimate polymorphism in CYP2E1. The relative risk (RR) was estimated by the odds ratio (OR), to determine the association between genotype of these genes and NPC development.The results of all above mentioned showed that lower allele frequency of YH1, CR2, NAG22 or NPCR could not become an individual marker to analyze the correlation between the polymorphism and NPC.GSTml C1270533T was discovered for the first time (the rare allele frequency is 22.2%), that the second genetic code in No.96 amino acid appears variation and makes this locus a missense mutation. The genotype displayed suggested there was no association between the phenotype and NPC susceptibility (RR=0.170, 95%CI =0.95-0.306 for homozygote TT).YH1 G1990158A and YH1 G1990398T are located in regulating region and the rare allele frequency is 22.2% in Chinese. The results indicated that homozygous variant GG in YH1 G1990158A was at a 2.3-fold risk of disease (95% confidence interval = 1.458-3.628). Similarly, homozygous variant GG in YH1 G1990398T was at 3.6-fold risk of developing NPC (95% confidence interval =1.97-6.693).CYP2E1 T505228A is located at coding region, its third genetic code in the 421th amino acid appears variation, making this locus a synonymous mutation, the R...
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