Browsing by Subject "DNA polymorphism"
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Item Open Access DNA repair gene polymorphisms and bladder cancer susceptibility in a Turkish population(International Institute of Anticancer Research, 2006) Karahalil, B.; Kocabas, N. A.; Özçelik, T.Background: Occupational exposure and life style preferences, such as smoking are the main known environmental susceptibility factors for bladder cancer. A growing list of chemicals has been shown to induce oxidative DNA damage. Base excision repair (BER) genes (X-ray repair cross complementing 1, XRCC1 and human 8-oxoguanine DNA glycosylase 1, OGG1) may play a key role in maintaining genome integrity and preventing cancer development. Materials and Methods: We tested whether polymorphisms in XRCC1 and OGG1 are associated with bladder cancer risk by using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In addition, the possible modifying affect of cigarette smoking was evaluated. Results: No studies, to date, have examined the association between genetic polymorphisms in DNA repair genes and bladder cancer susceptibility, in the Turkish population. We found the OGG1 Cys326Cys genotype to be more frequent among bladder cancer patients (odds ratio (OR): 2.41 (95% CI, 1.36-4.25)). However, in the case of XRCC1, there was no significant difference in susceptibility to bladder cancer development between patients with the Arg399 and these with the Gln399 allele (OR: 0.72 (95% CI, 0.41-1.26)). Conclusion: Our data showed that OGG1 genetic polymorphisms might be useful as prognostic genetic markers for bladder cancer in the clinical setting.Item Unknown Increased frequency of extremely skewed X chromosome inactivation in juvenile idiopathic arthritis(John Wiley & Sons, Inc., 2009) Uz, E.; Mustafa, C.; Topaloglu, R.; Bilginer, Y.; Dursun, A.; Kasapcopur, O.; Ozen, S.; Bakkaloglu, A.; Ozcelik, T.Objective. Juvenile idiopathic arthritis (JIA) is a childhood rheumatic disease of unknown etiology. Two subgroups of JIA, i.e., oligoarticular and polyarticular, are thought to have an autoimmune component, and show a higher female:male ratio. Skewed X chromosome inactivation (XCI) has previously been shown to be associated with scleroderma and autoimmune thyroiditis, 2 autoimmune disorders occurring predominantly in females. This study was undertaken to extend the analysis to the pediatric age group and to determine the XCI profiles of patients with JIA.Item Open Access p53 codon 72 polymorphism in bladder cancer-No evidence of association with increased risk or invasiveness(Springer, 2001) Törüner, G. A.; Uçar, A.; Tez, M.; Çetinkaya, M.; Özen, H.; Özçelik, T.We studied the effect of the p53 gene Arg72Pro polymorphism on bladder cancer susceptibility in a case control study of 121 bladder cancer patients and 114 age-sex matched controls to determine whether this polymorphism is a biomarker for the risk and how aggressive the disease is. Genomic DNA was obtained from venous blood samples for genotype determination by PCR and restriction digestion. The genotype frequencies in the patient group were Arg/Arg: 0.3553, Arg/Pro: 0.4711, Pro/Pro: 0.1736, and in the control group Arg/Arg: 0.3684, Arg/Pro: 0.4825, Pro/Pro: 0.1491. The distribution of genotypes between the two groups was not statistically different (χ2 = 0.260, df: 2, P = 0.878). The patient group was subdivided into two groups as superficial bladder cancer (n = 88) and invasive bladder cancer (n = 33), according to the presence of muscle invasion. The distribution of genotypes in the superficial group was Arg/Arg: 0.3409, Arg/Pro: 0.5114, Pro/Pro: 0.1477 and in the invasive group Arg/Arg: 0.3940, Arg/Pro: 0.3636, Pro/Pro: 0.2424. No association was observed with the invasiveness of the tumor (χ2 = 2.542, df: 2, P = 0.281). Stratification of the data by tobacco exposure did not result in a significant difference in genotype frequencies. These data do not support an association between the p53 Arg72Pro polymorphism and bladder cancer.Item Open Access PPAR-alpha L162V polymorphism in human hepatocellular carcinoma(Turkish Society of Gastroenterology, 2008) Koytak, E. S.; Mızrak, D.; Bektaş, M.; Verdi, H.; Arslan-Ergül, Ayça; İdilman, R.; Çınar, K.; Yurdaydın, C.; Ersöz, S.; Karayalçın, K.; Uzunalimoğlu, Ö.; Bozkaya, H.Background/aims: Several lines of evidence suggest that peroxisome proliferator-activated receptor alpha may be involved in hepatocarcinogenesis. L162V polymorphism of the peroxisome proliferator-activated receptor alpha gene enhances the transactivation activity of this transcription factor. The aim of this study was to determine the frequency and clinical correlates of peroxisome proliferator-activated receptor alpha L162V polymorphism in hepatitis virus-induced hepatocellular carcinoma. Methods: 90 hepatocellular carcinoma patients diagnosed at Ankara University Gastroenterology Clinic between January 2002 and July 2003 and 80 healthy controls with normal body mass index, blood chemistry and with negative viral serology were included. peroxisome proliferator-activated receptor alpha L162V polymorphism was determined by PCR-RFLP. Results: hepatocellular carcinoma etiologies were as follows: 56 HBV, 12 HBV+HDV, 22 HCV. Eighty-seven patients (97%) were cirrhotic, and 60 patients (67.5%) had advanced tumors. In 83 (92%) of 90 hepatocellular carcinoma patients, gene segment including polymorphic region could be amplified by PCR (50 HBV, 12 HBV+HDV, 21 HCV) and 6 of them (7.2%, all infected with HBV) had L162V polymorphism, while 2 (2.5%) of 80 controls had this polymorphism (p=0.162). This trend became more remarkable when only HBV (HBV+HDV)-infected patients were compared with controls (6/62, 9.7% vs. 2/80, 2.5%, respectively, p=0.071). Five of 6 patients with L162V had advanced disease. Conclusions: Peroxisome proliferator-activated receptor alpha L162V polymorphism tends to occur in HBV-induced epatocellular carcinoma and is absent in HCV-related epatocellular carcinoma. These findings may show clues for the existence of different carcinogenesis mechanisms in these two common etiologies. Frequent occurrence of advanced disease in patients with L162V polymorphism suggests a role for this polymorphism in tumor progression.Item Open Access Skewed X-chromosome inactivation in scleroderma(Springer New York, 2008) Uz, E.; Loubiere, L. S.; Gadi, V. K.; Ozbalkan, Z.; Stewart, J.; Nelson, J. L.; Ozcelik, T.Scleroderma is a female-prevalent autoimmune disease of unclear etiology. Two fundamental gender differences, skewed X-chromosome inactivation (XCI) and pregnancy-related microchimerism, have been implicated in scleroderma. We investigated the XCI patterns of female scleroderma patients and the parental origin of the inactive X chromosome in those patients having skewed XCI patterns (>80%). In addition, we investigated whether a correlation exists between XCI patterns and microchimerism in a well-characterized cohort. About 195 female scleroderma patients and 160 female controls were analyzed for the androgen receptor locus to assess XCI patterns in the DNA extracted from peripheral blood cells. Skewed XCI was observed in 67 (44.9%) of 149 informative patients and in 10 of 124 healthy controls (8.0%) [odds ratio (OR) = 9.3 (95% confidence interval (CI) 4.3-20.6, P < 0.0001)]. Extremely skewed XCI (>90%) was present in 44 of 149 patients (29.5%) but only in 3 of 124 controls (2.4%; OR = 16.9; 95% CI 4.8-70.4, P < 0.0001). Parental origin of the inactive X chromosome was investigated for ten patients for whom maternal DNA was informative, and the inactive X chromosome was of maternal origin in eight patients and of paternal origin in two patients. Skewed XCI mosaicism could be considered as an important risk factor in scleroderma.Item Open Access Turkish population data on the HLA-DQα, LDLR, GYPA, HBGG, D7S8, and GC loci(Springer, 1998) Vural, B.; Atlioǧlu, E.; Kolusayin, Ö.; Togan, I.; Büyükdevrim, S.; Özçelik, T.We have determined the allele and genotype frequencies of six PCR-based genetic markers HLA-DQα, LDLR, GYPA, HBGG, D7S8 and GC in the Turkish population (n = 361 for HLA-DQα, and n = 260 for PM). All loci meet Hardy- Weinberg expectations. The frequency data can be used in forensic analyses in the Turkish population.