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PubMed2006

Dinucleotide repeat polymorphism in intron II of human Toll-like receptor 2 gene and susceptibility to rheumatoid arthritis.

Human Toll-like receptors (TLRs) participate in innate immune response and signal the activation of adaptive immunity. The presence of a functional intronic polymorphism consisting of guanine-thymine repeats in TLR2 gene was recently reported. Here, we investigated a dinucleotide repeat polymorphism in intron II of TLR2 in Korean patients with rheumatoid arthritis (RA). The numbers of guanine-thymine [(GT)(n)] repeats in intron II of the TLR 2 gene were counted in 183 patients with RA and in 148 healthy controls, using the gene scanning technique. We classified alleles into two subclasses for further analysis, 12-16 GT repeats (S allele) and 17-28 repeats (L allele). By subgroup analysis, we also examined whether the S allele is associated with the presence of shared epitope (SE), rheumatoid factor (RF), joint erosion and extra-articular complications. S-allele frequency was significantly increased in patients with RA than in healthy controls [30.3% vs. 23.0%, P = 0.03, or 1.46, 95% confidence interval (CI) 1.03-2.07], and genotypes containing S alleles were more frequent in patients with RA than in healthy controls (54.4% vs. 46.5%. P = 0.04, or 1.57, 95% CI 1.01-2.42). A skewed S-allele distribution was not found to be related to the presence of SE. Subgroup analysis showed no genotypic or allele frequency differences between patients with/without RF, joint erosion, or extra-articular complications. Genotype containing shorter GT repeats in intron II of the TLR2 gene may confer susceptibility to RA in Koreans.

Adolescent↗
PubMed2007

No association between dinucleotide repeat polymorphism in intron 1 of the epidermal growth factor receptor gene EGFR and risk of lung cancer.

The tyrosine kinase receptor EGFR pathway is one of the oncogenic signaling cascades involved in lung cancer, mediating the epidermal growth factor receptor gene EGFR. First-intron polymorphisms with greater numbers of CA dinucleotide repeats tend to downregulate EGFR expression, which suggests that this polymorphism may modulate susceptibility to lung cancer. The present hospital-based case-control study evaluated the possible association of CA repeat polymorphism in the EGFR gene with risk of lung cancer in a Korean population. A bimodal pattern appeared, with a frequency of 57.1% for 20 CA repeats and 18.6% for 16 CA repeats. There was, however, no significant difference in distribution of allele genotypes between all lung cancer cases and the controls, nor among histological types for the cases.

Adenocarcinoma↗
PubMed1998

Influence of PvuII (intron 6) polymorphism of the lipoprotein lipase gene on cord plasma lipid and apolipoprotein levels in Indian and Chinese newborns of Singapore.

The influence of the PvuII polymorphism (intron 6) of the lipoprotein lipase (LPL) gene on cord plasma lipid traits was studied in 252 ethnic Chinese and 240 ethnic Indian newborns of Singapore. The allelic frequencies of P+ (presence of the restriction site) were 0.67 and 0.56 in the Chinese and Indian newborns, respectively, similar to their respective adult populations. The genotype distributions at the PvuII site were at Hardy Weinberg equilibrium in both ethnic Chinese (chi2 = 2.0) and ethnic Indians (chi2 = 3.6). Cord blood HDL-cholesterol (HDL-C) levels are higher in newborn Chinese than newborn Indians. In addition, cord blood LDL-cholesterol (LDL-C), apoB, and lipoprotein(a) levels are lower in newborn Chinese than newborn Indians. Both newborn Chinese and Indian male homozygotes for P- allele have higher cord blood LDL-C levels than newborns with the more common P+P+ or P-P+ genotypes. In Chinese male newborns, the LDL-C levels were 0.76 +/- 0.61 mmol/L, 0.53 +/- 0.29 mmol/L and 0.46 +/- 0.25 mmol/L, respectively (p = 0.01). In Indian male newborns, the LDL-C levels were 0.88 +/- 0.35 mmol/L for the P-P- genotype and 0.65 +/- 0.24 mmol/L for the P+P+ genotype (p = 0.003). In addition, the influence of the P- allele on LDL-C levels is remarkably similar in both ethnic groups, accounting for 8.48% of the population variance in the Chinese newborns and 8.09% in the Indian newborns. In contrast, no obvious effect of genotype is seen in this lipid parameter in the newborn females of either ethnic groups. There is presence of significant genotype specific influence on the LDL-C levels in cord plasma in male newborns, suggesting an early expression of the LPL gene locus.

Adult↗
PubMed2000

Pvu II intron 15 polymorphism at the LDL receptor gene is associated with differences in serum lipid concentrations in subjects with low and high risk for coronary artery disease from Brazil.

Coronary artery disease (CAD) has a high prevalence in the Brazilian population. Nevertheless, studies of genetic risk factors for CAD in this country have not been sufficiently conducted. We used the Pvu II polymorphism (intron 15) at the low-density lipoprotein receptor (LDLR) gene to study the effect of variation at this locus in determining plasma lipid concentrations in 128 white subjects presenting a lipid profile suggesting high risk for CAD (HRG) and 100 white normolipidemic individuals (controls, CG). The Pvu II polymorphism was detected by PCR-RFLP. The P1P1 genotype for Pvu II polymorphism (homozygous for absence of restriction site) was greater in HRG individuals than in CG subjects (57% vs. 38%, P<0.05). Moreover, the P1P1 genotype was strongly associated with high concentrations of total cholesterol (P=0.0001), triglycerides (P=0. 0295), LDL-C (P=0.0001), and VLDL-C concentrations (P=0.0280) and lower HDL-C concentrations (P=0.0051) in HRG subjects. Similarly, the CG individuals with P1P1 genotype presented high concentrations of total cholesterol and LDL-C compared to other genotypes (P=0. 0001). This study demonstrates the influence of Pvu II polymorphism of the LDLR on serum lipid concentrations of individuals with low and high risk for CAD from Brazil.

Adult↗
PubMed1999

Lack of association of presenilin-1 intron-8 polymorphism with neuropathological features of Alzheimer's disease.

Over 45 mutations within the coding region of presenilin-1 (PS-1) are associated with an autosomal dominant form of Alzheimer's disease. Recently allele 1 of a polymorphism within intron-8 was reported to be in disequilibrium with Alzheimer's disease in a group of patients with sporadic Alzheimer's disease. This association has been replicated in some, but not all, studies. To determine whether the PS-1 intronic polymorphism is overrepresented in Alzheimer's disease in an autopsy-proven series, and to examine whether allele 1 is associated with a specific neuropathological phenotype, polymerase chain reaction based technique was used to assess the genotype in 85 cases of Alzheimer's disease. The resulting genotypes were compared with age of onset, duration of illness, and quantitative neuropathological measures of Abeta(total), Abeta(1-40), Abeta(1-42), neurofibrillary tangle number and neuron number. The 1/1 genotype did not associate with any differences in the clinical or neuropathological phenotype. These data suggest that the PS-1 intron-8 polymorphism does not strongly impact the clinical or neuropathologic features of Alzheimer's disease.

Aged↗
PubMed2001

Endothelial nitric oxide synthase intron 4 polymorphism influences the progression of renal disease.

BACKGROUND/AIM: Nitric oxide is a potent regulator of intrarenal hemodynamics and may influence the renal function. We investigated whether polymorphism of intron 4 of the endothelial constitutive nitric oxide synthase (ecNOS) gene is related to the progression of chronic renal failure. METHODS: Polymorphism of ecNOS intron 4 was studied in 1,005 hemodialysis patients (710 with nondiabetic nephropathy and 295 with diabetic nephropathy) and was compared with the findings in 189 healthy subjects. ecNOS genotypes were determined by the polymerase chain reaction, followed by agarose gel electrophoresis. RESULTS: The frequencies of ecNOS4a/a, ecNOS4a/b, and ecNOS4b/b genotypes were, respectively, 0% (0/189), 13.8% (26/189), and 86.2% (163/189) in the control group; 1.7% (12/710), 22.1% (157/710), and 76.2% (541/710) in the nondiabetic nephropathy group, and 1.0% (3/295), 22.7% (67/295), and 76.3% (225/295) in the diabetic nephropathy group. The frequency of ecNOS4a (ecNOSa/a and ecNOSa/b) was significantly higher in both the nondiabetic group and in the diabetic group than in the controls (p = 0.0025 and p = 0.0438, respectively). CONCLUSION: There was a significantly higher frequency of the a allele of intron 4 in both nondiabetic and diabetic hemodialysis patients, so the polymorphism of intron 4 of the ecNOS gene may have a wide influence on the progression of renal disease.

Adult↗
PubMed2004

Intron 4 polymorphism of the endothelial nitric oxide synthase gene is associated with the development of lupus nephritis.

The objective was to investigate whether the functional polymorphism of intron 4 in the endothelial nitric oxide synthase (eNOS) gene is associated with susceptibility to systemic lupus erythematosus (SLE) and its clinical features. The 27-bp repeat polymorphism in intron 4 of the eNOS gene was determined by polymerase chain reaction in 88 SLE patients and 95 healthy control subjects. Clinical manifestations were analysed in each patient and correlated with the genotypes. The genotype distribution of the intron 4 of the eNOS did not differ between SLE patients and control subjects (aa, ab, bb genotypes 0, 15, 73 versus 2, 19, 74 controls respectively, chi-squared = 2.21, 2 df, P = 0.331). In the lupus patients according to the intron 4 genotypes of the eNOS, there was no clinically significant difference in age at onset, anti-dsDNA titre, C3, C4 level, SLEDAI, SLICC/ACR Damage Index, or autoantibodies such as RF, anti-Ro, La, RNP, Sm, or phospholipid antibodies. However, renal involvement was higher in patients with ab genotypes than in those with bb genotypes (53% versus 26%), but it did not reach statistical significance (P = 0.062). Logistic regression showed that having the ab genotype was a significant risk factor for the development of lupus nephritis (odds ratio = 3.28, 95%CI: 1.04-10.2, P = 0.04). In conclusion, our data show that the eNOS ab genotypes may be associated with the development of lupus nephritis, suggesting individuals who carry the 'a' allele are more susceptible to lupus nephritis than those with the 'b' allele.

Adolescent↗
PubMed2000

Evidence against association of the FE65 gene (APBB1) intron 13 polymorphism in Alzheimer's patients.

A genetic polymorphism in intron 13 of the FE65 gene (APBB1) was reported to be associated with Alzheimer's disease (AD). Our analyses of this polymorphism, both in a family-based or a case-control sample, fail to support the association between the FE65 intron 13 polymorphism and AD. We performed the sibship disequilibrium test (SDT, P=0.77) and the sib transmission/disequilibrium test (Sib-TDT, P=0.56) in a family-based study which included 526 subjects from 158 sibships. In addition, we compared the genotype and allele frequencies of this biallelic polymorphism in 311 AD patients to those of a control group consisting of 260 subjects and found no significant difference (chi(2), P=0.847 and P=0.586, respectively). Furthermore, our two-point linkage analysis in a family-based sample was in agreement with a genome wide scan for linkage to AD and showed no evidence for linkage to the short arm of chromosome 11 where the FE65 gene is located. We conclude that the association of the FE65 intron 13 polymorphism with AD, if any, is smaller than previously reported.

Aged↗
PubMed2003

Interethnic difference in the allelic distribution of human epidermal growth factor receptor intron 1 polymorphism.

PURPOSE: Epidermal growth factor receptor (EGFR) plays a critical role in signal transduction and is a target for a novel class of anticancer agents that aim to inhibit EGFR-mediated cancer cell growth. Previous studies have demonstrated a dinucleotide (CA)(n) repeat polymorphism in intron 1 of EGFR, ranging from 14 to 21 repeats, that has been suggested to regulate EGFR expression. The longer allele with 21 repeats showed an 80% reduction of gene expression compared with the shorter allele with 16 repeats. Therefore, the evaluation of the allelic distribution of this polymorphism in populations of various ethnic origins will be crucial to understand the interindividual variability in EGFR expression. EXPERIMENTAL DESIGN: We evaluated the influence of ethnicity on this polymorphism by genotyping individuals of Caucasian (n = 183), African-American (n = 84), and Asian (n = 66) background. RESULTS: The frequency of one of the longer alleles, allele 20 is significantly higher in Asian individuals (63% compared with 21% in Caucasians, P = 2 x 10(-18)). In confirmation of prior studies, the shorter allele 16 was the most common allele in Caucasians (43%) and African-Americans (42%), but its frequency was significantly lower in Asians (average 17%, P = 10(-7) compared with Caucasians). CONCLUSION: Major interethnic differences in the allelic frequencies of the EGFR intron 1 polymorphism exist. Our results may contribute to a better understanding of the molecular basis underlying ethnic differences in drug response and may be helpful for future strategies of individualized therapy with EGFR inhibitors.

Alleles↗
PubMed2003

Genetic polymorphism of CYP1A2 in Ethiopians affecting induction and expression: characterization of novel haplotypes with single-nucleotide polymorphisms in intron 1.

CYP1A2 polymorphism has been well studied in white persons and Asians but not in Africans. We performed CYP1A2 genotype and phenotype analysis using caffeine in Ethiopians living in Ethiopia (n = 100) or in Sweden (n = 73). We sequenced the CYP1A2 gene using genomic DNA from 12 subjects, which revealed a novel intron 1 single-nucleotide polymorphism (SNP), -730C>T. We developed SNP-specific polymerase chain reaction-restriction fragment length polymorphism genotyping and molecular haplotyping methods for the intron 1 SNPs, and four different haplotypes were identified: CYP1A2*1A (wild-type for all SNPs), CYP1A2*1F (-164A), CYP1A2*1J (-740G and -164A), and CYP1A2*1K (-730T, -740G, and -164A), having frequencies of 39.9, 49.6, 7.5, and 3.0%, respectively. The frequency of CYP1A2*1J and CYP1A2*1K among Saudi Arabians (n = 136) was 5.9% and 3.6%, and among Spaniards (n = 117) 1.3% and 0.5%, respectively. Functional significance of the different intron 1 haplotypes was analyzed. Subjects with CYP1A2*1K had significantly decreased CYP1A2 activity in vivo, and reporter constructs with this haplotype had significantly less inducibility with 2,3,7,8-tetrachlorodibenzo-p-dioxin in human B16A2 hepatoma cells. Electrophoretic mobility shift assay using nuclear extracts from B16A2 cells revealed a specific DNA binding protein complex to an Ets element. Efficient competition was obtained using oligonucleotide probes carrying the wt sequence and Ets consensus probe, whereas competition was abolished using probes with the -730C>T SNP alone or in combination with -740T>G (CYP1A2*1K). The results indicate a novel polymorphism in intron 1 of importance for Ets-dependent CYP1A2 expression in vivo and inducibility of the enzyme, which might be of critical importance for determination of interindividual differences in drug metabolism and sensitivity to carcinogens activated by CYP1A2.

Adult↗
PubMed1996

Detection and evaluation of p53 intron 2 polymorphism in lung carcinomas in Hong Kong.

A polymorphism in intron 2 of the p53 gene, which gives rise to 2 alleles, A1 and A2, was analyzed by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and direct DNA-sequencing techniques. The distribution of this allele in the peripheral blood in the Chinese population comprising 27 healthy individuals, 30 bronchiectasis patients, 34 non-small-cell lung cancer (NSCLC) patients and 27 SCLC patients was analyzed. The genotypic distributions for this marker were significantly different between the blood of healthy individuals and SCLC patients. There was no significant difference between genotypes of Caucasians and Chinese. Tumors, normal lungs and peripheral blood of 83 adenocarcinoma and 10 squamous cell carcinoma patients were also studied. There was a significant difference in the distribution of the genotypes detected in tumor tissues vs. blood of adenocarcinoma patients. The frequency of detection of the A1/A1 genotype in the tumor tissues was increased in adenocarcinoma patients as compared with the blood of adenocarcinoma patients and was decreased in the blood of SCLC patients as compared with the blood of healthy individuals. Survival rates in Hong Kong adenocarcinoma patients with the A1/A1 genotype were lower than those in patients with A1/A2 and A2/A2 genotypes up to 30 months post-operation. Point mutations were detected at the p53 intron 2 polymorphic locus in NSCLC specimens, with a mutation rate of 15.4% (8/52). All mutations were GC transversions. The significance of this instability in p53 intron 2 remains to be elucidated.

Adenocarcinoma↗
PubMed2006

Evolution of an intronic microsatellite polymorphism in Toll-like receptor 2 among primates.

Nonhuman primates express varying responses to Mycobacterium tuberculosis: New World monkeys appear to be resistant to tuberculosis (TB) while Old World monkeys seem to be particularly susceptible. The aim of this study was to elucidate the presence of the regulatory guanine-thymine (GT) repeat polymorphisms in intron 2 of Toll-like receptor 2 (TLR2) associated with the development of TB in humans and to determine any variations in these microsatellite polymorphisms in primates. We sequenced the region encompassing the regulatory GT repeat microsatellites in intron 2 of TLR2 in 12 different nonhuman primates using polymerase chain reaction amplification, TA cloning, and automatic sequencing. The nonhuman primates included for this study were as follows: chimpanzee (Pan troglodytes), bonobo (Pan paniscus), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), Celebes ape (Macaca nigra), rhesus monkey (Macaca mulatta), pigtail macaque (Macaca nemestrina), patas monkey (Erythrocebus patas), spider monkey (Ateles geoffroyi), Woolly monkey (Lagothrix lagotricha), tamarin (Saguinus labiatus), and ring-tailed lemur (Lemur catta). Nucleotide sequences encompassing the regulatory GT repeat region are similar across species and are completely conserved in great apes. However, Old World monkeys lack GT repeats altogether, while New World monkeys and ring-tailed lemurs have much more complex structures around the position of the repeats. In conclusion, the genetic structures encompassing the regulatory GT repeats in intron 2 of human TLR2 are similar among nonhuman primates. The sequence is most conserved in New World monkeys and less in Old World monkeys.

Animals↗
PubMed2004

Endothelial nitric oxide synthase gene intron 4 polymorphism in patients with end-stage renal disease.

BACKGROUND: Nitric oxide (NO) synthesized by endothelial cell NO synthase (ecNOS) is a potent regulator of intrarenal haemodynamics. A polymorphism in intron 4 of the ecNOS gene is a candidate gene in cardiovascular and renal diseases. We investigated a potential involvement of this polymorphism in chronic renal failure. METHODS: We performed a case-control study involving 706 patients with end-stage renal disease (ESRD) and 321 healthy controls. All subjects were genotyped for the ecNOS4 polymorphism by the polymerase chain reaction followed by agarose gel electrophoresis. RESULTS: The analysis revealed that the frequencies of the ecNOS4 genotypes were significantly different in ESRD patients, both diabetic and non-diabetic, than in controls. In all dialysis patients for aa, ab and bb genotypes the frequencies were, respectively, 6.5, 35 and 58.5% in the patient group, and 1, 25 and 74% in control subjects. The a allele carriers (aa + ab) were more frequent among ESRD patients than in controls (OR 1.95; 95% CI 1.13-3.4; P = 0.0031). No significant association was found when hypertensive ESRD patients were compared with normotensive patients. The distribution of genotypes was similar in both subgroups (P = 0.21). CONCLUSION: There was a significantly higher frequency of the ecNOS4a allele carriers among ESRD patients, both diabetic and non-diabetic, than in control subjects. This suggests that the ecNOS gene polymorphism may be associated with an increased risk of chronic renal failure.

Case-Control Studies↗
PubMed2000

p53 intron 7 polymorphisms in urinary bladder cancer patients and controls. Stockholm Bladder Cancer Group.

A C-->T polymorphism in intron 7 of the human tumour suppressor gene p53 was studied in 159 urinary bladder cancer patients and 171 non-cancer controls. The polymorphism was found in 15% of both patients and controls, suggesting that it has no relevance in urinary bladder cancer pathogenesis or aetiology. A second polymorphism, a T-->G change located 20 bp downstream of the C-->T change, was found in all samples with the C-->T change. Our findings indicate that the C-->T and the T-->G changes occur simultaneously and belong to the same allelotype.

Adult↗
PubMed2003

Endothelial nitric oxide synthase gene intron 4 polymorphism in type 2 diabetes mellitus.

INTRODUCTION: Endothelial nitric oxide synthase (ecNOS) is a key regulator of vascular nitric oxide production. Polymorphism in intron 4 of the ecNOS gene is implicated in cardiovascular and renal diseases. We investigated a potential involvement of this polymorphism in the development of type 2 diabetes mellitus and its renal complications. METHODS: This preliminary study involved 410 individuals with type 2 diabetes and 330 healthy control subjects. From the diabetes group 178 patients had diabetic nephropathy. All subjects were genotyped for the ecNOS4 polymorphism by the polymerase chain reaction (PCR) followed by gel electrophoresis. Genotype and allele frequencies were compared between diabetes patients with and without nephropathy and the control group. All calculations were performed using the Statistical Package for the Social Sciences (SPSS, Inc., Chicago, IL, USA) for Windows 5.0. The chi-square test and Fisher's exact test were used for case-control comparisons. The Kruskal-Wallis test was used for the comparison of subgroups of patients with diabetes. RESULTS: The analysis revealed that patients with diabetes, regardless of their nephropathy status, were significantly different in genotype distribution and 4a allele frequencies compared with controls (p < 0.05). The frequency of aa genotype was 8.2% in diabetic patients without nephropathy, 8.4% with those with nephropathy and 1.2% in controls. The 4a allele showed a significant effect on diabetic nephropathy, with odds ratio of 2.24 (95% confidence interval 1.12-3.40). There were no significant differences in the 4a allele frequency between the normotensive and hypertensive patients with diabetes. CONCLUSION: Our results suggest that the ecNOS gene polymorphism can serve as a useful genetic marker of increased susceptibility to type 2 diabetes and its renal complications.

Adult↗
PubMed2004

WNK4 intron 10 polymorphism is not associated with hypertension.

A polymorphism in intron 10 of the serine-threonine kinase with no lysine (K) 4 gene WNK4 (G-->A, base 1156666 on chromosome 17) has recently been associated with essential hypertension in a white American population. We have attempted to replicate this finding in a well characterized cohort of 184 unrelated hypertensive Australians of British extraction in which biological power was enhanced by them each having 2 hypertensive parents. Controls were 219 normotensive ethnically matched subjects whose parents were both normotensive. Genotyping was performed using the homogeneous MassEXTEND Assay. This showed a frequency of 0.10 for the minor allele in each group (P=0.88). Moreover, blood pressure, body mass index, sex, and plasma lipid levels were similar across genotypes. In conclusion, our study provides no support for an association of the intron 10 variant of WNK4 with essential hypertension in the Anglo-Australian population studied.

Adult↗
PubMed2003

A LRPAP1 intronic insertion/deletion polymorphism and phenotypic variability in Alzheimer disease.

Alzheimer disease (AD) is a neurodegenerative disorder, characterized by dementia. AD exhibits variability in age at onset, rate of progression, and specific cognitive, functional, and behavioral features. Genetic variants are potential modulators of phenotypic variability. The purpose of this study was to explore the relationship between a polymorphism in the Low Density Lipoprotein Receptor Related Protein-Associated Protein (LRPAP1) gene (4p16.3) and repeated measures of cognition, function, and behavior in persons with AD, using outcome data collected in two caregiver intervention studies. Thirty-seven subjects diagnosed with probable or possible AD were recruited. All subjects were genotyped for a 37 basepair insertion/deletion polymorphism in intron 5 of the LRPAP1 gene. No differences in allele or genotype frequencies by gender or by age at onset were identified. No statistically significant genotype effects upon cognition or behavior were identified. However, trends were noted in measures of language, with the LRPAP1 insertion-positive subjects exhibiting poorer language scores (average score difference = 28%, p = .158). LRPAP1 insertion-positive subjects also were more functionally impaired than subjects without the LRPAP1 insertion allele (F1,7 = 7.36, p = .030). These results suggest genetic variations at the LRPAP1 locus may modulate AD phenotype beyond risk for disease.

Activities of Daily Living↗