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At least 145 records · Page 8Linked to original sources
PubMed2003

Simultaneous detection of the exon 10 polymorphism and a novel intronic single base insertion polymorphism in the XPD gene using single strand conformation polymorphism.

We developed a new method based on the single strand conformation polymorphism (SSCP) technique for the detection of a G23591A (Asp312Asn) polymorphism in exon 10 of the XPD gene. In the process we also identified a novel polymorphism 23623C-ins (IVS10+17C-ins) in intron 10 of the same gene. With this newly developed SSCP-based method of genotyping we could detect both polymorphisms in the same assay and thus consequently determine the haplotype. In order to determine the population frequency of the novel polymorphism and the haplotype frequency, 302 healthy individuals were genotyped. The allelic frequency of the 23623C-ins intronic polymorphism was 0.16, whereas the frequency of the variant allele for the G23591A polymorphism was 0.39. Forty-three individuals (14%) were heterozygous for both polymorphisms but none carried polymorphic variants for both G23591A and 23623C-ins on the same allele. The effect of the novel intronic insertion polymorphism, which is located 16 nt downstream of the 3'-end of exon 10 of the XPD gene and involves a mononucleotide C repeat sequence, on expression remains to be determined.

Adult↗
PubMed1999

Single-nucleotide polymorphisms in intron 2 of CYP21P: evidence for a higher rate of mutation at CpG dinucleotides in the functional steroid 21-hydroxylase gene and application to segregation analysis in congenital adrenal hyperplasia.

BACKGROUND: Intron 2 of CYP21, the functional steroid 21-hydroxylase gene contains several single-nucleotide polymorphisms (SNPs). We tested the hypothesis that intron 2 of the pseudogene, CYP21P, might also be polymorphic and provide markers for segregation analysis of this region of the genome, including observable markers for segregation analysis of CYP21 gene deletions. A comparison of SNPs in both genes might provide insights into the rates of mutation in these duplicated genes. METHODS: After amplification with PCR, we examined restriction site polymorphisms in intron 2 of CYP21P in 24 members of the parental generation of the Centre d'Etude du Polymorphisme Humain families and selected offspring. RESULTS: Intron 2 of CYP21P contains frequent SNPs around nucleotide 398 and nucleotide 509, which can be typed by PCR/restriction enzyme digestion with HaeIII. Of the 48 CYP21P alleles examined, 44 could be characterized unambiguously. Of these 44 alleles, 4 were deleted, and the frequencies of restriction at the polymorphic HaeIII sites were 20 of 40 at nucleotide 398 and 30 of 40 at nucleotide 509. Both polymorphisms result from C-->T transitions that occur at CpG dinucleotides. The frequencies of C at these nucleotides in CYP21P are significantly higher than at the corresponding nucleotides in CYP21 of the same individuals (P <0.01). CONCLUSION: These data suggest that these CpG dinucleotides are more frequently mutated in CYP21 than in CYP21P, and that several mutations at CpG dinucleotides in the coding regions of CYP21 might result from CpG instability rather than the more usually proposed mechanism of gene conversion. These frequent SNPs provide useful markers for studying both allelic segregation of CYP21, particularly for chromosomes with known CYP21 deletions, and for investigating the origin of these polymorphisms.

Adrenal Hyperplasia, Congenital↗
PubMed2006

C2028T polymorphism in exon 12 and dinucleotide repeat polymorphism in intron 13 of the HIF-1alpha gene define HIF-1alpha protein expression in non-small cell lung cancer.

OBJECTIVES: In this study, we investigated whether polymorphisms of the HIF-1alpha gene may account for the patterns of HIF-1alpha protein expression in non-small cell lung carcinomas (NSCLC) and the expression of HIF-1alpha down-stream proteins. METHODS: Specific HIF-1alpha polymorphisms were assessed in a series of patients with NSCLC: (a) the C to T transition at nucleotide 1744 (position 2028 according to sequence with accession number , which gives rise to Pro/Ser variation at codon 582), (b) the G to A nucleotide substitution at point 1790 (position 2046 according to sequence with accession number , which gives rise to Ala/Thr variation at codon 588), and (c) the dinucleotide GT repeat polymorphism in intron 13. Immunohistochemistry for HIF-1alpha and down-stream proteins (VEGF, LDH-5, GLUT-1) was also performed in tumor material. RESULTS: A strong association of the P582S polymorphism and of GT repeat polymorphism higher than 14/14 with increased HIF-1alpha expression was noted. HIF-1alpha polymorphism did not relate to the expression of the HIF-1alpha downstream proteins analysed, but significant association of HIF-1alpha expression with LDH-5 was confirmed (p=0.008). CONCLUSIONS: HIF-1alpha polymorphisms may have an important impact on HIF-protein stability and, eventually, function.

Aged↗
PubMed2001

Single nucleotide polymorphisms in intron 2 of the human interleukin-1 receptor antagonist (IL-1Ra) gene: further definition of the IL-1 beta and IL-1Ra polymorphisms in North American Caucasians and Taiwanese Chinese.

Previous studies have suggested that a variable number tandem repeat (VNTR) polymorphism in the second intron of the interleukin-1 receptor antagonist (IL-1Ra) gene and the single nucleotide polymorphisms at positions -511 and +3954 of the IL-1beta gene might be associated with increased risks of chronic inflammatory diseases, autoimmune diseases and gastric cancer. In the present study, IL-1beta and IL-1Ra genotypes were analyzed among Asians in Taiwan and Caucasians in North America. We identified a novel polymorphism with 3 nucleotide substitutions in the IL-1Ra VNTR 2-repeat allele. One of the substitutions corresponds with the fourth 3' end nucleotide of the reverse primer that is often used for analysis of the IL-1Ra-associated VNTR locus. Mismatching between this primer and the 2-repeat allele can cause misleading amplification results when stringent conditions are used for annealing. The estimated haplotype frequencies of the variant IL-1 genes were significantly different between Taiwanese and Caucasians. The frequency of the pro-inflammatory IL-1Ra 2-repeat allele was significantly lower in Taiwanese than in Caucasians. In contrast, the frequencies of the pro-inflammatory IL-1beta -511T allele and +3954C allele were significantly higher among Taiwanese compared with Caucasians.

Asian People↗
PubMed1998

Insertion/deletion polymorphism in intron 16 of the ACE gene and left ventricular hypertrophy in patients with end-stage renal disease.

We studied the relationship between polymorphism in intron 16 of the angiotensin-converting enzyme (ACE) gene and left ventricular (LV) hypertrophy in uremic patients treated with hemodialysis therapy. The LV parameters were not different for age-, hematocrit-, and blood pressure-matched patients in DD, ID, and II genotype groups. The most important factor for LV hypertrophy was systolic blood pressure, which correlated with the posterior wall thickness (r=0.35; P=0.001) and LV mass index (LVMI; r=0.23; P=0.032). Among nonhypertensive patients, the frequency of interventricular septum (IVS) hypertrophy (>12 mm) and hypertrophy in LVMI (>145 g/m2) was significantly greater in patients with the DD genotype than in I allele-positive (+) patients. The odds rate for IVS hypertrophy was 5.04 (95% confidence interval, 1.15 to 24.8). These data suggest that the DD genotype of the ACE gene polymorphism is a contributory factor for the development of LV hypertrophy in patients with end-stage renal disease (ESRD).

Age Factors↗
PubMed2003

Polymorphism in intron 2 of the fetal interleukin-1 receptor antagonist genotype influences midtrimester amniotic fluid concentrations of interleukin-1beta and interleukin-1 receptor antagonist and pregnancy outcome.

OBJECTIVE: Preterm labor in experimental models is initiated by intra-amniotic interleukin-1beta (IL-1beta) and inhibited by interleukin-1 receptor antagonist (IL-1ra). The IL-1ra gene is polymorphic and the different alleles are associated with variations in IL-1beta and IL-1ra production. The relationship among the IL-1ra genotype of the fetus, concentrations of IL-1beta and IL-1ra in second-trimester amniotic fluid, and pregnancy outcome was determined. STUDY DESIGN: Amniotic fluids from 291 consecutive women with singleton pregnancies, obtained at 15 to 17 weeks' gestation, were tested for IL-1beta and IL-1ra concentrations by enzyme-linked immunosorbent assay. DNA from fetal cells was analyzed for a length polymorphism in intron 2 of the IL-1ra gene by polymerase chain reaction. Pregnancy outcomes were obtained after completion of testing. RESULTS: The distribution of fetal IL-1ra genotypes was similar to that found in other populations: 50.9% (148) were homozygous for allele 1 (IL1RN*1), 39.5% (115) were IL1RN*1/allele 2 (IL1RN*2) heterozygotes, 6.9% (20) were IL1RN*2 homozygotes, whereas 2.7% (8) had combinations of other alleles. Fetal possession of IL1RN*2 was associated with a greater than 50% increase in midtrimester intra-amniotic IL-1beta levels (P=.006) and a smaller increase in IL-1ra levels (P=.01) compared with fetuses who were IL1RN*1 homozygotes. Despite the low sample size, IL1RN*2 homozygosity, but not midtrimester intraamniotic levels of IL-1beta and IL-1ra, was related to an increased rate of preterm birth (P<.0001). In the 11 pregnancies that were subsequently terminated because of major malformations, there was a decreased frequency of IL1RN*1 homozygosity (P=.04). Birth weight was unrelated to IL-1ra genotype. CONCLUSION: Possession by the fetus of the IL1RN*2 allele is associated with enhanced intraamniotic IL-1beta production. Induction of an intra-amniotic proinflammatory immune response might be more likely to lead to preterm labor in fetuses carrying the IL1RN*2 allele.

Amniotic Fluid↗
PubMed2002

Smoking status-dependent association of the 27-bp repeat polymorphism in intron 4 of endothelial nitric oxide synthase gene with plasma nitric oxide concentrations.

BACKGROUND: Both positive and negative associations between a rare allele of 27-bp repeat polymorphism (eNOS4b/a polymorphism) in intron 4 of endothelial nitric oxide synthase and plasma nitric oxide (NO) concentrations were previously reported. Although these conflicting results were suggested to be partly accounted for smoking status of subjects, no further studies have been accomplished. METHODS: We analyzed eNOS4b/a polymorphism in a group of 393 healthy Korean subjects and measured their plasma nitrite and nitrate (NO(x)) concentrations. NO(x) concentrations were measured by the Griess method and the genotypes of eNOS4b/a polymorphism determined by the banding pattern on gel electrophoresis. RESULTS: The frequency of eNOS4a allele in this study was 11.6%. The plasma NO(x) concentrations (in micromol/l) in subjects with eNOS4a allele was found to be significantly higher relative to those in eNOS4b allele (49.68 +/- 18.62 and 55.25 +/- 20.87, respectively, P < 0.05), which was valid only in smokers. Multiple regression analysis revealed that the most predictive contributing factor for plasma NO(x) concentrations was eNOS4a allele (P < 0.01), followed by smoking (P < 0.05), total cholesterol (P < 0.05), and triglycerides (P < 0.05). CONCLUSION: Our data indicate that there is substantial effect of eNOS4b/a polymorphism on the variance of plasma NO(x) concentrations in Korean population and that this effect is dependent on smoking status.

Adult↗
PubMed2006

No evidence for angiotensin type 2 receptor gene polymorphism in intron 1 in patients with coarctation of the aorta and Ullrich-Turner syndrome.

In male patients with congenital anomalies of the kidney and urinary tract, an increased incidence of a polymorphism in the angiotensin type 2 receptor gene (AT2R) has been identified. The AT2R has been shown to be involved in apoptosis, particularly during embryogenesis. The aim of this study was to examine the A-->1675G transition polymorphism in intron 1 of the AT2R gene that is located on the X chromosome in patients with coarctation of the aorta (CoA) with and without Ullrich-Turner syndrome (UTS). Screening of DNA samples was performed with restriction fragment length polymorphism analysis. Ninety-seven patients with CoA, 28 girls with UTS, 10 girls with UTS and CoA, and 96 control individuals were studied. There was no significant difference in the distribution of A and G-genotypes in any of the patient groups compared to controls. An A-->1675G transition in the AT2R gene seems not to be involved in the pathogenesis of aortic coarctation.

Aortic Coarctation↗
PubMed1997

Intron-length polymorphism at the actin gene locus mac-1: a genetic marker for population studies in the marine mussels Mytilus galloprovincialis Lmk. and M. edulis L.

A novel intron-length polymorphism at the actin gene locus mac-1 is here reported and used as a genetic marker for population studies in mussels of the genus Mytilus. Two closely related genes subsequently identified as alleles, mac-1a1 and mac-1b1, from a genomic library of M. galloprovincialis were partially cloned and sequenced. They mainly differed from each other by a 65-bp insertion within their first intron. Polymerase chain reaction (PCR) primers were designed outside the insertion. The PCR analysis of 166 individual mussels from M. galloprovincialis and M. edulis populations revealed three size-classes of alleles or allelomorphs, two of which were of the expected sizes for mac1a1 and mac-1b1. One allelomorph was absent from M. edulis samples, although it was present at substantial frequencies in M. galloprovincialis populations. The frequencies of the two other allelomorphs significantly differed between M. galloprovincialis and M. edulis populations. The comparison of six mac-1 intron sequences over 277 bp showed at once that allelomorphs encompassed alleles differing from one another by substantial numbers of mutations, and that identical alleles were present in both M. galloprovincialis and M. edulis individuals, a probable result of the recent introgression between the two species.

Actins↗
PubMed2000

An insertion/deletion polymorphism in intron 18 of the type B human natriuretic peptide receptor gene is not associated with cerebral infarction.

The natriuretic peptide (NP) system may play a crucial role in the development of cardiovascular and renal diseases. C-type NP dilates arteries and lowers blood pressure, and it inhibits the proliferation of vascular smooth muscle cells via the type B NP receptor (NPRB). We determined and analyzed the structure of the NPRB gene and found an insertion/deletion (I/D) polymorphism in intron 18. In this experiment, we studied this I/D polymorphism in the NPRB gene in 241 subjects, including 118 patients with cerebral infarction (the CI group) and 123 control subjects (the non-CI group). Our goal was evaluate the association of this polymorphism with cerebral infarction. Our findings showed that genotype frequencies of the I/D polymorphism were in Hardy-Weinberg equilibrium. The frequencies for the II, ID, and DD alleles were 0.569, 0.374, and 0.057, respectively, in the non-CI group and 0.576, 0.356, and 0.068, respectively, in the CI group. No association was found between this polymorphism and cerebral infarction. These results suggest that this polymorphism in the NPRB gene is not linked to a pathogenic CI gene.

Aged↗
PubMed1998

Lack of association between atopy and RsaI polymorphism within intron 2 of the Fc(epsilon)RI-beta gene in a Spanish population sample.

BACKGROUND: The B genotype of RasI polymorphism located within intron 2 of the Fc-IgE receptor I (Fc(epsilon)RI) gene was previously found to be increased in atopic patients from a Japanese population sample. METHODS: We studied these A/B genotypes in 70 Spanish atopic patients, and the results were compared to those of 51 nonatopic controls. RasI polymorphisms were studied by specific digestion of polymerase chain reaction fragments followed by polyacrylamide gel electrophoresis. RESULTS: The polymorphism frequency (A/A: 25/70, A/B: 28/70, B/B: 17/70) found in patients did not differ from the frequency in nonatopic control subjects. CONCLUSIONS: We did not find RasI polymorphisms associated with atopic disease. The genetic findings in atopy and asthma may be very different according to ethnic and local characteristics, and they must be carefully verified in different population samples.

Adolescent↗
PubMed2000

[Study on the Polymorphism of Intron 22 (CA)n Repeat within FVIII Gene in Dai, Yi and Han Populations of Yunnan Province]

This study was designed to investigate the polymorphism of intron 22 (CA)n repeat within FVIII gene in Dai, Yi and Han populations of Yunnan province. PCR, DNA sequencing technique and PAGE were used in this study. The results showed that three different alleles corresponding to 24, 25 and 26 dinucleotides were found at this locus and the allele frequency ranged from 1.20% to 57.7% in Dai and from 16.43% to 63.00% in Yi populations. In Han population, five different alleles with 24, 25, 26, 27 and 28 (CA)s were found, the allele frequency ranged from 8.97% to 32.00%. Heterozygotes of intron 22 (CA) repeat within FVIII gene were not found in the three populations. In conclusion, it was obvious that the locus cannot be acted as DNA genetic marker of FVIII gene in the three populations in Yunnan.

Journal Article↗
PubMed2002

A polymorphism within intron 11 of the tau gene is not increased in frequency in patients with sporadic Alzheimer's disease, nor does it influence the extent of tau pathology in the brain.

There are numerous polymorphisms within the tau gene but these are in complete linkage disequilibrium and exist as two common extended haplotypes H1 and H2. We have investigated the frequency of these haplotypes in 83 cases of sporadic Alzheimer's disease (AD) using the +34 polymorphism in intron 11 of the tau gene as a marker of H1 and H2 haplotypes. The total amount of hyperphosphorylated tau protein (tau load), present as neurofibrillary tangles, neuropil threads or plaque neurites, was quantified in the frontal cortex of these patients and related to tau haplotype. We found no increase in H1H1 haplotype in this autopsy population of cases with AD compared to published control data. Stratification of cases for apolipoprotein E (APO E) genotype showed a slight, but not statistically significant, overrepresentation of epsilon 4 allele amongst bearers of H2 haplotype. There were no overall differences in tau load between haplotype groups though cases within each haplotype group bearing APO E epsilon 4 allele had a significantly higher tau load than those without epsilon 4 allele. Neither age at onset or duration of illness differed according to tau haplotype. We conclude that the frequency of tau gene H1 haplotype is not elevated in AD and possession of this has no impact upon the amount of tau pathology in AD.

Adult↗
PubMed2004

Association between polymorphism in intron 1 of cocaine- and amphetamine-regulated transcript gene with alcoholism, but not with bipolar disorder and schizophrenia in Korean population.

Cocaine- and amphetamine-regulated transcript (CART) peptide is a novel neuropeptide involved in feeding, drug reward, and stress. We hypothesized that the polymorphism of CART gene might be related with susceptibility to neuropsychiatric diseases such as alcoholism, bipolar disorder, and schizophrenia. The polymorphism (rs2239670) in intron 1 was selected for study among other single nucleotide polymorphisms (SNPs) located at the area of CART gene, because it had not been tested until to date. The study included patients of alcoholism (100), bipolar disorder (76) and schizophrenia (169) from the Korean population. Healthy controls for bipolar disorder and schizophrenia consisted of 333 individuals. For alcoholism, both patient group and control subjects included only male. The restriction fragment length polymorphism (RFLP) using the AvaII restriction enzyme was designed to analyze the selected SNP. The distribution of GG, GA, and AA genotypes in the 333 controls was 50.2, 41.1, and 8.7%, respectively. The frequency of G and A alleles in the 333 controls was 70.7 and 29.3%, respectively. The distribution of genotype and allele frequencies of the AvaII polymorphism showed a significant difference between alcoholism and controls (P = 0.037 and P = 0.044). However, the AvaII polymorphism of the CART gene did not show association with bipolar disorder and schizophrenia. In conclusion, we report for the first time that the AvaII polymorphism (rs2239670) in intron 1 of the CART gene is associated with alcoholism in the Korean male population.

Alcoholism↗
PubMed1995

Two single base polymorphisms in introns 41 and 16 of the NF1 gene.

We have characterized two intragenic polymorphisms in the neurofibromatosis type 1 (NF1) gene by direct sequencing of PCR products. The variants for these polymorphisms were initially detected on Hydrolink gels. One of the polymorphisms involves a G to A transition in intron 41 at the 28th base upstream of exon 42 with an observed 'G'/'A' heterozygosity of 0.42. The other polymorphism is a T to C transition in intron 16 at the 16th base upstream of exon 17 with an observed 'T'/'C' heterozygosity of 0.09. In combination with other documented polymorphisms in the NF1 gene, these variants should assist in genetic analysis of NF1 families.

Base Sequence↗