A polymorphism in intron 6 of the CYP17 gene.
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Asian↗
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Results for “intronic polymorphism”
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A polymorphism in intron 2 of the TP53 gene.
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Alleles↗
Molecular basis of ESD*5 and ESD*7 and haplotype analysis with new polymorphisms in introns.
The two polymorphic alleles of esterase D (ESD), ESD*5 and ESD*7, are specific to Europeans and Asians, respectively. In this study the molecular basis was characterized: ESD*5, arising from ESD*1, has a G to A transition, resulting in Gly257(GGT) --> Asp(GAT); and ESD*7, originating from ESD*2, has an A to G transition, resulting in Asp231(GAT) --> Gly(GGT). Glycine is also involved in the common ESD*1/ESD*2 polymorphism [Gly190(GGA) --> Glu(GAA)]. Haplotype analysis using a few novel intragenic polymorphisms showed strong associations among polymorphic sites, suggesting that recombination has been less frequent in the human ESD gene, although it spans about 25 kb from exon 1 to exon 10. A marked difference was observed in the distribution of haplotype frequencies between Germans and Japanese.
Animals↗
[p53 gene intron 7 polymorphism and its association with oral neoplasms].
OBJECTIVE: To investigate the association between oral neoplasm genetic susceptibility and genetic polymorphism of p53 intron 7. METHODS: The intron 7 ApaI polymorphism of p53 was analyzed in 95 oral neoplasm patients and 105 healthy individuals by utilizing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotyping assay technique, and direct sequencing was performed in 30 cases which were selected from the patients and controls by random sampling. RESULTS: In oral neoplasms cases, haplotype combinations were T-G 43.2%, C-T 56.8%, and frequencies of genotype were T-G/T-G 15.8%, C-T/T-G 54.7%, C-T/C-T 29.5%, while in controls they were T-G 30.9%, C-T 69.1% and T-G/T-G 10.5%, C-T/T-G 41.0%, C-T/C-T 48.5%. There was a significant difference in the allelic frequency and the genotypical distributions between the oral neoplasm patients and the controls. The individuals with the T-G allele had a slight increasing neoplasm risk than individuals with C-T allele; the OR for T-G versus C-T was 1.69 (95% CI, 1.12 - 2.51). The risk of suffering from oral neoplasms was higher in the individuals of T-G/T-G genotype and of T-G/C-T genotype than in individuals of C-T/CT genotype with odds ratio of 2.48 versus 2.20. CONCLUSIONS: There are two polymorphic points in the 7th intron of human p53 gene, which could be associated with genetic susceptibility of oral neoplasms. T-G allele may be the risk factor of oral neoplasms.
Adult↗
Genetic variation of the methylenetetrahydrofolate reductase and cystathionine beta-synthase genes in Korean patients with coronary artery disease and a new polymorphism in intron 7.
We investigated polymorphisms of methylenetetrahydrofolate reductase (MTHFR) and cystathionine beta-synthase (CBS) genes in Korean patients with coronary artery disease (CAD) and identified a new polymorphism (c-->t) in intron 7 of the CBS gene using the single-strand conformation polymorphism method. No significant differences were found in allele frequencies for either gene between the CAD and normal groups although the frequency of the so-called thermolabile MTHFR polymorphism, a proposed risk factor for CAD, was higher in Koreans than in other populations studied. The relatively low incidence of CAD in Korea suggests that this MTHFR polymorphism is not causative in this population.
Coronary Disease↗
Intron 3 16 bp duplication polymorphism of p53 is associated with an increased risk for breast cancer by the age of 50 years.
We used a large population-based case-control study to determine whether three known p53 polymorphisms, intron 3 16 bp duplication, codon 72(Arg/Pro) and intron 6 MspI restriction fragment length polymorphism, alter the risk for breast cancer in German women. For all three polymorphisms, the odds ratios (ORs) for breast cancer were increased in women carrying the rare allele; however, this was statistically significant only for the 16 bp duplication polymorphism. Compared with the 16 bp duplication wild-type A1/A1 genotype, ORs for A1/A2 genotype and A2/A2 genotype were 1.3 [95% confidence interval (CI) 1.0-1.7] and 1.7 (95% CI 0.8-3.4), suggesting an allele dosage effect (trend test, P = 0.03). Significant evidence was found for a differential effect by family history of breast cancer (P = 0.03 for interaction), with the OR being 5.3 among women with a first degree family history. Our data suggest that inheritance of an intronic polymorphism in the p53 gene increases breast cancer risk appreciably in women by the age of 50 years with a family history of breast cancer in the German population.
Breast Neoplasms↗
Haplotypes defined by promoter and intron 1 polymorphisms of the COLIA1 gene regulate bone mineral density in women.
CONTEXT: The COLIA1 gene is a strong candidate for susceptibility to osteoporosis. The causal genetic variants are currently unclear, but the most likely are functional polymorphisms in the promoter and intron 1 of COLIA1. OBJECTIVE: The objective of the study was to determine whether promoter and intron 1 polymorphisms of COLIA1 or haplotypes defined by these polymorphisms regulate bone mineral density (BMD) in women. DESIGN: This was a population-based association study involving 3270 women from the United Kingdom who took part in a regional osteoporosis screening program. MAIN OUTCOME MEASURES: BMD at the lumbar spine (LS-BMD) and femoral neck (FN-BMD) was measured on two occasions approximately 6 yr apart, in relation to polymorphisms and haplotypes defined by polymorphisms within the COLIA1 intron 1 (+1245G/T; rs1800012) and promoter (-1997G/T; rs1107946; -1663IndelT; rs2412298). RESULTS: The polymorphisms were in strong linkage disequilibrium, and three haplotypes accounted for more than 95% of alleles at the COLIA1 locus. The individual polymorphisms were associated with BMD, but the most consistent associations were with haplotypes defined by all three polymorphisms. Homozygote carriers of haplotype 2 (-1997G/-1663delT/+1245T) had reduced BMD at baseline (P = 0.007 for LS-BMD; P = 0.008 for FN-BMD), whereas homozygotes for haplotype 3 (-1997T/-1663insT/+1245G) had increased BMD (P = 0.007 for LS-BMD). Similar associations were observed at follow-up for haplotype 3, but the association with haplotype 2 was weaker due to increased uptake of hormone replacement therapy in homozygotes for this haplotype. CONCLUSIONS: Two haplotypes defined by polymorphisms in the 5' flank of the COLIA1 regulate BMD in a bidirectional manner in women.
Absorptiometry, Photon↗
Identification of a polymorphism in intron 2 of the p53 gene.
A polymorphism in intron 2 of the p53 gene was identified by single-strand conformation polymorphism analysis. The result is a G-to-C transversion at bp +38 following the splice donor site of exon 2.
Alleles↗
Ambulatory blood pressure, left ventricular mass and vascular phenotypes in relation to the endothelial nitric oxide synthase gene Glu298Asp and intron 4 polymorphisms in a population-based family study.
Reduced nitric oxide production is associated with pathological changes in the cardiovascular system. In a study of randomly chosen families, we analysed the relationship between two polymorphisms (Glu298Asp and intron 4) of the endothelial nitric oxide synthase (eNOS) and ambulatory blood pressure (ABP), left ventricular mass index (LVMI) and vascular phenotypes. The study population consisted of 127 parents and 167 offspring. All subjects underwent 24 h ABP monitoring using a SpaceLabs 90207 device. 2D and M-mode echocardiograms were obtained. Pulse wave velocity between the common carotid and femoral artery was measured with the Complior device, and the carotid intima-media thickness (IMT) was assessed by ultrasound. For statistical analysis, covariables and correlations between relatives were taken into account. The frequency of genotypes was as follows: for Glu298Asp: 55.1%-Glu/Glu, 40.1%-Glu/Asp and 4.8%-Asp/Asp; for intron 4: 65.0%-4 b/b, 33.3%-4 b/a and 1.7%-4 a/a, being in Hardy-Weinberg equilibrium (P > or = 0.29). There was no relationship between the eNOS gene polymorphisms and ABP or LVMI either in parents or their offspring. Among parents, carriers of the 298Asp allele had higher IMT values as compared with Glu/Glu homozygotes (0.94 vs 0.70 mm; P = 0.007). Among offspring, there was a similar tendency (0.60 vs 0.53 mm; P = 0.10), which was confirmed by transmission disequilibrium tests for quantitative variables (P > or = 0.07). Our findings indicate that the Glu298Asp polymorphism of eNOS identifies patients with larger carotid IMT, also in younger subjects.
Adolescent↗
A serotonin transporter gene intron 2 polymorphic region, correlated with affective disorders, has allele-dependent differential enhancer-like properties in the mouse embryo.
Polymorphic regions consisting of a variable number of tandem repeats within intron 2 of the gene coding for the serotonin transporter protein 5-HTT have been associated with susceptibility to affective disorders. We have cloned two of these intronic polymorphisms, Stin2.10 and Stin2.12, into an expression vector containing a heterologous minimal promoter and the bacterial LacZ reporter gene. These constructs were then used to produce transgenic mice. In embryonic day 10.5 embryos, both Stin2.10 and Stin2.12 produced consistent beta-galactosidase expression in the embryonic midbrain, hindbrain, and spinal cord floor plate. However, we observed that the levels of beta-galactosidase expression produced by both the Stin2.10 and Stin2.12 within the rostral hindbrain differed significantly at embryonic day 10.5. Our data suggest that these polymorphic variable number of tandem repeats regions act as transcriptional regulators and have allele-dependent differential enhancer-like properties within an area of the hindbrain where the 5-HTT gene is known to be transcribed at this stage of development.
Animals↗
Endothelial nitric oxide synthase intron 4 polymorphism is a marker for coronary artery disease in African-American and Caucasian men.
OBJECTIVES: We investigated the association of the intron 4 polymorphism of the endothelial nitric oxide synthase (eNOS) gene with coronary artery disease (CAD). BACKGROUND: Genetic alterations in the gene encoding for eNOS could contribute to the development and progression of CAD. METHODS: We genotyped for the eNOS intron 4 polymorphism in 194 subjects undergoing coronary angiography. Genotyping was performed with polymerase chain reaction-restriction fragment length polymorphism for the variable number of tandem repeats in intron 4. Coronary artery disease (CAD) was assessed by quantitative coronary angiography, and endothelial function was measured by brachial ultrasonography. We performed logistic regression analysis for the effect of eNOS intron 4 polymorphism and other coronary risk factors on multi-vessel CAD and endothelial function. RESULTS: The 4a-allele frequency in African Americans was 0.31, while the 4a-allele frequency in Caucasians was 0.15 (P<.001). The prevalence of the 4a-allele was highest among subjects with multi-vessel disease both for African Americans and for Caucasians. A race-adjusted comparison of the prevalence of the 4a-allele among subjects with multi-vessel disease vs those without was statistically significant (P=.03). No correlation was found between the eNOS intron 4 polymorphism and endothelial function. CONCLUSIONS: The eNOS intron 4 polymorphism may be a marker of multi-vessel CAD in African Americans and Caucasians.
Adult↗
Lack of independent associations of apolipoprotein E promoter and intron 1 polymorphisms with Alzheimer's disease.
Several studies have demonstrated genetic associations between Alzheimer's disease (AD) and polymorphisms in the promoter/enhancer regions of the apolipoprotein E (APOE) gene. These studies raise the possibility that APOE transcription control may be involved in altered risks for AD. We evaluated polymorphic sites in the intron-1 enhancer element (IE-1G/C) and in the APOE promoter (-219G/T). For the IE-1 polymorphism, we analyzed 433 individuals (183 AD and 250 controls), and found a strong linkage between the IE-1G allele and APOE-epsilon4. When we controlled for this linkage using log-linear model analysis, we found no independent association between the IE-1 polymorphism and AD. For the -219 polymorphism, we analyzed 475 individuals (168 AD cases, 234 controls, and 73 cases of cerebral amyloid angiopathy (CAA)). We found strong linkages between the -219G allele and APOE-epsilon2 and between the -219 T allele and APOE-epsilon4. Controlling for these linkages, we found no independent association between the -219 polymorphism and AD or CAA. Thus, our studies do not support independent associations between AD and either the IE-1 or the -219 polymorphisms.
Alleles↗
Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR.
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Animals↗
Genetic mapping of the human tryptophan hydroxylase gene on chromosome 11, using an intronic conformational polymorphism.
The identification of polymorphic alleles at loci coding for functional genes is crucial for genetic association and linkage studies. Since the tryptophan hydroxylase (TPH) gene codes for the rate-limiting enzyme in the biosynthesis of the neurotransmitter serotonin, it would be advantageous to identify a polymorphism in this gene. By examining introns of the human TPH gene by PCR amplification and analysis by the single-strand conformational polymorphism (SSCP) technique, an SSCP was revealed with two alleles that occur with frequencies of .40 and .60 in unrelated Caucasians. DNAs from 24 informative CEPH families were typed for the TPH intron polymorphism and analyzed with respect to 10 linked markers on chromosome 11, between p13 and p15, with the result that TPH was placed between D11S151 and D11S134. This region contains loci for several important genes, including those for Beckwith-Wiedemann syndrome and tyrosine hydroxylase.
Animals↗
Interleukin-4 intron 3 polymorphism is not related to susceptibility to febrile seizures.
Interleukin-4 (IL-4) is a cytokine with anti-inflammatory properties. This study was undertaken to investigate whether IL-4 intron 3 gene polymorphism could be used as markers of susceptibility to febrile seizures and epilepsy of children. Children were divided into three groups: group 1, febrile seizures (n = 51); group 2, epilepsy (n = 43); and group 3, normal control group (n = 83). Polymorphisms for IL-4 intron 3 were detected by polymerase chain reaction. Genotypes and allelic frequencies for IL-4 intron 3 gene polymorphism in three groups were compared. We found that proportions of different IL-4 intron 3 polymorphisms in three groups were nonsignificantly different. Proportions of RP1 homozygote/heterozygote/RP2 homozygote for IL-4 intron 3 in three groups were as follows: group 1, 56.9/41.2/1.9%; group 2, 62.8/32.6/4.6%; and group 3, 62.7/33.7/3.6%. The proportion of RP1/RP2 for IL-4 intron 3 in three groups were as follows: group 1, 77.5/22.5%, group 2, 79.1/20.9%, and group 3, 79.5/20.5%. We concluded that the association of IL-4 polymorphisms with febrile seizures and epilepsy of children does not exist. IL-4 intron 3 polymorphism is not a useful marker for prediction of the susceptibility of febrile seizure and epilepsy of children.
Chi-Square Distribution↗
The zone of sympatry and hybridization of Mytilus edulis and M. galloprovincialis, as described by intron length polymorphism at locus mac-1.
Intron-size variation at the actin gene locus mac-1 was used to characterize mussel, Mytilus spp., populations in the approximately 2000-km wide zone of contact and hybridization ('hybrid zone') between M. edulis and M. galloprovincialis in western Europe. Twenty-five samples were collected in 1995-99 in locations within the hybrid zone and from reference populations of each species. We used correspondence analysis on the matrix of allelic frequencies to determine which alleles are characteristic of each species, and to characterize samples along the genetic gradient between M. edulis and M. galloprovincialis. In the hybrid zone, some samples exhibited mac-1 allele frequencies that were typical of M. edulis; other samples were distributed along the M. edulis/M. galloprovincialis gradient and displayed variable levels of intergradation that were not correlated with geography. Some of the latter samples exhibited significant heterozygote deficiencies. The simple admixture hypothesis (Wahlund effect) could not be rejected for two-fifths of the samples. The hybrid zone thus appeared as a mosaic of populations which are either pure M. edulis, or hybrid between M. galloprovincialis and M. edulis, or a mixture of the foregoing with M. galloprovincialis individuals. These results were consistent with published allozyme data, suggesting that they can be extended to the entire nuclear genome. M. edulis mac-1 alleles were present at moderate frequency in Atlantic M. galloprovincialis, and at significantly lower frequency in some Mediterranean samples. This pattern was homogeneous over a broad geographical range within each basin. It was not evident that introgression of M. edulis into M. galloprovincialis presently occurs south of the zone of contact. We propose that the distinctness of the Atlantic M. galloprovincialis population results from past introgression by M. edulis alleles.
Actins↗
Characterization of frequent polymorphisms in intron 2 of CYP21: application to analysis of segregation of CYP21 alleles.
The gene encoding adrenal steroid 21-hydroxylase, CYP21, is located in the MHC class III region. Most cases of congenital adrenal hyperplasia (CAH) are caused by mutations in this gene, and most mutations appear to arise from gene conversion-like events involving the transfer of deleterious sequences from the pseudogene, CYP21P, which is located within 30 kb of CYP21. Approximately 20-30% of mutations are caused by deletions of CYP21. The second intron of CYP21 is polymorphic, and several base substitutions that include nt395, nt453, and nt601 have been reported; however, the frequencies of these polymorphisms are unknown. Using a combination of cleavase fragment length polymorphism analysis and direct sequencing, we examined the sequence of intron 2 in seven wild-type CYP21 genes and determined the frequency of polymorphisms at nt395, nt453, and nt601 in 48 chromosomes from the parental generation of Centre d'Etude du Polymorphisme Humain families. The observed frequencies of bases at these positions were as follows: 395C, 0.17; 395T, 0.83; 453C, 0.71; 453T, 0.29; 601A, 0.1; and 601C, 0.9. Using a PCR/restriction digestion approach to examine these intragenic markers, we could follow the segregation of alleles in informative families with 21-hydroxylase deficiency and identify deletions of CYP21. We emphasize that this method should be used in conjunction with other molecular genetic techniques for diagnosis of CAH. In addition to their potential use in families with CAH, these markers may be of use in genetic studies of the MHC in humans.
Adrenal Hyperplasia, Congenital↗
Functional significance of a C-->A polymorphism in intron 1 of the cytochrome P450 CYP1A2 gene tested with caffeine.
AIMS: The cytochrome P450 enzyme CYP1A2 metabolises several drugs and carcinogens. We wanted to determine how much of the variability of CYP1A2 activity is explained by a newly discovered gene polymorphism in intron 1. METHODS: A single nucleotide polymorphism in intron 1 of the CYP1A2 gene at position 734 downstream of the first transcribed nucleotide was identified by DNA sequence analysis. The functional significance of this C/A polymorphism was assessed in 185 healthy Caucasian non-smokers and in 51 smokers by genotyping and phenotyping using caffeine (100 mg oral dose). RESULTS: Out of the total sample, 46% were homozygous for the variant A, 44% were heterozygous, and 10% were homozygous for the variant C. The ratio of 1,7-dimethylxanthine (17X) plus 1,7-dimethyluric acid divided by caffeine in 0-5 h urine samples from 185 non-smokers did not differ significantly between the three CYP1A2 genotypes. In the 51 smokers, analysis of variance revealed significant differences in the 5 h plasma 17X/caffeine ratios between the genotypes (P=0.008, F-test). The mean ratio was 1.37 in carriers of the A/A genotype, 0.88 in heterozygotes and 0.82 in carriers of C/C. The mean difference between the A/A and C/A groups was 0.48 (95% confidence interval 0. 15-0.81; P=0.01). CONCLUSIONS: The A/A genotype, which may represent a CYP1A2 high inducibility genotype, may either be a direct cause of increased CYP1A2 activity, or be genetically linked to polymorphisms conferring high inducibility. Further studies are needed to define the role of this polymorphism on the pharmacokinetics of drugs metabolised by CYP1A2 and in the activation of carcinogens.
Caffeine↗