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PubMed1999

Identification of a novel polymorphism in the promoter region of the tau gene highly associated to progressive supranuclear palsy in humans.

An intronic polymorphism and other changes in the transcribed region of the tau gene forming a haplotype have been previously described associated to progressive supranuclear palsy (PSP). These results raised the possibility that a change at or near the tau gene could be responsible for an increased risk to develop PSP. We initiated the present work in research for potential changes in the promoter region of the tau gene that could further extend the previously described haplotype. The tau promoter region was analyzed through single strand conformation polymorphism followed by direct sequencing in PSP patients (n = 35), in controls (n = 195) and in Alzheimer's disease (AD; n = 74) patients. We have been able to identify a G to C change at position -221 of the tau gene promoter region. The CC genotype has been detected to be present with a significantly higher frequency in PSP patients (91.4%; P < 0.00001; OR = 11.8), but not in AD patients, as compared with controls (49.74%). Subsequently we have detected that the CC -221 tau promoter genotype is significantly associated to the tau intronic A0/A0 genotype (P < 0.00001). The detected -221 tau G to C change occurs within a potential c-myb proto-oncogene element present in the promoter region. Thus, in addition to extending the previously described haplotype associated to PSP, this -221 G to C change is an interesting candidate that could provide a potential explanation for the association of the haplotype to increased risk for developing PSP.

Base Sequence↗

PubMed2002

Lack of impact of CYP1A2 genetic polymorphism (C/A polymorphism at position 734 in intron 1 and G/A polymorphism at position -2964 in the 5'-flanking region of CYP1A2) on the plasma concentration of haloperidol in smoking male Japanese with schizophrenia.

The impact of genetic polymorphism of CYP1A2 that are related to the induction of the isozyme on the plasma levels of haloperidol (HAL) in 40 male smokers with schizophrenia was investigated. A point mutation from C to A in intron 1 at position 734 and a point mutation from G to A at position -2964 in the 5'-flanking region of CYP1A2 were identified by polymerase chain-reaction-restricted fragment length polymorphism method. Regarding C/A polymorphism in intron 1 at position 734, no significant difference was found in the plasma concentrations of HAL corrected for dose and weight among the subjects with A/A (n = 21), A/C (n = 14) and C/C (n = 5) genotypes (one-way analysis of variance: 63.1 +/- 18.5, 47.8 +/- 12.5 and 50.8 +/- 15.1 ng/ml/mg/kg, respectively, F(2,37) = 2.556, P = .09). Regarding G/A polymorphism at position -2964 in the 5'-flanking region, no significant difference was found in the plasma concentrations of HAL corrected for dose and weight between subjects with G/G (n = 24) and G/A (n = 15) (two-tailed t test: G/G and G/A = 51.2 +/- 16.6 and 59.0 +/- 17.6 ng/ml/mg/kg, respectively, df = 28, P = .22). The present study suggests that the genotyping of CYP1A2 cannot predict the steady state plasma levels of HAL in male smoking schizophrenics.

5' Flanking Region↗

PubMed2004

Two functional variants of the superoxide dismutase genes in Finnish families with asthma.

BACKGROUND: Functional polymorphisms in the genes encoding superoxide dismutases (SOD)-that is, superoxide scavenging antioxidant enzymes-may play an important role in the development of inflammatory airway diseases such as asthma. METHODS: The allele frequencies of two missense polymorphisms of SOD genes (Ala16Val in MnSOD (SOD2) and Arg213Gly in ECSOD (SOD3)) were investigated in Finnish patients with asthma and compared with family based controls. Both variants have been shown to be functionally interesting in the lung. The polymorphism at the exon-intron 3 boundary of a third SOD, CuZnSOD (SOD1), was also included in the analysis. RESULTS: None of the SOD genetic variants studied appeared to be major genetic regulators in the development of asthma. We could exclude all models of inheritance that increased the risk of asthma more than 1.2 fold for MnSOD*Val (frequency of allele 0.74 in the population) and more than 6.6 fold for ECSOD*Gly213 (frequency of allele 0.03 in the population) compared with non-carriers. For the intronic polymorphism in CuZnSOD, a relative risk of more than 3.3 (frequency of allele 0.10 in the population) could be excluded. CONCLUSIONS: It is highly unlikely that the functionally important genetic variants Ala16Val and Arg213Gly of SODs play a major role in the genetic susceptibility of asthma.

Adolescent↗

PubMed1995

Structural analysis of the 5' region of mouse and human Huntington disease genes reveals conservation of putative promoter region and di- and trinucleotide polymorphisms.

We have previously cloned and characterized the murine homologue of the Huntington disease (HD) gene and shown that it maps to mouse chromosome 5 within a region of conserved synteny with human chromosome 4p16.3. Here we present a detailed comparison of the sequence of the putative promoter and the organization of the 5' genomic region of the murine (Hdh) and human HD genes encompassing the first five exons. We show that in this region these two genes share identical exon boundaries, but have different-size introns. Two dinucleotide (CT) and one trinucleotide intronic polymorphism in Hdh and an intronic CA polymorphism in the HD gene were identified. Comparison of 940-bp sequence 5' to the putative translation start site reveals a highly conserved region (78.8% nucleotide identity) between Hdh and the HD gene from nucleotide -56 to -206 (of Hdh). Neither Hdh nor the HD gene have typical TATA or CCAAT elements, but both show one putative AP2 binding site and numerous potential Sp1 binding sites. The high sequence identity between Hdh and the HD gene for approximately 200 bp 5' to the putative translation start site indicates that these sequences may play a role in regulating expression of the Huntington disease gene.

Animals↗

PubMed2002

The complex history of a gene proposed to participate in a sexual isolation mechanism in house mice.

Previous behavioral experiments showed that mouse salivary androgen-binding protein (ABP) was involved in interindividual recognition and might play a role in sexual isolation between house mouse (Mus musculus) subspecies. The pattern of evolution of Abpa, the gene for the alpha subunit of ABP, was found to be consistent with this hypothesis. Abpa apparently diverged rapidly between species and subspecies with a large excess of nonsynonymous substitutions, a lack of exon polymorphism within each of the three subspecies, and a lack of intron polymorphism in the one subspecies studied (M. musculus domesticus). Here we characterized the intron and exon sequence variations of this gene in house mouse populations from central Eurasia, a region yet unsampled and thought to be close to the cradle of the radiation of the subspecies. We also determined the intron and exon sequences in seven other species of the genus Mus. We confirmed the general pattern of rapid evolution by essentially nonsynonymous substitutions, both inter- and intraspecifically, supporting the idea that Darwinian selection has driven the evolution of this gene. We also observed a uniform intron sequence in five samples of M. musculus musculus, suggesting that a selective sweep might have occurred for that allele. In contrast to previous results, however, we found extensive intron and exon polymorphism in some house mouse populations from central Eurasia. We also found evidence for secondary admixture of the subspecies-specific alleles in regions of transition between the subspecies in central Eurasia. Furthermore, an abnormal intron phylogeny suggested that interspecific exchanges had occurred between the house mouse subspecies and three other Palearctic species. These observations appear to be at variance with the simple hypothesis that Abpa is involved in reproductive isolation. Although we do not rule out a role in recognition, the situation appears to be more complex than previously thought. Thus the selective mechanism behind the evolution of Abpa remains to be resolved, and we suggest that it may have changed during the recent colonization history of the house mouse.

Amino Acid Sequence↗

PubMedDate not supplied

Polymorphisms in the human homologue of the drosophila Indy (I'm not dead yet) gene.

Insertion of a P element in one copy of the Drosophila Indy gene results in a significant increase in Drosophila lifespan. In order to examine whether mutations or polymorphisms in the human Indy gene promoted human longevity, the Indy gene was sequenced in 13 subjects of age 90-99, 12 subjects between age 38-49 and 18 subjects <age 23. Three coding region polymorphisms resulting in an amino acid change, F62L, V80L and I550V, two silent coding region polymorphisms, A99A and I551I, and three intron polymorphisms, IVS2+10 C deletion, IVS9+40T/A and IVS10+38C/T were identified. The I550V polymorphism occurred in whites, Hispanics, Asians and African-Americans at allele frequencies of 0.3514, 0.5104, 0.4274 and 0.5375, respectively. The I550V polymorphism was genotyped in 2366 subjects and examined for its association with age and weight.

Adult↗

PubMed2003

Novel tau polymorphisms, tau haplotypes, and splicing in familial and sporadic frontotemporal dementia.

BACKGROUND: A subset of familial cases (FTDP-17) of frontotemporal dementia (FTD) are caused by mutations in the tau gene. The role of tau gene mutations and haplotypes in sporadic FTD and the functional consequences of tau polymorphisms are unknown. OBJECTIVES: To investigate (1) the frequency of known FTDP-17 mutations in familial and sporadic FTD and compare these results with previous studies; (2) whether the tau H1 haplotype is associated with FTD; and (3) the functional effect of intronic tau sequence variations. PATIENTS AND METHODS: Patients with familial and sporadic FTD were screened for mutations in the microtubule-binding region of tau. The frequencies of tau haplotypes and genotypes were compared between patients with FTD and control subjects. We analyzed the splicing effect of novel intronic polymorphisms associated with FTD. RESULTS: The P301L mutation was detected in 11% of familial FTD cases. The H1 haplotype was not overrepresented in patients with FTD, but the P301L mutation appeared on the background of the H2 tau haplotype. We identified 4 novel single nucleotide polymorphisms in intron 9 and a 9-base pair deletion in intron 4A. A C-to-T transition 177 base pairs upstream from exon 10 was significantly increased in patients with FTD compared with controls. Direct analysis of brain tissue from a patient with this variant showed an increase in exon 10-containing tau transcripts. CONCLUSIONS: Sequence variations in intronic or regulatory regions of tau may have previously unrecognized consequences leading to tau dysfunction and neurodegeneration.

Adult↗

PubMed2006

Association of VEGF and eNOS gene polymorphisms in type 2 diabetic retinopathy.

PURPOSE: Vascular endothelial growth factor (VEGF) is a major mediator of angiogenesis, and nitric oxide (NO) is an upstream and downstream regulator of VEGF mediated angiogenesis. VEGF and NO have been suggested to play an important role in the pathogenesis of microvascular complications in diabetic retinopathy (DR). The objective of this study was to examine the genetic variations of the VEGF and eNOS gene and assess their possible relationship to DR in type 2 diabetic patients in the Indian population. METHODS: In this study, 210 unrelated patients were enrolled and categorized into two study groups: a DR group, consisting of patients with proliferative diabetic retinopathy, and a diabetic without retinopathy (DWR) group comprised of patients with type 2 diabetes of more than 15 years duration who showed no signs of DR or had fewer than five dots or blot hemorrhages. Association of the genetic polymorphisms in the promoter and 5' UTR region of VEGF and the intron4 region of eNOS were studied. Total genomic DNA was isolated from peripheral blood leukocytes. PCR-RFLP analysis was performed for all samples to evaluate the genotypes. The distributions of the genotypes were compared using the chi2 test. Haplotype estimation and multiple logistic regression analysis were carried out to analyze the significance of polymorphisms. RESULTS: We investigated four reported polymorphisms in the VEGF (5' UTR, promoter) and one reported polymorphism (intron 4) in the eNOS gene in Type 2 diabetes patients with (n=120) and without (n=90) retinopathy. The genotype distribution of the C(-7)T, T(-1498)C, and C(-634)G polymorphisms of VEGF differed significantly between patients with DR and DWR (p=0.001, p=0.0001, and p=0.021, respectively). Allele C in the -1498 region (p=0.0001) and T in -7 region (p=0.002) were also found to be significantly increased in patients with retinopathy. Calculated odds ratios (OR) for three heterozygous genotypes of C(-7)T, T(-1498)C, and C(-634)G regions were 4.17 (95% CI: 1.90-9.18, p=0.0001), 4.37 (95% CI: 2.44-7.84, p=0.0001), and 2.33 (95% CI: 1.24-4.36, p=0.008), respectively, and was found to be significantly higher in the DR group when compared with the DWR group. Multiple logistic regression analysis revealed that the nongenetic parameters, age (p=0.024) and duration of diabetes (p=0.009), and the genetic parameters, like VEGF C(-7)T (p=0.002) and T(-1498)C (p=0.001) polymorphisms, were significantly associated with DR. The frequencies of haplotype consisting of the majority of alleles in VEGF were found to be significantly associated with DR. The genotype distribution of eNOS did not differ significantly between the two study groups, and therefore the eNOS intron 4 polymorphism was considered to be less significant. CONCLUSIONS: This is the first study to report VEGF and eNOS gene polymorphisms in patients with DR in the Indian population. The data suggest that the polymorphisms in the 5' UTR and promoter region of VEGF could be regarded as a major genetic risk factor for DR.

5' Untranslated Regions↗

PubMed2002

Genetic control of IL-1beta bioactivity through differential regulation of the IL-1 receptor antagonist.

Regulation of IL-1 bioactivity by the IL-1 receptor antagonist (IL-1Ra) is critical for the preservation of normal vascular structure and function in mice. In humans, IL-1 bioactivity may be further fine-tuned by genetic polymorphisms. We recently proposed that an intronic polymorphism of the human gene encoding the IL-1R antagonist (IL1RN) is a genetic risk factor for the development of chronic cardiac allograft rejection. Here we aimed to establish a physiological basis for this susceptibility. Plasma and peripheral blood mononuclear cells (PBMC) were obtained from 55 healthy human volunteers, whose genotypes for four polymorphisms of IL1 family genes (IL1B, IL1R1 and IL1RN) were determined by PCR. IL-1beta and IL-1Ra production and release in PBMC cultures were studied by flow cytometry and ELISA. Functional and genotypic data were pooled and analyzed first by multivariate and, subsequently, by univariate statistical tests. We were able to confirm our observed association of IL1RN genotype with chronic cardiac allograft rejection using multivariate statistics. IL1RN genotype also emerged as the principal regulator of both constitutive and stimulated IL-1Ra and IL-1beta release. Allele IL1RN*2 was consistently associated with higher IL-1Ra and lower IL-1beta release, in a dosage-dependent manner. Conversely, IL1RN*2 carriage was associated with reduced production of the intracellular isoform of IL-1Ra. These genotypic effects were only observed with prolonged culture prior to stimulation and were not appreciably influenced by the presence of exogenous modulators of IL-1beta production. We conclude that IL1RN genotype is the principal determinant of IL-1beta bioactivity within theIL1 gene cluster in humans and discuss its putative role in disease.

Adult↗

PubMed1999

Linkage disequilibrium at the ADH2 and ADH3 loci and risk of alcoholism.

Two of the three class I alcohol dehydrogenase (ADH) genes (ADH2 and ADH3) encode known functional variants that act on alcohol with different efficiencies. Variants at both these genes have been implicated in alcoholism in some populations because allele frequencies differ between alcoholics and controls. Specifically, controls have higher frequencies of the variants with higher Vmax (ADH2*2 and ADH3*1). In samples both of alcoholics and of controls from three Taiwanese populations (Chinese, Ami, and Atayal) we found significant pairwise disequilibrium for all comparisons of the two functional polymorphisms and a third, presumably neutral, intronic polymorphism in ADH2. The class I ADH genes all lie within 80 kb on chromosome 4; thus, variants are not inherited independently, and haplotypes must be analyzed when evaluating the risk of alcoholism. In the Taiwanese Chinese we found that, only among those chromosomes containing the ADH3*1 variant (high Vmax), the proportions of chromosomes with ADH2*1 (low Vmax) and those with ADH2*2 (high Vmax) are significantly different between alcoholics and controls (P<10-5). The proportions of chromosomes with ADH3*1 and those with ADH3*2 are not significantly different between alcoholics and controls, on a constant ADH2 background (with ADH2*1, P=.83; with ADH2*2, P=.53). Thus, the observed differences in the frequency of the functional polymorphism at ADH3, between alcoholics and controls, can be accounted for by the disequilibrium with ADH2 in this population.

Alcohol Dehydrogenase↗

PubMed2002

Association of polymorphisms in the collagen region of human SP-A1 and SP-A2 genes with pulmonary tuberculosis in Indian population.

Surfactant protein A (SP-A) binds to and modulates phagocytosis of Mycobacterium tuberculosis by macrophages. We investigated the relationship between polymorphisms in the collagen regions of SP-A1 and SP-A2 genes and pulmonary tuberculosis. In the present study, seven single nucleotide polymorphisms (SNPs) (4 exonic and 3 intronic) have been identified in the collagen regions of SP-A1 and SP-A2 genes in Indian population. Two intronic polymorphisms, SP-A1C1416T ((p = 0.0000, odds ratio (OR) = 20.767,95% CI: 8.315-OR<51.870) and SP-A2C1382G (p = 0.0054; OR = 3.675, 95% CI: 1.400< OR<9.644), showed significant association with pulmonary tuberculosis (number of patients = 10, number of controls = 7). A redundant SNPA1660G of SP-A2gene showed significant association with pulmonary tuberculosis (number of patients = 17, number of controls = 19, p = 0.0000, OR = 8.94,95% CI: 3.311<OR<24.126). This polymorphism, when existing along with a non-redundant polymorphism, SP-A2G1649C (Ala91Pro) resulted in a stronger association with pulmonary tuberculosis (number of patients = 17, number of controls = 19, p = 0.000, OR = 16.3, 95% CI: 7.8644<OR<33.9244). The results indicated that these SNPs in the collagen region of SP-A2 may be one of the contributing factors to the genetic predisposition to pulmonary tuberculosis.

Amino Acid Sequence↗

PubMed2002

Dual transcription of b2a2 and b3a2 BCR-ABL transcripts in chronic myeloid leukaemia is confined to patients with a linked polymorphism within the BCR gene.

We propose a mechanism for dual expression of b2a2 and b3a2 BCR-ABL in chronic myeloid leukaemia (CML). We have identified a BCR allele, present in approximately 29% of the population, which includes an adenine to guanine polymorphism in the putative branchpoint of BCR intron 13. CML patients who expressed both b2a2 and b3a2 transcripts had the allele, which was also associated with alternative transcription of the normal BCR allele. We conclude that the BCR intronic polymorphism is associated with activation of a cryptic branchpoint resulting in reduced efficiency of RNA splicing and exon 14 (b3) skipping in BCR and BCR-ABL.

Alternative Splicing↗

PubMed1997

No association between the intronic presenilin-1 polymorphism and Alzheimer's disease in clinic and population-based samples.

Mutations in the Presenilin 1 (PS1) gene on chromosome 14 cause most early-onset familial Alzheimer's disease (AD). An intronic polymorphism in the PS1 gene was recently identified and reported to be associated with late-onset AD [Wragg et al., Lancet 347: 509-512, 1996]. The authors found an excess of homozygotes for the more common allele (allele 1) in AD cases, associated with an approximate doubling of risk. In the present study, we report the PS1 polymorphism distributions in clinic and population-based samples. We were not able to replicate the findings of Wragg et al. [1996]. Our results are consistent with those of other researchers and do not support the conclusion that the PS1 polymorphism is associated with late-onset AD.

Alleles↗

PubMed2001

Genetic variation of the human glycine receptor subunit genes GLRA3 and GLRB and susceptibility to idiopathic generalized epilepsies.

Alterations of glycine receptor alpha1 and beta subunit genes have been associated with hypertonic motor disorders in both mice and humans. Mutations in genes encoding other ligand- and voltage-gated ion channels have been identified in rare monogenic forms of idiopathic generalized epilepsies (IGE). We tested the hypothesis that allelic variants of the glycine receptor subunit genes, GLRA3 and GLRB, both localized on chromosome 4q, confer susceptibility to common subtypes of IGE. Mutation screening was carried out in index patients of 14 IGE families. No pathogenic mutation was found, but two intronic polymorphisms were detected in the GLRB gene, and four intronic, three exonic, and one 3'-UTR polymorphisms were identified for the GLRA3 gene. Subsequent screening for exonic and 3'-UTR polymorphisms in GLRA3 showed no statistical difference between a group of sporadic IGE patients (n = 104) and a control group (n = 141). The genotype frequencies for exonic and 3'-UTR polymorphisms in GLRA3 showed no statistically significant difference between IGE patients (n = 104) and an ethnically matched control group (n = 141). Thus, no association between IGE and alterations in GLRA3 or GLRB genes could be detected, indicating that both genes do not play a major causative role in the epileptogenesis of common IGE subtypes. Still, these novel single nucleotide polymorphisms may be useful markers for candidate gene analyses of other disorders.

Alleles↗

PubMed2004

Lack of association between acetylcholine receptor epsilon polymorphisms and early-onset myasthenia gravis.

A patient with mutations in the acetylcholine receptor (AChR) epsilon subunit, who subsequently developed autoimmune myasthenia gravis (MG), led us to search for epsilon AChR mutations and polymorphisms in 167 patients with early-onset MG. No epsilon-subunit mutations or increased incidence of exonic epsilon-subunit polymorphisms were found. The allelic frequency of the intron polymorphism IVS11+ 20del20 was more prevalent in non-United Kingdom subjects, both patients and healthy individuals, than in United Kingdom subjects (15.8 vs. 6.2%, P = 0.0008) but not between MG patients and healthy individuals. These data provide no evidence that heteroallelic mutations or polymorphisms in the AChR epsilon subunit are involved in the development of autoimmune early-onset MG but raise issues for future studies.

Adult↗

PubMed1997

Sequence, splice site and population frequency distribution analyses of the polymorphic human tryptophan hydroxylase intron 7.

A human tryptophan hydroxylase intron seven polymorphism previously associated with low CSF 5-HIAA and suicidal behavior was sequenced and characterized for its potential role in TPH pre-mRNA splicing. Two polymorphic sites were identified: A218C and A779C. The 779A allelic frequency in various populations ranged from 0.43 to 0.61 and was in strong linkage disequilibrium with the A218C site. A218C provides a site for restriction fragment length polymorphism analysis. TPH mRNA was reverse-transcribed and sequenced. No aberrant splice products from the 779A or 779G TPH genes were detected nor were any other polymorphic nucleotides found.

Base Sequence↗

PubMed2004

[Genetic tau-variants in patients with frontotemporal dementia].

OBJECTIVE: [corrected] To evaluate tau-associated genetic polymorphisms in patients with sporadic frontotemporal dementia (FTD) and healthy control subjects. METHOD: Tau-gene sequence of 30 patients with FTD and 30 healthy controls was analysed by polymerase-chain-reaction (PCR). Subsequent sequencing was performed to identify exonic and intronic differences between both groups. RESULTS: The following polypmorphisms, which are localized closely to each exon-intron-border, have been identified: In 37 % (n = 11) of the control subjects three different intronic polymorphisms occur simultaneously (Intron 2, 263, C --> Y; Intron 3, 590, A --> R; Intron 11, 150, G --> A). In the FTD group, this coexistance has been observed only in 17 % (n = 5). CONCLUSIONS: In how far there exists a significant correlation between the newly identified triple polymorphism in the Tau gene and an alternated risk for FTD must be evaluated in a lager population. The proximity of these polymorphisms to the exon-intron border would facilitate functional influences on gene expression patterns. These preliminary results described, above potentially point to further pathogenetic factors in the genesis of FTD.

Adult↗

PubMed2004

Left ventricle mass index and the common, functional, X-linked angiotensin II type-2 receptor gene polymorphism (-1332 G/A) in patients with systemic hypertension.

A common intronic polymorphism, (-1332 G/A) of the angiotensin type-2 receptor gene, located on the X-chromosome, has been reported to be functional. The aim of our study was to evaluate this polymorphism for an association with left ventricular hypertrophy. Left ventricle (LV) mass was measured in 197 patients with systemic hypertension and 60 normal volunteers using a 1.5-Tesla Philips MRI system. Genotyping was performed using a restriction enzyme digestion of an initial 310-bp polymerase chain reaction product that included the angiotensin type-2 (-1332 G/A) locus. The mean LV mass index for the male patients was 94.3+/-19.6 g/m2 (n=125) and for the female patients was 71.2+/-12.0 g/m2 (n=72). Seventy-three (37.1%) of all patients had an elevated LV mass index, defined as the mean LV mass index for normal volunteers plus 2 SD (males 77.8+/-9.1 g/m2, n=30; females 61.5+/-7.5 g/m2, n=30). Comparison of LV mass index of the A_/AA genotype (mean LV mass index=82.4+/-21.1 g/m2; n=123) against that of the G_/GG genotype (mean LV mass index=88.1+/-19.0 g/m2; n=89) as a continuous variable was significant by ANOVA (P=0.044). chi2 Comparison between subjects with and subjects without left ventricular hypertrophy revealed an excess of the G_/GG genotype among the group with LV hypertrophy (P=0.031). We observed an association between the angiotensin type-2 receptor (-1332 G) allele and the presence of left ventricular hypertrophy in hypertensive subjects.

Adult↗