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PubMed2001

Variable expression of presenilin 1 is not a major determinant of risk for late-onset Alzheimer's disease.

We have previously reported a significant association between early-onset Alzheimer's disease (EOAD) and an allele in the promoter of presenilin 1 (PSEN1) significantly decreasing PSEN1 expression in vitro. For late-onset Alzheimer's disease (LOAD), numerous studies have reported inconsistent associations with a PSEN1 intronic polymorphism. We therefore hypothesized that linkage disequilibrium between the intronic PSEN1 polymorphism and the functional promoter polymorphism might explain the conflicting reports in LOAD. We analysed both variations in 356 LOAD patients and 230 controls in a population-based case-control study. In addition, we re-analysed all published literature on the PSEN1 intronic polymorphism in a meta-analysis. No significant association was found with the PSEN1 intronic or promoter polymorphism in our case-control sample. In the meta-analysis no major differences between patients and controls were found for the PSEN1 intronic variation. Together, our results do not support a major role for variable expression of PSEN1 in LOAD.

Age of Onset↗
PubMed1995

Exonic MHC-DRB polymorphisms and intronic simple repeat sequences: Janus' faces of DNA sequence evolution.

The evolution of highly polymorphic gene loci is following routes that cannot be extrapolated from the existing knowledge of single copy genes. In addition, interpreting the evolution of the most polymorphic loci in vertebrates requires a plethora of data from different taxa. We evaluate here the rules for the evolution of Major Histocompatibility Complex (MHC-)DRB genes recently established in humans and other primates on the basis of sequences from several artiodactyl species. MHC genes encode essential molecules for self/altered-self/non-self discrimination in the interaction of the organism with its environment. The necessity to effectively present various different antigens to immunocompetent cells causes positive selection pressure on the variability of these genes in the population. Artiodactyls represent the third mammalian order in which this phenomenon was evidence independently. A further incentive to investigate also the surroundings of MHC-DRB loci was the presence of a particular repetitive sequence stretch in the vicinity of the polymorphic exon--in addition to the evolutionarily old alleles, ancient polymorphisms and the mechanisms for their generation and/or maintenance. Besides their utility for indirect gene diagnosis (MHC-DRB typing), the closely linked stretches of simple repetitive DNA in the neighborhood of the highly polymorphic MHC-DRB genes are also interesting remains of the evolutionary history. Evolutionary development is different in genetically inert intronic DNA compared to the exonic counterparts, despite their close vicinity. The persistence of these simple repeats over nearly 100 million years in one location preserving the same basic motif structure is startling. Indirect evidence is weighed that biological meaning should be considered for these elements. The combined analysis of the polymorphic DRB genes and the (highly variable but persistent) simple repeat stretches deepen our understanding of the complexities within a unique genomic compartment encoding essential molecules for self/non-self differentiation in the interaction of the organism with its environment.

Amino Acid Sequence↗
PubMedDate not supplied

C to A single nucleotide polymorphism in intron 18 of the human MST1R (RON) gene that maps at 3p21.3.

The MST1R (RON) gene, that maps at 3p21.3, encodes a protein tyrosine kinase receptor comprised of an extra-cellular domain that contains the ligand binding pocket and an intracellular region where the kinase domain is located. It controls cell survival and motility programs related to invasive growth. With the single strand conformation polymorphism (SSCP) method, a C to A nucleotide polymorphism (SNP) was found in intron 18 of the gene. The SNP has a frequency of 0.28 among African-American, 0.25 among Caucasian CEPH and 0.09 among Asian healthy individuals. During these studies, an alternatively spliced cDNA of MST1R, lacking exon 19, was also found that may result from this change.

Alternative Splicing↗
PubMed2003

CTLA4 gene and Graves' disease: association of Graves' disease with the CTLA4 exon 1 and intron 1 polymorphisms, but not with the promoter polymorphism.

OBJECTIVE: Recent studies have shown that Graves' disease (GD) is linked to and associated with alleles of the cytotoxic T lymphocyte antigen-4 (CTLA4) locus. However, the true pathogenic polymorphism(s) at this locus remains uncertain. Moreover, the association studies of the promoter CTLA4(-318)C/T polymorphism in white GD populations have produced conflicting results. Therefore, we have analysed three CTLA4 single nucleotide polymorphisms, including promoter CTLA4(-318)C/T, exon 1 CTLA4(49)A/G and intron 1 CTLA4(1822)C/T in our GD cohort from the UK. PATIENTS AND METHODS: We studied 301 white patients with GD and 349 healthy ethnically matched local controls. Amongst GD probands, 129 had significant thyroid-associated orbitopathy (TAO; NOSPECS class III or worse). The CTLA4(-318)C/T, CTLA4(49)A/G and CTLA4(1822)C/T polymorphisms were genotyped by using the restriction enzymes MseI, Bst71I and HaeIII, respectively. RESULTS: We found no association between GD and alleles of CTLA4(-318)C/T. GD was found to be associated with the G allele of CTLA4(49)A/G[P = 5.9 x 10(-6), odds ratio (OR) 1.65] and the T allele of CTLA4(1822)C/T (P = 7.7 x 10(-6), OR 1.64). The frequencies of these alleles were significantly higher in GD probands with significant TAO than in those without TAO (G allele: P = 0.001, OR 1.68; T allele: P = 0.001, OR 1.70). CONCLUSIONS: The promoter CTLA4(-318)C/T polymorphism is not in linkage disequilibrium with the pathogenic polymorphism(s) at the CTLA4 locus. The alleles of both the exon 1 CTLA4(49)A/G and the intron 1 CTLA4(1822)C/T polymorphisms are associated with GD, which is stronger in patients with TAO.

Abatacept↗
PubMed1998

Insertional polymorphism in introns 4 and 10 of the maize beta-glucosidase gene glu1.

The major beta-glucosidase isozyme Glu1 is encoded by a highly polymorphic gene (glu1) in maize. The glu1 gene comprises 12 exons and 11 introns. Two of these introns, introns 4 and 10, show insertional polymorphism: those in allele glu1-1 (represented by inbred line OH7B) are longer than those in other inbred genotypes and in two teosintes (Zea mexicana and Zea parviglumis) surveyed. Sequence data revealed that an increase in the length of intron 4 from 150 to 477 bp in OH7B is due to a short (11 bp) tandem duplication and a large insertion sequence of 313 bp plus a 4-bp (5' ATAG 3') direct repeat. The 313-bp insertion sequence (referred to as mzsTn-1) has all the features of a transposon, having a 25-bp well-conserved (3/25 mismatches) inverted repeat sequence at its termini flanked by a 4-bp direct repeat. The increase in length from 1041 to 1302 bp in intron 10 of OH7B is due to a 259-bp insertion sequence (referred to as mzsTn-2) plus a 2-bp (5' TA 3') direct repeat. The mzsTn-2 element also possesses all the hallmarks of a transposon: a 34-bp well-conserved (3/34 mismatches) inverted repeat sequence at its termini flanked by a 2-bp direct repeat. The mzsTn-1 element belongs to a new family of inverted repeat elements, while mzsTn-2 belongs to the Stowaway family of inverted repeat elements. Analysis of PCR products from amplifications off genomic-DNA templates, using primers derived from the inverted repeat termini, and Southern blotting data suggest that both small transposons are members of a multigene family. The occurrence of two different small transposons in introns of the same glu1 allele in inbred OH7B and their absence in other genotypes suggest that they have moved into this glu1 allele recently through mediation of their autonomous counterparts that are active in OH7B or in its ancestry.

Base Sequence↗
PubMed1993

Low expression allele alpha LELY of red cell spectrin is associated with mutations in exon 40 (alpha V/41 polymorphism) and intron 45 and with partial skipping of exon 46.

The alpha V/41 polymorphism of erythroid alpha-spectrin has been characterized initially by an increased susceptibility to proteolysis of the alpha IV-alpha V domain junction (Alloisio N., L. Morlé, J. Maréchal, A.-F. Roux, M.-T. Ducluzeau, D. Guetarni, B. Pothier, F. Baklouti, A. Ghanem, R. Kastally, et al. 1991. J. Clin. Invest. 87:2169-2177). Until now, it has been found associated invariably with a low expression level of the corresponding alpha chain. Among 61 chromosomes investigated in French and North African individuals or kindreds, we observed 19 chromosomes with the alpha V/41 polymorphism. With no single exception, the latter displayed a point mutation in exon 40 (Leu-->Val; CTA-->GTA) at position alpha 1857. According to the triple helical model of spectrin structure, this change accounts for the peptide maps' abnormalities. Sequencing the entire alpha V domain cDNA disclosed, in addition, a partial skipping of exon 46. At the gene level, a substitution (C-->T) was evidenced at nucleotide -12 of intron 45. This mutation appeared linked to the exon 40 mutation in 17 chromosomes, again with no single exception, among 53 examined chromosomes. We hypothesized that the lack of exon 46 would hamper the nucleation process and eventually account for the low expression feature. The present doubly mutated allele was renamed allele alpha LELY (low expression, Lyon).

Alleles↗
PubMed2006

Mutational screening of the CYP26A1 gene in patients with caudal regression syndrome.

BACKGROUND: The retinoic acid (RA)-catabolizing enzyme Cyp26a1 plays an important role in protecting tailbud tissues from inappropriate exposure to RA. Cyp26a1-null animals exhibit caudal agenesis and spina bifida, imperforate anus, agenesis of the caudal portions of the digestive and urogenital tracts, and malformed lumbosacral skeletal elements. This phenotype closely resembles the most severe form of caudal agenesis in humans. In view of these findings, we investigated a potential involvement of the human CYP26A1 gene in the pathogenesis of caudal regression syndrome (CRS). METHODS: Mutational screening of 49 CRS patients and 132 controls was performed using denaturing high-performance liquid chromatography and sequencing. Differences in the genotype and allele frequency of each SNP were evaluated by chi(2) analysis. The biological significance of the intronic variants was investigated by transfection assays of mutant constructs and by analysis of the splicing patterns with RT-PCR. RESULTS: Mutational screening allowed us to identify 6 SNPs, 4 of which (447 C>G, 1134 G>A, IVS 1+10 G>C, and IVS 4+8 AG>GA) are new. In addition, we describe a novel 2-site haplotype consisting of the 2 intronic SNPs. Both single-locus and haplotype analyses revealed no association with increased risk for CRS. The consequences of the 2 intronic polymorphisms on the mRNA splicing process were also investigated. Moreover, using functional and computational methods we demonstrated that both of these intronic polymorphisms affect the intron splicing efficiency. CONCLUSIONS: Our research did not provide evidence that CYP26A1 has implications for the pathogenesis of human CRS. However, the relationship between CRS risk and the CYP26A1 genotype requires further study with a larger number of genotyped subjects.

Cytochrome P-450 Enzyme System↗
PubMed1997

T/G polymorphism at intron 9 of presenilin 1 gene is associated with, but not responsible for sporadic late-onset Alzheimer's disease in Japanese population.

To investigate whether presenilin 1 (PS1) gene, a major causative gene of familial early-onset Alzheimer's disease (AD), also contributes to the etiology of sporadic AD, we evaluated associations between Japanese AD and polymorphisms located at 14q24.3. While the D14S43 and FOS loci showed no association with either early- or late-onset AD, late-onset AD carrying no APOE-epsilon4 allele was associated with the G allele of the T/G polymorphism located at intron 9 of the PS1 gene (P = 0.016). Considering another study showing a positive association between AD and the T allele, this polymorphism is associated with, but not responsible for sporadic late-onset Alzheimer's disease.

Age of Onset↗
PubMed1996

Allele-specific PCR for simultaneous amplification of both alleles of a deletion polymorphism in intron 6 of the human dopamine 2 receptor gene (DRD2).

The human dopamine 2 receptor gene (DRD2) is an important candidate gene for drug addiction and alcoholism. So far, no mutations within the coding region of DRD2 have been found to be associated with addiction disorders. To identify sequence polymorphisms for further haplotype analyses and to analyze the importance of possible intron sequence variations of the human DRD2 gene (>260kb) in greater cohorts and in a routine manner we established an optimized methodological procedure for polymerase chain reaction (PCR) amplification and direct non-radioactive sequencing followed by a bidirectional allele-specific PCR protocol; the latter one allows the simultaneous amplification of several alleles in one reaction tube. Overall, the sequences of the DRD2 introns 3-7 are highly conserved. Nevertheless, in each of the analyzed intron sequences we found substitution variants as well as a one base-pair deletion polymorphism in intron 6. The allele-specific PCR allowed the reliable testing of 95 healthy control individuals and 270 alcoholics for analyzing a possible genetic association of this newly characterized polymorphic DRD2 marker with alcoholism in an ethnically and clinically homogenous group of patients. However, the observed allele frequencies for the 1bp deletion polymorphism were 15.9% for the alcoholics and 15.3% for the controls suggesting no association of the deletion to alcoholism.

Alleles↗
PubMed2001

Ethnic variation in genotype frequencies of a p53 intron 7 polymorphism.

Using a PCR-restriction enzyme-based method we found large ethnic variations when a C-->T polymorphism in the human p53 gene at position 14181 in intron 7 was studied in Finnish, Polish, Hungarian, Italian, Japanese, Indian and Chinese populations. The largest variations were found between Caucasian and Asian, genotype frequencies varied from C 0.95 and T 0.05 in the Finnish population to C 0.67 and T 0.33 in the Chinese population, the relative risk (RR) for T being 6.5 (95% CI 3.4-12.3, P < 0.001). Variations were also found between Finnish and Italian and between Italian and Chinese (RR for T 2.4, 95% CI 1.2-4.9 and 2.7, 95% CI 1.7-4.2, respectively).

Asian People↗
PubMed1996

Allelic ladder characterization of the short tandem repeat polymorphism in intron 6 of the lipoprotein lipase gene and its application in an Austrian Caucasian population study.

The short tandem repeat (STR) polymorphism HumLPL (TTTA)n, which is located in intron 6 of the lipoprotein lipase gene, was investigated by AMPFLP (amplification fragment length polymorphism)-technique using an allelic ladder consisting of amplified alleles of this locus as a standard size marker. The allelic ladder was prepared by pooling equal concentrations of six separate alleles, which were identified by their different electrophoretic mobility in native polyacrylamide gel, eluted and subsequently amplified. Sequence analysis of the ladder alleles and allele 7, which is not included in the ladder, showed a regular repeat structure with 7 and 9 to 14 repetitions of the core repeat. The allelic ladder was employed in the analysis of the genotypes of 550 unrelated Caucasoids of Austria. No new alleles were found. The population investigated showed no deviation from Hardy-Weinberg equilibrium (P = 0.195).

Alleles↗
PubMed2000

Modulation of factor VII levels by intron 7 polymorphisms: population and in vitro studies.

Previous studies have established that factor VII gene (F7) polymorphisms (5'F7 and R353Q) contribute about one-third of factor VII (FVII) level variation in plasma. However, F7 genotyping in patients with cardiovascular disease has produced conflicting results. Population and expression studies were used to investigate the role of intron 7 (IVS7 ) polymorphisms, including repeat and sequence variations, in controlling activated FVII (FVIIa) and antigen (FVIIag) levels. Genotype-phenotype studies performed in 438 Italian subjects suggested a positive relation between the IVS7 repeat number and FVII levels. The lowest values were associated with the IVS7 + 7G allele. The screening of 52 patients with mild FVII deficiency showed an 8-fold increase in frequency (8%) of this allele, and among heterozygotes for identical mutations, lower FVII levels were observed in the IVS7 + 7G carriers. This frequent genetic component participates in the phenotypic heterogeneity of FVII deficiency. The evaluation of the individual contribution of polymorphisms was assisted by the expression of each IVS7 variant, as a minigene, in eukaryotic cells. The novel quantitative analysis revealed that higher numbers of repeats were associated with higher mRNA expression levels and that the IVS7 + 7G allele, previously defined as a functionally silent polymorphism, was responsible for the lowest relative mRNA expression. Taken together, these findings indicate that the IVS7 polymorphisms contribute to the plasmatic variance of FVII levels via differential efficiency of mRNA splicing. These studies provide further elements to understand the control of FVII levels, which could be of importance to ensure the hemostatic balance under pathologic conditions.

Amino Acid Substitution↗
PubMed2001

[Importance of 5569G/A polymorphism in intron 4 of HFE gene in the diagnosis of hereditary hemochromatosis].

BACKGROUND: The presence of the 5569A polymorphism may lead to misdiagnosis of patients susceptible of hereditary hemochromatosis (HH). For that reason, samples containing the Cys282Tyr mutation were revised and the frequency of this polymorphism in our environment was assessed. PATIENTS AND METHOD: Twenty samples were retested and 56 controls were included. The study was performed by PCR-RFLP. RESULTS: The diagnosis was confirmed in 8 cases susceptible of error. However, an amplification deficiency of normal alleles was detected in 2 heterozygous (17%). The allelic frequency of the 5569A polymorphism in the control population was 14.3%. CONCLUSIONS: Although misdiagnosis was not committed, we recommend changing to any primer that does not include the 5569G/A polymorphism in the study of HH.

Adult↗
PubMed1999

Aggression and anger-related traits associated with a polymorphism of the tryptophan hydroxylase gene.

BACKGROUND: Central nervous system (CNS) serotonergic activity correlates inversely with human aggressive behavior, and individual differences in aggressive disposition are at least partially heritable. This study was conducted to evaluate the possible association between measures of antagonistic behavior and an intronic polymorphism of the gene coding for tryptophan hydroxylase (TPH), the rate-limiting enzyme in serotonin biosynthesis. METHODS: Locally recruited men and women (n = 251) were genotyped for the A218C polymorphism located in intron 7 of the TPH gene. All subjects were administered standard interview and questionnaire indices of aggression and anger-related traits of personality; in a portion of subjects, CNS serotonergic activity was assessed by neuropsychopharmacologic challenge (prolactin response to fenfluramine hydrochloride). RESULTS: Persons having any TPH U allele scored significantly higher on measures of aggression and tendency to experience unprovoked anger and were more likely to report expressing their anger outwardly than individuals homozygous for the alternate L allele. In men, but not women, peak prolactin response to fenfluramine was also attenuated among subjects having any U allele, relative to LL homozygotes. CONCLUSIONS: Individual differences in aggressive disposition are associated with an intronic polymorphism of the TPH gene in a nonpatient sample of community-derived volunteers.

Aggression↗