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PubMed2002

Identification of an intronic TG repeat polymorphism in the human proteasome core particle PROS-27K gene.

A TG dinucleotide repeat was identified in intron 6 of the human proteasome core particle PROS-27K (IOTA, PSMA6) gene. We present data on the length polymorphism of this repeat in 120 individuals from Latvia and 197 individuals from Finland. A combination of PCR and fluorescent gel electrophoresis was utilized to type the polymorphism. Twelve alleles were observed, varying in length from 10 to 23 TG repeats. Similar allele frequencies were observed in Latvian and Finnish subjects, with 17 and 20 repeats being the most frequent in both populations. We suggest that this TG dinucleotide repeat could be utilized as a prospective marker for genetic linkage and association studies of common diseases.

Cysteine Endopeptidases↗
PubMed1999

Re-sequencing of DNA from a diverse panel of cattle reveals a high level of polymorphism in both intron and exon.

In order to assess the extent of DNA sequence variation in cattle, introns and exons from both the leptin and Amyloid Precursor Protein (APP) genes have been sequenced in a panel of DNAs derived from 22 diverse animals. Direct DNA sequencing of PCR products was used; thus, 44 chromosomes were studied. Polymorphisms were identified by manual scanning of sequence chromatograms and computerized sequence analysis. Twenty Single Nucleotide Polymorphisms (SNPs) were detected in 1788 bp sequenced from the leptin gene, giving a frequency of 1 SNP per 89 bp. Twenty-four SNPs were detected in a 458-bp fragment of the APP gene; 23 of the polymorphisms were contained in a 302-bp intron 16 fragment. This equates to an SNP frequency of 1 per 13 bp for the intron. We can thus conclude that this portion of the bovine APP gene constitutes a hypermutable region. Nucleotide sequence diversity values of 0.019 and 0.0026 were obtained for APP and leptin respectively.

Amino Acid Substitution↗
PubMed2002

Description of three new polymorphisms in the intronic and 3'UTR regions of the human interferon gamma gene.

Interferon-gamma (IFN-gamma) is a key regulator of the development and functions of the immune system. In particular, this cytokine plays a major role in immune defense against infections by various human pathogens and polymorphisms in the IFN-gamma gene, including the transcription regulatory region, and might affect host resistance to infectious agents such as schistosomes. In this study on the genetics of human schistosomiasis we uncovered three new single nucleotide polymorphisms in the IFN-gamma genes. Two polymorphisms are located in the third intron and the third is in the 3'UTR region of this gene: an A to G transition at position +2109 from the transcription start and two G to A transitions at positions +3810 and +5134. In a SUDANESE population living in an endemic area of malaria and schistosomiasis, the allelic frequenciesare: 0.85 (+2109A), 0.15 (+2109G), 0.92 (+3810G), 0.08 (+3810A), (+5134G) and 0.04 (+5134A).

3' Untranslated Regions↗
PubMed2001

An intron 4 gene polymorphism in endothelial cell nitric oxide synthase might modulate lipid metabolism in nondiabetic patients on hemodialysis.

We investigated the relationship between endothelial constitutive nitric oxide synthase (ecNOS) gene polymorphism and lipid metabolism in patients with nondiabetic chronic renal failure on hemodialysis. Serum from 181 nondiabetic patients on hemodialysis were examined. A genomic DNA fragment was amplified by polymerase chain reaction (PCR) for determining the ecNOS genotype. The PCR products were designated as a and b alleles by electrophoresis. In hemodialysis patients, the frequency of the ecNOS4 for b/b, b/a and a/a genotype was 76.6, 22.8 and 0.6%, respectively. There was not significant difference in the levels of total cholesterol (TC), triglyceride (TG) and calculated low-density lipoprotein cholesterol (LDL-c) in sera between patients (aa and ba) with the a allele and patients (bb) without the a allele. On the other hand, the levels of serum high-density lipoprotein cholesterol (HDL-c) in patients with the a allele (51.9 +/- 3.33 mg/dl) were significantly higher than those in patients without the a allele (43.05 +/- 1.40 mg/dl) (p = 0.005). The frequency of patients with the a allele and low levels of serum HDL-c among patients with a long duration of dialysis (> or =10 years) was significantly lower than that in patients with short duration of dialysis (<10 years) (p = 0.05). It appears that an intron 4 gene polymorphism in ecNOS may modulate lipid metabolism in nondiabetic patients on hemodialysis and the a allele of ecNOS gene polymorphism may affect the prognosis of hemodialysis patients with low levels of serum HDL-c.

Alleles↗
PubMed1994

Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene.

At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the small alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, we observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of "cooperative" changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

Adult↗
PubMed2002

T(-786)-->C polymorphism of the endothelial nitric oxide synthase gene influences the progression of renal disease.

BACKGROUND/AIMS: Polymorphism of the endothelial nitric oxide synthase (ecNOS) gene may be involved in renal disease. Recently, T(-786)-->C polymorphism affecting ecNOS gene transcription has been reported. To clarify the role of T(-786)-->C polymorphism in renal disease, we investigated hemodialysis patients and healthy controls for this polymorphism and we compared its frequency with that of intron 4 polymorphism in the hemodialysis patients. METHODS: The subjects were 252 patients who had been on hemodialysis for less than 2 years (168 with nondiabetic nephropathy and 84 with diabetic nephropathy) and 187 healthy controls. T(-786)-->C polymorphism was detected using polymerase chain reaction-restriction fragment length polymorphism analysis. RESULTS: The frequencies of the T/C and C/C genotypes were significantly higher in the nondiabetic hemodialysis patients than in the controls (odds ratio 1.41; 95% Cl 1.03-2.00), and were also significantly higher in the diabetic hemodialysis patients than in the controls (odds ratio 1.56; 95% Cl 1.02-2.41). In addition, T(-786)-->C polymorphism and intron 4 polymorphism showed strong linkage disequilibrium. CONCLUSION: T(-786)-->C polymorphism may be involved in the progression of both nondiabetic and diabetic nephropathy, along with intron 4 polymorphism.

Adult↗
PubMed1993

Strong association between polymorphisms in an intronic microsatellite and in the coding sequence of the BoLA-DRB3 gene: implications for microsatellite stability and PCR-based DRB3 typing.

A highly polymorphic microsatellite in the bovine DRB3 gene was characterized by polymerase chain reaction (PCR) analysis and DNA sequencing. A very strong association between expressed DRB3 polymorphism and microsatellite alleles was revealed by PCR analysis of genomic DNA from 116 animals representing three breeds of cattle. The results indicated a low frequency of microsatellite length mutations as the association was consistent over breeds. The DRB3 microsatellite may be utilized in a PCR-based typing method of bovine class II alleles. The microsatellite polymorphism did not distinguish all known DRB3 alleles, but it was shown that this method may be complemented by the use of allele-specific PCR based on the extensive polymorphism in the DRB3 exon 2. The DNA sequences of seven microsatellite alleles, associated with different class II haplotypes, were determined. The DRB3 microsatellite is composed of three repeat motifs, a stretch of at least 10 uninterrupted (TG)n dinucleotides, a long but interrupted stretch of (GA)n dinucleotides, and a few (CAGA)n tetranucleotides. There were pronounced sequence differences between alleles and the results indicated that the evolution of this microsatellite has involved length mutations of the dinucleotide repeats as well as point mutations causing interruptions in the dinucleotide repeats.

Alleles↗
PubMed1999

Biallelic polymorphism in the intron region of beta-tubulin gene of Cryptosporidium parasites.

Nucleotide sequencing of polymerase chain reaction amplified intron region of the Cryptosporidium parvum beta-tubulin gene in 26 human and 15 animal isolates revealed distinct genetic polymorphism between the human and bovine genotypes. The separation of 2 genotypes of C. parvum is in agreement with our previous genotyping data based on the thrombospondin-related adhesion protein (TRAP-C2) gene, indicating these genotype characteristics are linked at 2 genetic loci. Characterization of Cryptosporidium muris and Cryptosporidium serpentis has further shown that non-parvum Cryptosporidium parasites have beta-tubulin intron sequences identical to bovine genotype of C. parvum. Thus, results of this study confirm the lineage of 2 genotypes of C. parvum at 2 genetic loci and suggest a need for extensive characterization of various Cryptosporidium spp.

Alleles↗
PubMed2003

Intronic single nucleotide polymorphisms in the RET protooncogene are associated with a subset of apparently sporadic pheochromocytoma and may modulate age of onset.

Approximately 75% of pheochromocytomas are sporadic. Germline mutations in RET, VHL, SDHB, and SDHD have been shown to cause the 25% that are hereditary. Germline high penetrance gain-of-function RET mutations cause multiple endocrine neoplasia type 2, of which medullary thyroid carcinoma (MTC) and pheochromocytoma are components, whereas loss-of-function mutations cause Hirschprung disease (HSCR). A low-penetrance founder locus, in linkage disequilibrium with a RET ancestral haplotype comprising specific alleles at three intron (IVS) 1 single nucleotide polymorphisms (SNPs) (haplotype 0) and SNP A45A, predisposes to the majority of isolated HSCR. A different low-penetrance locus, in linkage disequilibrium with IVS 1 haplotype 2 and SNP S836S, was associated with a subset of sporadic MTC. We, therefore, sought to determine whether RET might also be a low-penetrance gene for apparently sporadic pheochromocytoma. We analyzed 104 pheochromocytoma cases without germline mutations in RET, VHL, SDHD, and SDHB for their status at A45, S836, three IVS 1 SNPs, and a novel upstream insertion/deletion variant. Pheochromocytoma cases were not associated with either A45A or S836S, but we found that cases were associated with haplotype 0 (P = 0.032). However, unlike HSCR, this pheochromocytoma-associated haplotype 0 was not associated with A45A. Taken together with the strengthening of association with the addition of the 5' insertion/deletion variant data (P = 0.016), our observations suggest the presence of a low-penetrance pheochromocytoma susceptibility locus in a region upstream of the putative loci for HSCR and apparently sporadic MTC.

Adrenal Gland Neoplasms↗
PubMed2004

Molecular basis of the size polymorphism of the first intron of the Adh-1 gene of the mediterranean fruit fly, Ceratitis capitata.

The first intron of the gene encoding one of the alcohol dehydrogenase isoenzymes (ADH-1) in Ceratitis capitata is highly polymorphic in size. Five size variants of this intron were isolated from different strains and populations and characterized. Restriction map and sequence analysis showed that the intron size polymorphism is due to the presence or absence of (a) a copy of a defective mariner-like element, postdoc; (b) an approximately 550-bp 3' indel which exhibits no similarity to any known sequence; and (c) a central duplication of 704 bp consisting of part of the 3' end of the postdoc element, the region between postdoc and the 3' indel, and the first 20 bp of the 3' indel. The homologous Adh-1 intron was amplified from the congeneric species, Ceratitis rosa, in order to obtain an outgroup for comparative and phylogenetic analyses. The C. rosa introns were polymorphic in size, ranging from about 1100 to 2000 bp, the major difference between them being the presence or absence of a mariner-like element Crmar2, unrelated to the postdoc element. Phylogenetic analysis suggests that the shorter intron variants in C. capitata may represent the ancestral form of the intron, the longest variants apparently being the most recent.

Alcohol Dehydrogenase↗
PubMed2005

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

The nature of any long palindrome that might exist in the human genome is obscured by the instability of such sequences once cloned in Escherichia coli. We describe and validate a practical alternative to the analysis of naturally-occurring palindromes based upon cloning and propagation in Saccharomyces cerevisiae. With this approach we have investigated an intronic sequence in the human Neurofibromatosis 1 (NF1) locus that is represented by multiple conflicting versions in GenBank. We find that the site is highly polymorphic, exhibiting different degrees of palindromy in different individuals. A side-by-side comparison of the same plasmids in E.coli versus. S.cerevisiae demonstrated that the more palindromic alleles were inevitably corrupted upon cloning in E.coli, but could be propagated intact in yeast. The high quality sequence obtained from the yeast-based approach provides insight into the various mechanisms that destabilize a palindrome in E.coli, yeast and humans, into the diversification of a highly polymorphic site within the NF1 locus during primate evolution, and into the association between palindromy and chromosomal translocation.

Alleles↗
PubMed2005

A 5' intronic splice site polymorphism leads to a null allele of the P2X7 gene in 1-2% of the Caucasian population.

The P2X(7) gene is important for the innate immune response but known polymorphisms do not explain all subjects with loss of P2X(7) function. A splice site mutation (g-->t) was found at position +1 of the first intron of the P2X(7) gene in 7 of 336 Caucasians and 1 of 39 subjects of Indian ethnicity. All eight subjects were heterozygous for the uncommon 1513A-->C polymorphism of the P2X(7) gene. RT-PCR and sequencing showed the splice site mutation was on the 1513C allele in the Caucasians and on the 1513A allele in the Indian subject. The splice site mutation is an inherited polymorphism and gives rise to a P2X(7) null allele in 1-2% of the Caucasian population.

Adult↗
PubMedDate not supplied

Practical application of three polymorphic microsatellites in intron 40 of the human von Willebrand factor gene.

Intron 40 of the human von Willebrand factor gene contains a region with variable-number tandem repeats (VNTR), type (ATCT)n, showing length polymorphism. In order to carry out family studies of von Willebrand's disease, we performed PCR procedures to analyze 3 previously described microsatellites from that region, both in normal individuals and in von Willebrand disease patients. Three pairs of primers were used to amplify independently nucleotides 1890-1991 (VNTR 1), 2215-2380 (VNTR 2) and 1640-1794 (VNTR 3) from intron 40. The observed heterozygosities (0.75, 0.73 and 0.86 for VNTRs 1, 2 and 3, respectively) were in good agreement with the expected heterozygosities derived from the allele frequencies (0.70, 0.73 and 0.79, respectively). Furthermore, the combination of the 3 VNTRs showed 96% of heterozygosity, which correspond with the 98% expected value under linkage equilibrium. Therefore, our conclusion is that the use of these 3 markers, especially VNTR 3, constitutes a rapid and reliable method for performing segregation studies in von Willebrand disease families.

Alleles↗