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PubMed2001

Glycogen storage disease type Ia: molecular study in Brazilian patients.

Mutations in the glucose-6-phosphatase (G6Pase) gene are responsible for glycogen storage disease type Ia (GSDIa). This disease is characterized by growth retardation, hepatomegaly, hypoglycemia, hyperlipidemia, and lactic acidosis. In this study, we report mutations in the G6Pase gene in 8 of 25 Brazilian patients with clinical symptoms of GSDIa. Five previously described mutations (R83C, Q347X, V338F, D38V, and G68R) were detected. The two most common mutations identified were R83C and Q347X, accounting for 8 of 14 (57.14%) mutant alleles. A 1,176 single-nucleotide polymorphism and two intronic mutations (IVS3-58T>A and IVS4+10G>A) were also analyzed. We used the minigene strategy in order to verify the effect of these intronic mutations on the splicing mechanism. This study emphasizes that molecular genetic analysis is a reliable and convenient alternative to the assay of enzyme activity in a fresh liver biopsy specimen for diagnosing GSDIa.

Alleles↗
PubMed2000

Consequences of vitamin D receptor gene polymorphisms for growth inhibition of cultured human peripheral blood mononuclear cells by 1, 25-dihydroxyvitamin D3.

OBJECTIVE: In the vitamin D receptor (VDR) gene a BsmI restriction fragment length polymorphism (RFLP) in intron 8 and a translational start-site polymorphism, identified as a FokI RFLP, have been described. Crucial for a proper interpretation of these polymorphisms in association studies is the knowledge whether they have direct consequences for 1,25-(OH)2D3 action at cellular level. The present study was designed to assess functional significance of the FokI and BsmI VDR gene polymorphisms in peripheral blood mononuclear cells (PBMC) with a natural occurring VDR genotype for cell growth inhibition by 1,25-(OH)2D3. DESIGN: PBMC of women were isolated, VDR genotyped and in vitro inhibition by 1,25-(OH)2D3 of Phytohemagglutinin (PHA)-stimulated growth of PBMC was examined in relation to VDR genotype. RESULTS: PHA-stimulated growth and maximal growth inhibition were independent of VDR genotype. However, the FF genotype had a significant lower ED50 than the Ff genotype corresponding to an allele dose effect of 0.32 nM per f allele copy (P = 0.0036). For BsmI genotypes no differences in ED50 were observed. CONCLUSION: The present study demonstrates for the first time in cells with a natural VDR genotype a direct functional consequence of the VDR gene translational start-site polymorphism for the action of 1,25-(OH)2D3. Especially under conditions of vitamin D insufficiency these findings might have clinical implications.

Aged↗
PubMed2000

Uncommon mutations and polymorphisms in the hemochromatosis gene.

Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron metabolism. Iron absorption from the gut is inappropriately high, resulting in increasing iron overload. The hemochromatosis gene (HFE) was identified in 1996 by extensive positional cloning by many groups over a period of about 20 years. Two missense mutations were identified. Homozygosity for one of these, a substitution of a tyrosine for a conserved cysteine (C282Y), has now clearly been shown to be associated with HH in 60-100% of patients. The role of the second mutation, the substitution of an aspartic acid for a histidine (H63D), is not so clear but compound heterozygotes for both these mutations have a significant risk of developing HH. Here we review other putative mutations in the HFE gene and document a number of diallelic polymorphisms in HFE introns.

Amino Acid Substitution↗
PubMed2005

Association study between the novel functional polymorphism of the serotonin transporter gene and suicidal behaviour in schizophrenia.

A serotonin transporter gene linked polymorphic region (5-HTTLPR) has been investigated in several genetic association studies, including studies of schizophrenia and suicidality. The current study was designed to examine whether the new long (A/G) variant polymorphism of the 5-HTT gene may be associated with suicide attempts of 290 Caucasian schizophrenic patients. Among these patients, 92 had a history of suicide attempt. No association with history of suicide attempt was found in the multiallelic 5-HTTLPR (p = 0.305), however we found significant association with the intron 2 VNTR polymorphism (p = 0.018). When we performed a haplotype analysis, we found association between suicide attempt and haplotype distribution (p = 0.031). These findings suggest that the intron 2 VNTR polymorphism in serotonin transporter gene may influence suicidal behaviour in schizophrenia.

Adult↗
PubMed1998

A polymorphism in a DNA polymerase alpha gene intron differentiates between murine virulent and avirulent strains of Toxoplasma gondii.

The IC intron, found within the DNA polymerase alpha gene of Toxoplasma gondii, was used to evaluate the genetic relationship among 10 strains of T. gondii. Sequence comparison detected polymorphisms within this 652 bp intron which correlated with murine virulence. The results reported here suggest that T. gondii contains two lineages, corresponding with their virulence, evolving independently following their separation. The extensive homology of the IC sequences within the virulent and avirulent groups affirms the close relationship of the strains within the group, as reflected by the identical nucleotide substitutions and dinucleotide insertions/deletions observed. In addition, the presence of the Nde I restriction enzyme site within the IC intron of avirulent strains allows definition of a T. gondii strain as murine virulent or avirulent without needing to test it in vivo.

Animals↗
PubMed2003

Analysis of the human folate receptor beta gene for an association with neural tube defects.

The folate receptor beta (FRbeta) gene encodes a receptor that binds and transports 5-methyltetrahydrofolate. FRbeta polymorphisms may potentially alter folate delivery and are likely candidates for an association with neural tube defect (NTD) risk. To look for association between FRbeta polymorphisms we studied NTD-affected children and their parents (254 triads) recruited throughout Ireland and a control population of 296 pregnant women who did not give birth to an NTD-affected child. Five potential single nucleotide polymorphisms (SNPs) were examined. These were located within the coding, intronic and 3(')-untranslated regions of the FRbeta gene. Four of these SNPs were not found to be variable within our Irish cohort. SNP rs651646 (A-->T), located upstream of exon 2 within an intronic region, is polymorphic and is thus a marker for an FRbeta NTD association study. The frequency of the SNP rs651646 "A" allele was not significantly different in cases (odds ratio [OR] 1.07, 95% CI. 0.84-1.36; P=0.60), their mothers (odds ratio [OR] 1.09, 95% CI. 0.86-1.38; P=0.51) or fathers (odds ratio [OR] 1.09, 95% CI. 0.86-1.38; P=0.50) when compared to controls. Comparisons of allele transmission from 255 informative heterozygous parents of NTD cases showed no preferential transmission of either the A or T alleles (A: 50.2%, n=128; T: 49.8%, n=127; P=1.00, McNemar chi(2) 0.0). We also measured allele frequencies in a sample of American-Caucasians and African-Americans. Highly significant allele frequency differences were observed between populations. In conclusion, SNP rs651646 within the FRbeta gene is polymorphic but is not associated with neural tube defects within the Irish population.

3' Untranslated Regions↗
PubMed2000

Polymorphism in the interleukin-1 receptor antagonist gene is associated with alcoholism in Spanish men.

BACKGROUND: A polymorphism located in intron 2 of the interleukin-1 receptor antagonist (IL1RN) gene recently has been associated with the development of hepatic fibrosis in Japanese alcoholics. In the present study, we analyzed whether there is an association between this polymorphism, alcoholism, and alcoholic liver disease in a Spanish male population of alcoholics. METHODS: The IL1RN genotype was assessed by polymerase chain reaction by using oligonucleotides that flank a variable nucleotide tandem repeat polymorphism located in intron 2 of this gene in 90 male alcoholic patients from Spain: 30 alcohol-dependent men, 30 alcohol abusers, and 30 alcoholics with liver cirrhosis. We also studied 40 healthy subjects. RESULTS: The distribution of the IL1RN allelic frequencies in Spanish healthy subjects is similar to that previously reported in White subjects. However, the A1 allele is overrepresented in Spanish alcoholics when compared with healthy subjects. No significant differences in allelic frequencies were observed between alcoholics with liver cirrhosis and alcoholics without liver disease or between alcohol-dependent subjects and alcohol abusers. CONCLUSION: The presence of the A1 allele of the IL1RN gene is associated with a higher risk of alcoholism in Spanish men.

Adult↗
PubMed2000

[Genetic polymorphisms of Rb and susceptibility of esophageal cancer].

OBJECTIVE: To assess the possible association between the polymorphisms of Rb (intron 20, 17) and susceptibility of esophageal cancer so as to provide clues for genetic markers of esophageal cancer. METHODS: Samples were taken from 56 normal Han people of Shaanxi, 47 esophageal cancer samples, and 31 peri-cancerous non-tumor. DNAs were analysed by using PCR technique. RESULTS: Ten alleles fragments were found in Han population of Shannxi by using primer Rb gene (intron 20). PIC was 0.86. Heterozygosity was 0.7. In esophageal cancer tissues, PIC was 0.82. Heterozygosity was 0.55. In peri-cancerous non-tumor, PIC was 0.87. Heterozygosity was 0.74. Distribution of genotype frequency was significantly different between Han population of Shaanxi and esophageal cancer (P < 0.01). Two alleles (945 bp, 630 bp + 315 bp) fragments were found in Han population of Shaanxi by using primer Rb gene (intron 17). Genotype frequency of Han population of Shaanxi was A/A: 0.28, A/B: 0.52, B/B: 0.20. Genotype frequency of esophageal cancer was A/A: 0.11, A/B: 0.77, B/B: 0.12. Distribution of genotype frequency was significantly different between Han population of Shaanxi and esophageal cancer (P < 0.05). Mutation of Rb gene was found in 7 cases. CONCLUSIONS: Polymorphism of Rb (intron 20) VNTR and Rb (intron 17) could be used as valuable markers. There should bea relationship between polymorphism of Rb VNTR and esophageal cancer susceptibility.

Esophageal Neoplasms↗
PubMed2000

Polymorphisms in the human aromatase cytochrome P450 gene (CYP19) and breast cancer risk.

The aromatase enzyme catalyses the conversion of androgens to oestrogens in the oestrogen biosynthesis pathway. Because increased exposure to oestrogens is considered to be a risk factor for breast cancer, the human aromatase gene (CYP19) is a plausible candidate for low penetrance breast cancer susceptibility. Preliminary reports have suggested that specific alleles of a TTTA repeat may be associated with differences in breast cancer risk. We have identified two new polymorphisms in the CYP19 gene: a TCT insertion/deletion in intron 4 and a G-->T substitution in intron 6, which have rare allele frequencies of 0.35 and 0.45, respectively, in the British population. Comparison was made between the frequencies of these alleles and those of the TTTA repeat in up to 599 breast cancer cases and 433 normal controls from the East Anglian, British population. We found strong linkage disequilibrium between the alleles of these three loci, but no significant association of any alleles with breast cancer risk. The maximum odds ratios observed were: 1.03 (95% CI 0.68-1.55) for the intron 4 TCT insertion/deletion polymorphism [del/del versus ins/ins]; 1.56 (95% CI 0.63-3.83) for the intron 4 [TTTA](10) allele; 1.29 (95% CI 0. 75-2.21) for the intron 6 G-->T polymorphism [TT versus GG]. We conclude that the CYP19 gene has no major role in common breast cancer incidence in the British population.

Adult↗
PubMed2003

Higher stromal expression of transforming growth factor-beta type II receptors is associated with poorer prognosis breast tumors.

Transforming growth factor-beta (TGFB) is a potent inhibitor of normal epithelial cell proliferation, and may be one of the regulatory factors that are perturbed during tumor development. While many tumor cell lines no longer respond to the inhibitory effects of TGFB due to a reduction or absence of the type II receptor (TGFBR2), the role of TGFBR2 in tumors from patients with breast cancer is less clear. The objective of this study was to screen human breast tumors to determine if there was a TGFBR2 mutation and/or altered expression of TGFBR2 protein. Using 10 unique primers, SSCP-PCR was used to detect heterozygosity in the complete coding sequence from 72 tumors and normal DNA from 20 individuals. One region of the promoter was also examined. Expression of TGFBR2 in the same breast tumors was examined by immunohistochemistry. Sequence variations were identified among normal and tumor tissue samples by SSCP-PCR within coding regions of exon 4 (1/72 samples) and within non-coding regions of intron 2 (1/72), intron 3 (72/72), and intron 6 (1/72). A new polymorphism was identified in intron 3. Observed allele frequencies were consistent with Hardy-Weinberg equilibrium in both the tumors and normal DNA. TGFBR2 was expressed in the epithelium and stroma of tumor tissue. The percentage of cells expressing TGFBR2 in stroma was higher in patients that had a positive lymph node status and/or negative estrogen and progesterone receptor expression. There was no relationship between TGFBR2 expression in the epithelium and these variables.

Breast↗
PubMed2004

An association study of a polymorphism in the heparan sulfate proteoglycan gene (perlecan, HSPG2) and Alzheimer's disease.

Accumulating evidence indicates that the heparan-sulfate-proteoglycan (perlecan, HSPG2), as well as other specific proteoglycans, are involved in amyloidogenesis and tau aggregation in Alzheimer's disease (AD). Moreover, the HSPG2 is located on chromosome 1p36, a region of linkage to late-onset AD (LOAD). These two criteria, pathological and positional, make the HSPG2 an interesting candidate for an association with AD. We performed a case-control association study between the common intron 6 BamHI polymorphism at a region of putative heparan-sulfate (HS) attachment sites in the HSPG2 gene and sporadic AD in Jews. No association was detected with AD, neither as a risk factor nor as a modifier gene affecting the age at disease onset and disease progression. In addition, no interactive effect was found with the known risk factor for AD, the apolipoprotein E (APOE) epsilon4. These findings show no evidence for association between HSPG2 intron 6 BamHI polymorphism and AD in our population.

Age of Onset↗
PubMed2000

Identification of a novel polymorphism of estrogen receptor-alpha gene that is associated with calcium excretion in urine.

A novel variation of the estrogen receptor-alpha (ERalpha) gene was identified by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). It is one base substitution in codon 325 (CCC [allele M] to CCG [allele m]) in exon 4 of the human ERalpha gene. This substitution did not cause an amino acid change. We categorized 306 unrelated Japanese postmenopausal women into three genotypes: MM, Mm, and mm; the frequency of each genotype was 26.5%, 43.1%, and 30.4%, respectively. Then, the association of this polymorphism with bone mineral density (BMD) of lumbar spine and bone-calcium metabolic markers was studied. There was no significant difference in BMD of the lumbar spine or most of the bone metabolic markers. However, the urinary calcium (Ca) excretion ratio (u-Ca/Cre) corrected by creatinine was significantly lower in the genotype mm group compared with the genotype MM group (MM vs mm, 0.247 +/-0.158 vs 0.200 +/- 0.105; P < 0.05). We examined the relationship of restriction fragment length polymorphisms (RFLPs) (PvuII, XbaI) in intron 1 and the polymorphism in exon 4. The frequency of genotype MM was higher in the genotype PPxx, which was reported to be associated with lower BMD in the same population of Japanese postmenopausal women. The ER polymorphism identified in this study might be related to some biological mechanisms that regulate calcium metabolism.

Bone Density↗
PubMed2000

Bovine CAPN1 maps to a region of BTA29 containing a quantitative trait locus for meat tenderness.

Micromolar calcium activated neural protease (CAPN1) was investigated as a potential candidate gene for a quantitative trait locus (QTL) on BTA29 affecting meat tenderness. A 2,948-bp bovine cDNA containing the entire coding region of the gene was obtained, showing 91% identity to human CAPN1. The 716 AA protein predicted from this sequence shows 97% similarity (95% identity) to the 714 AA human protein. Analysis of the gene structure revealed that CAPN1 mRNA is encoded by at least 19 exons, and 11,055 bp of the gene were sequenced, including 17 introns. Two single nucleotide polymorphisms (SNP) were detected in intron 12 and were used to map bovine CAPN1 to the telomeric end of the BTA29 linkage group. This approximately coincides with the position of the QTL, demonstrating that CAPN1 protease is a positional candidate gene potentially affecting variation in meat tenderness in a bovine resource mapping population.

Amino Acid Sequence↗
PubMed1986

Polymorphisms in the apolipoprotein AI-CIII gene complex.

We report the presence of five restriction fragment length polymorphisms in the apolipoprotein AI-CIII (apo AI-CIII) gene complex as well as their respective allelic frequencies in a German population (pi) that we studied: an SstI (BanII) polymorphism in the 3' non-coding region of apo CIII q1(pi) = 0.13); an MspI polymorphism in the third intron of apo AI (q2(pi) = 0.12); a PvuII polymorphism in the first intron of apo CIII (q3(pi) = 0.30); and two XmnI polymorphisms in the 5' side of apo AI (q4(pi) = 0.20 and q5(pi) = 0.05).

Apolipoprotein A-I↗
PubMed1999

Detection of three genetic polymorphisms in the 5'-flanking region and intron 1 of human CYP1A2 in the Japanese population.

Interindividual variability of the activity of CYP1A2 may be expected to affect cancer susceptibility, since the enzyme is capable of activating several carcinogens. In the present study, we found three new polymorphisms in the 5'-flanking region (CYPIA2/B) and intron 1 (CYPIA2/C and CYP1A2/D) of CYP1A2 in Japanese by using polymerase chain reaction-single strand conformation polymorphism. We developed methods to detect these polymorphisms by polymerase chain reaction-restriction fragment length polymorphism and performed a population study (159 subjects) to estimate the frequencies of the alleles. The frequencies of the CYP1A2/A (adenine), CYP1A2/B (thymine-deleted), CYP1A2/C (guanine) and CYP1A2/D (adenine) variants were 21.1, 42.0, 8.2 and 61.3%, respectively. The results of family study supported the idea that these CYP1A2 genotypes are inherited with an autosomal codominant transmission.

Cytochrome P-450 CYP1A2↗
PubMed1989

Complete sequence of the human tissue factor gene, a highly regulated cellular receptor that initiates the coagulation protease cascade.

Tissue factor (TF) is the high-affinity receptor for plasma factors VII and VIIa. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade. Outside the vasculature, TF expression is highly dependent upon cell type. TF can also be induced by inflammatory mediators to appear on monocytes and vascular endothelial cells as a component of cellular immune responses. As an initial step toward elucidating the regulatory regions involved in control of TF gene expression, we have established the organization of the 12.4 kbp human TF gene and its complete DNA sequence. There are six exons separated by five introns. Within intron 5, we have mapped the single nucleotide difference which leads to the previously described MspI polymorphism; the same intron also contains an apparently polymorphic PstI site. The TF gene also contains three full-length Alu repeats and one partial Alu repeat. A single major transcription start site was identified 26 bp downstream from a TATA consensus promoter element. The putative promoter and first exon are located within a 1.2 kbp region of very high G + C content which fits the criteria of an HTF island. A cluster of predicted binding sites for a number of known transcription factors was found to coincide with this putative promoter region. These factors included AP-1 and AP-2 which can mediate the effects of phorbol esters, agonists known to induce TF expression in monocytes and vascular endothelial cells.

Amino Acid Sequence↗