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PubMed2004

A_16_C haplotype in the FcepsilonRIbeta gene confers a higher risk for atopic asthma in the Indian population.

We conducted a case-control study aimed at identifying polymorphisms and haplotypes in the FcepsilonRIbeta gene associated with asthma and its associated phenotypes such as serum IgE levels. A G/A polymorphism in intron 2, a (CA)n repeat polymorphism in intron 5, and a C/T polymorphism in 3'-UTR, encompassing a length of 8.74 Kb, were genotyped, and haplotypes were generated for unrelated patients and healthy volunteers in two independent cohorts. A significant association was observed at the level of alleles and genotypes studied with asthma independently in the two cohorts (p < 0.05). A change in CC_AA genotype combination to a non-CC_AA genotype was associated with reduced risk for asthma. Interestingly, a three-locus haplotype, A_16_C, was found to be significantly associated with asthma (p = 10(-5) in cohort A and p = 0.004 in cohort B). On the other hand, the haplotype G_18_T was found to be negatively associated with asthma (p = 0.007 in cohort A and p = 0.0004 in cohort B). This is the first study identifying a haplotype A_16_C that predisposes individuals to asthma in the Indian population.

Adolescent↗
PubMed2000

An intron 4 gene polymorphism in endothelial cell nitric oxide synthase might modulate volume-dependent hypertension in patients on hemodialysis.

Nitric oxide (NO) has some relevance to the pathophysiology of hypertension. We examined the distribution of endothelial nitric oxide synthase (ecNOS4) gene polymorphism in patients with essential hypertension (n = 107) in comparison with healthy subjects (n = 362), and then studied the possibility that ecNOS4 gene polymorphism affects changes in blood pressure (BP) due to water load in hemodialysis patients. Though the NO metabolite (NOx) level in subjects with the a allele (31.2 +/- 1.76 micromol/l) was significantly lower than in those without the a allele (35.6 +/- 0.90 micromol/l) (p = 0.0263), we found no association between this gene polymorphism and essential hypertension. However, there still remains the possibility that the NO response to elevation of BP might be suppressed in patients with hypertension. In order to examine the association between ecNOS4 gene polymorphism and volume-dependent hypertension, 181 hemodialysis patients with complete anuria were recruited. Depending on the increase in mean BP (mm Hg) divided by percent increase in body weight (deltaBP/deltaBW), patients were divided into high responders (High-R: deltaBP/deltaBW >2.0 mm Hg; n = 90) and low responders (Low-R: deltaBP/deltaBW <2.0 mm Hg; n = 91). In the High-R group, the frequencies of a/a, b/a and b/b genotypes were 1.1, 32.1 and 66.8%, respectively, and in the Low-R group, these frequencies were 1.1, 9.4 and 89.5%, respectively. The relative risk for those in the High-R group conferred by the ecNOS4 a allele (b/a + a/a) was 3.64 (95% confidence intervals: 1.60-8.24, p = 0.0089). This study did not show a strong involvement of ecNOS4 gene polymorphism, at least in the basal NO production in patients with essential hypertension, however, it indicated that ecNOS4 gene polymorphism might modulate changes in BP due to water load in patients on hemodialysis, thus indicating that these polymorphisms may be involved in the pathophysiology of volume-dependent hypertension.

Alleles↗
PubMed2001

A prospective evaluation of the interleukin-1 receptor antagonist intron 2 gene polymorphism and the risk of myocardial infarction.

While an interleukin-1 receptor antagonist gene polymorphism (IL1RN-VNTR) has recently been hypothesized to be a risk factor for coronary artery disease, no prospective data relating this polymorphism to subsequent risk of coronary events are available. We therefore investigated the association between IL1RN-VNTR genotype and the incidence of myocardial infarction (MI) in a large, prospective cohort of initially healthy men. The IL1RN-VNTR was evaluated among 385 MI case subjects and an equal number of age- and smoking-matched control subjects during a 12-year follow-up. Overall, the allele and genotype distributions were similar among cases and controls, both in the total cohort and in all subgroups evaluated. All observed genotype frequencies were in Hardy-Weinberg equilibrium. Furthermore, the relative risk in a comparison of homozygous mutant to homozygous wild-type was 0.89 (95%CI = 0.5-1.6; P = 0.9). In this large, prospective study, the IL1RN-VNTR gene polymorphism is not associated with risks of future MI. These data also highlight the importance of hypothesis testing studies in genetic epidemiology, particularly for hypotheses generated from small samples or post hoc subgroup analyses.

Adult↗
PubMed2000

No association between a presenilin 1 polymorphism and Alzheimer disease.

BACKGROUND: Homozygosity of allele 1 of a presenilin 1 intron 8 polymorphism (PS1-1) has been associated with doubling of the risk of sporadic late-onset Alzheimer disease (LOAD), in some, but not all studies. OBJECTIVE: To genotype the PS1 intron 8 polymorphism in predominantly Hispanic families with LOAD to test for association and for linkage between this polymorphism and LOAD. DESIGN: A family-based, case-control, genetic-linkage study. SETTING: Predominantly Hispanic families were selected from probands who were part of a random sample of 2128 Medicare beneficiaries aged 65 years or older who were residing in the community of Washington Heights, which is located in the northern part of Manhattan, NY. PARTICIPANTS: Fifty-one families with 103 affected family members, 67 unaffected family members, and 7 family members with other diagnoses were genotyped for the PS1 polymorphism. All patients met National Institute of Neurological and Communicative Disorders and Stroke-Alzheimer's Disease and Related Disorders Association criteria for either probable or possible Alzheimer disease. Age was truncated at 55 years or older. MAIN OUTCOME MEASURES: Association analyses, conditional logistic regression, and traditional linkage methods were applied to the families for the PS1 polymorphism and for the presence of the gene for apolipoprotein E (APOE). Results of the association and conditional logistic regression analyses of PS1 intron 8 polymorphism were subsequently adjusted for the effect of APOE-epsilon4, sex, age, and education of each sibling. RESULTS: No association between the PS1 intron 8 polymorphism and LOAD was observed (relative risk, 0.99; 95% confidence interval, 0.3-3.4). An association between presence of the APOE-epsilon4 allele and LOAD (relative risk 4.05; 95% confidence interval, 1.3-12.5) was observed. CONCLUSION: We could not confirm the relationship between the PS1 intron 8 polymorphism and LOAD in this collection of families.

Aged↗
PubMed2004

Associations between IL12B polymorphisms and tuberculosis in the Hong Kong Chinese population.

BACKGROUND: Interleukin (IL)-12 plays a vital role in regulating cell-mediated immunity against tuberculosis (TB). METHODS: To test whether IL12B genetic polymorphisms might contribute to human TB susceptibility, we examined the genotype frequencies of 5 IL12B polymorphisms (at promoter, intron 2, intron 4, exon 5, and 3' untranslated region [UTR]) in 516 patients with TB and 514 healthy control subjects from the Hong Kong Chinese population. RESULTS: Individuals homozygous for the IL12B intron 2-repeat marker (ATT)8 had a 2.1-fold increased risk of developing TB (P < .001) (odds ratio, 2.14 [95% confidence interval, 1.45-3.19]). Estimation of the frequencies of multiple-locus haplotypes composed of IL12B promoter, intron 2, intron 4, and 3' UTR alleles revealed potential risk haplotypes (designated "A" and "K") and protective haplotypes (designated "B") for TB. Furthermore, combining the genotype data of the 4 informative IL12B loci revealed a strong association between a specific genotype pattern, termed "diplotype I" (heterozygous A and K haplotypes), and TB. In contrast, diplotype II (homozygous BB haplotypes) appeared protective against TB. CONCLUSIONS: These findings support the association between IL12B intron 2 polymorphism and TB and between specific IL12B haplotypes and TB.

Asian People↗
PubMed1995

A novel polymorphism (6376 G/T) in intron 7 of the human protein C gene.

A novel polymorphism (6376 G/T) in intron 7 (17) of the human PROC gene has been identified by direct DNA sequencing. Restriction analysis with the use of mutagenic primers indicate that the allele frequencies are 0.17 (allele T) and 0.83 (allele G), with a calculated heterozygosity of 28%.

Base Sequence↗
PubMed2001

An intronic poly (AT) polymorphism of the DNA repair gene XPC and risk of squamous cell carcinoma of the head and neck: a case-control study.

Inherited polymorphisms of DNA repair genes may contribute to variations in DNA repair capacity and genetic susceptibility to cancer. In a hospital-based case-control study of 287 non-Hispanic white patients with newly diagnosed SCCHN and 311 control subjects matched on age, sex, ethnicity, and smoking status, we investigated the role of a newly identified variant allele of XPC, XPC-PAT+. We found that the frequency of the XPC-PAT+ allele was higher in the cases (0.409) than in the controls (0.333; P = 0.007). Fifty cases (17.4%) and 37 controls (11.9%) were XPC-PAT+/+, and 135 (47.0%) cases and 133 controls (42.8%) were XPC-PAT+/-. XPC-PAT+/- and XPC-PAT+/+ subjects were at significantly increased risk for SCCHN [adjusted odds ratios = 1.44 and 1.85, respectively (95% confidence intervals, 1.01-2.05 and 1.12-3.05, respectively; trend test, P = 0.007)]. We did not find ethnic difference in the frequency of XPC-PAT+ allele among four groups aged between 19 and 75 years: non-Hispanic whites, 294; African-Americans, 178; Hispanic-Americans, 103; and native Chinese, 119 (0.333, 0.281, 0.296, and 0.353, respectively). The case-control findings support the hypothesis that the XPC-PAT+ allele may contribute to the risk of developing SCCHN.

Aged↗
PubMedDate not supplied

Association between an atrial natriuretic peptide gene polymorphism and normal blood pressure in subjects of African ancestry.

AIM: The roles of the atrial natriuretic peptide (ANP) gene and the clearance receptor of the ANP (NPRC) gene in hypertensive groups of African ancestry are unclear. The aim of the present study was to assess the relationship between both ANP and NPRC gene polymorphisms and hypertension in Black South Africans. METHODS: 298 patients, diagnosed as having essential hypertension according to 24-hour ambulatory blood pressure (BP) measurements (mean daytime diastolic BP> 90 mm Hg) whilst off medication, and 278 normotensive control subjects of a similar African ancestry, were genotyped for polymorphic markers in intron 2 (which is in complete linkage disequilibrium with a potentially functional exon 1 variant) and exon 3 (which leads to the extension of ANP by two additional arginines) of the ANP gene. Moreover, 64 hypertensives and 63 control from the same groups were genotyped for the cis-acting promoter/enhancer element of the NPRC gene. RESULTS: No relationship between the exon 3 variant and either the presence (odds ratio = 1.075) or the severity (24-hour BP) of hypertension was noted. The intron 2 polymorphism occurred at a low frequency in the control group (frequency of subjects heterozygous for the variant = 6.1%), but was almost absent in the hypertensive group (frequency of heterozygotes = 1.7%). Consequently, a relationship between a normal BP and the intron 2 variant was noted (odds ratio = 0.28, confidence interval = 0.10-0.76, p < 0.01, <1% chance of false positive results). The NPRC gene variant occurred with an equally low frequency in both the hypertensive (4.7%) and the control (4.8%) groups. CONCLUSIONS: The results of the present study suggest that the ANP, but not the NPRC locus contributes to BP in subjects of African ancestry.

Africa↗
PubMed2006

Global distribution of a novel trinucleotide microsatellite polymorphism (ATA)n in intron 8 of the SLC11A1 gene and susceptibility to pulmonary tuberculosis.

We identified a novel trinucleotide (ATA)n repeat polymorphism in intron 8 of SLC11AI, a candidate gene for susceptibility to tuberculosis (TB) infection. We characterized the frequency of this polymorphism in 485 individuals originating from eight globally diverse human populations and compared the distribution of (ATA)n alleles in 146 adults and in 80 cord blood samples from newborns in the Gambian population. Lastly, we tested for association of this microsatellite with pulmonary TB in 318 TB cases and 146 controls in the Gambian population. We found no significant difference in frequency or distribution of alleles in adult and cord blood samples, and we found no significant association between this marker and pulmonary TB.

Case-Control Studies↗
PubMed1994

Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequences.

A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 tree [Gyllensten and Erlich, Hum Immunol 36:1-10, 1989]. Thus 3' DQA1 intron 1 and exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource.

Algorithms↗
PubMed1999

CA repeat allele polymorphism in the first intron of the human interferon-gamma gene is associated with lung allograft fibrosis.

Interferon-gamma (IFN-gamma) is an inflammatory cytokine that has been implicated in the development of fibrosis in inflamed tissues. In this study we have analysed the association between genetically-determined high IFN-gamma production and development of fibrosis in lung transplants. The human IFN-gamma gene has a variable length CA repeat in the first intron. Our previous study showed that polymorphism of this microsatellite is associated with individual variation in the levels of IFN-gamma production. In vitro production of IFN-gamma showed significant correlation with presence of allele #2 (p < 0.01). In this study allele #2 was found to be associated with allograft fibrosis defined by transbronchial biopsy. An analysis of two groups of lung transplant recipients showed a significant increase in the frequency of allele #2 in the group which developed fibrosis after transplantation compared to the group that did not (p < 0.005). We postulate that the production of IFN-gamma, which is under genetic control, can influence the development of fibrosis in lung allografts.

Adenine↗
PubMed2001

The phospholipase C-gamma1 gene (PLCG1) and lithium-responsive bipolar disorder: re-examination of an intronic dinucleotide repeat polymorphism.

Twin, family and adoption studies have indicated that genetic susceptibility plays an important role in the etiology of bipolar disorder. Turecki et al. (1998) recently published preliminary evidence suggesting that bipolar patients with an excellent response to lithium treatment have a higher frequency of a specific dinucleotide repeat allele in the phospholipase Cgamma-1 (PLCG1) genomic region. The present work was undertaken to re-examine the finding by Turecki et al. in a sample of Norwegian lithium-treated bipolar patients sub-classified as lithium responders, non-responders, or partial responders/unclassified. The overall distribution of the PLCG1 dinucleotide repeat alleles was not significantly different between different categories of subjects. When analyzed according to presence or absence of different dinucleotide alleles, a PLCG1-8 repeat was more frequent among lithium responders vs controls. In line with Turecki et al., we also noticed a moderately over-representation of the PLCG1-5 repeat among the bipolar patients as compared to the controls.

Bipolar Disorder↗
PubMedDate not supplied

BalI and MspI polymorphisms of the dopamine D3 receptor gene in African Blacks and Caucasians.

An exonic BalI polymorphism and an intronic MspI polymorphism of the dopamine D3 gene were genotyped in 101 Caucasians from the Alsace and in 56 people from the Congo. This is the first study of the BalI polymorphism in sub-Saharan Africa and the first population study of the MspI site. BalI allele 1 was rare in the Congo (0.12) whereas it is the most frequent allele in all studies in Europe and Asia. MspI allele 1 was also significantly less frequent in the Congolese (0.24) than in Caucasians (0.52). D3 gene alleles show different frequencies in sub-Saharan Africa and may be useful for population studies.

Alleles↗
PubMed2003

An intron splice acceptor polymorphism in hMSH2 and risk of leukemia after treatment with chemotherapeutic alkylating agents.

PURPOSE: We sought to determine whether the -6 exon 13 T>C polymorphism in the DNA mismatch repair gene hMSH2 modulates susceptibility to acute myeloid leukemia after therapy and particularly after O(6)-guanine alkylating chemotherapy. We also determined the extent of microsatellite instability (MSI) in therapy-related acute myeloid leukemia (t-AML) as a marker of dysfunctional DNA mismatch repair. EXPERIMENTAL DESIGN: Using a novel restriction fragment length polymorphism, verified by direct sequencing, we have genotyped 91 t-AML cases, 420 de novo acute myeloid leukemia cases, and 837 controls for the hMSH2 -6 exon 13 polymorphism. MSI was evaluated in presentation bone marrow from 34 cases using the mononucleotide microsatellite markers BAT16, BAT25, and BAT26. RESULTS: Distribution of the hMSH2 -6 exon 13 polymorphism was not significantly different between de novo acute myeloid leukemia cases and controls, with heterozygotes and homozygotes for the variant (C) allele representing 12.2 and 1.6%, respectively, of the control population. However, the variant (C) hMSH2 allele was significantly overrepresented in t-AML cases that had previously been treated with O(6)-guanine alkylating agents, including cyclophosphamide and procarbazine, compared with controls (odds ratio, 4.02; 95% confidence interval, 1.40-11.37). Thirteen of 34 (38%) t-AML cases were MSI positive, and 2 of these 13 cases were homozygous for the variant (C) allele, a frequency substantially higher than in the control population. CONCLUSIONS: Association of the hMSH2 -6 exon 13 variant (C) allele with leukemia after O(6)-guanine alkylating agents implicates this allele in conferring a nondisabling DNA mismatch repair defect with concomitant moderate alkylation tolerance, which predisposes to the development of t-AML via the induction of DNA mismatch repair-disabling mutations and high-grade MSI. Homozygosity for the hMSH2 variant in 2 of 13 MSI-positive t-AML cases provides some support for this model.

Adolescent↗
PubMed2000

Probable involvement of a germ-line mutation of an unknown mismatch repair gene in a Japanese Muir-Torre syndrome phenotype.

A combination of haplotype analysis and direct sequencing were conducted on Japanese Muir-Torre syndrome kindred. In the kindred, two females revealed a hereditary non-polyposis colon cancer (HNPCC) phenotype and one male had a sebaceous tumor in addition to a HNPCC phenotype. Haplotype analysis and direct sequencing failed to show involvement of the known mismatch repair genes, with the exception of MSH5, in this kindred. Analysis of large fragments (from 3.9 to 6. 2 kb) covering the entire 25 kb MSH5 gene in the proband revealed the absence of gross changes in the promoter region and exons. The direct sequencing of the promoter region and all 25 exons failed to demonstrate any mutations in the coding regions except for a CA repeat polymorphism in intron 3 and a C/A polymorphism in intron 15. Taken together present results indicate that a novel and yet unknown mismatch repair gene is likely involved in the HNPCC in this kindred.

Adult↗
PubMed1996

p53 allelotypes and enhanced detection of allelic loss in ovarian cancer: lack of correlation with familial and clinical factors.

To develop a mapping strategy for improved detection of p53 allelic loss associated with ovarian carcinoma, we utilized multiple intragenic polymorphisms and single-strand conformation polymorphism (SSCP) analysis. p53 allelotype distributions were defined for 80 ovarian cancer patients from germ-line DNA. All polymorphic sites studied had polymorphism information content (PIC) rates of greater than 0.25. Tumor loss of heterozygosity (LOH) was determined from informative polymorphisms and migratory shifts on SSCP screening of exons 5-9. Of the four polymorphisms analyzed, the intron 1 (alu) was the most informative (PIC = 0.66). A novel allele of 110 base pairs was found in 4.4% of our ovarian cancer cohort at this site. The intron 3 (16-base pair repeat) and intron 6 (MSP1) polymorphisms were in relative equilibrium; thus, we chose to use only the intron 3 polymorphic site in the mapping strategy. Family cancer history did not influence the allelotype distribution frequencies. Overall, 56 of 61 tumors (91.8%) were informative for allelic loss, and LOH was observed in 66.1 %. A reduction to homozygosity at the p53 locus did not correlate with familial or clinical factors. These observations are consistent with the multiple mechanisms by which p53 dysfunction can occur.

Adult↗