Restriction fragment length polymorphisms associated with immunoglobulin C gamma genes reveal linkage disequilibrium and genomic organization.

We have demonstrated that restriction fragment length polymorphisms (RFLPs) produced by BamHI can be used as markers for constant (C) region heavy chain genes C psi gamma (C gamma pseudogene), C gamma 2, and C gamma 4. These RFLPs were found nonrandomly associated in the population sample studied. Of the eight combinations (haplotypes) of RFLPs theoretically possible, only two accounted for a total of 88% of the 116 chromosomes examined, a value greater than the total of 25% expected from random segregation of alleles. This indicates considerable linkage disequilibrium between C psi gamma, C gamma 2, and C gamma 4. Quantitative assessment of the degree of association between C gamma gene RFLPs, Gm markers, and switch region RFLPs adjacent to C mu and C alpha 1 revealed that C psi gamma is most tightly associated with C gamma 2 (r = 0.81 and 0.95 for the two common haplotypes), suggesting that C psi gamma maps to a position lying between C alpha 1 and C gamma 2. The association analysis used here should have general applicability for studying the genomic organization of other multigene families.     

Polymorphism at NRAMP1 and D2S1471 loci associated with juvenile rheumatoid arthritis

OBJECTIVE: To examine the role of NRAMP1 in susceptibility to juvenile rheumatoid arthritis (JRA). METHODS: DNA from 119 JRA patients (72 pauciarticular, 47 polyarticular) and 111 healthy controls from Latvia was genotyped for a functional repeat polymorphism in the promoter of NRAMP1 and a linked (<150 kb) microsatellite D2S1471. The findings were compared with those from HLA-DQ alleles typed previously. Chi-square analyses were performed using the Mantel-Haenszel test and stratification according to pure Latvian or pure Russian descent. Haplotype analysis was performed using the Associate program to implement the expectation-maximization algorithm based on the gene-counting technique. RESULTS: Allele 3 at NRAMP1 conferred increased risk (odds ratios [ORs] 2.26, 2.31, and 2.19; P = 0.0006, 0.003, and 0.019) of disease in the JRA, pauciarticular, and polyarticular patient groups, respectively. Allele 2 conferred protection (OR 0.44, 0.43, and 0.46). Alleles at D2S1471 that conferred susceptibility (6 and 12) or protection (11) did so only when on a haplotype with alleles 3 or 2, respectively, at NRAMP1. Allele 3 at NRAMP1 was additive with HLA-DQ7 for susceptibility (OR 3.71, 3.71, and 4.02), and allele 2 at NRAMP1 was additive with HLA-DQ5 for protection (OR 0.19, 0.08, and 0.12). CONCLUSION: The NRAMP1 allele conferring susceptibility to JRA drives high levels of NRAMP1 expression, while the allele associated with protection drives low levels. These 2 alleles are inversely associated with susceptibility to infectious disease, consistent with their maintenance in populations through balancing selection.     

Single nucleotide polymorphisms and haplotypes of protein C and protein S genes in the Thai population.

Protein C (PC) and protein S (PS) play key roles in an anticoagulant pathway in order to control the haemostatic system. We identified single nucleotide polymorphisms (SNPs) and/or haplotypes in the promotor and exons of the whole PC and PS genes and in the 3'-untranslated region of the PS gene in 55 Thai individuals. The PC gene revealed 10 haplotypes. One synonymous SNP at 2196 was found in the normal Thai population with a minor allele frequency of 4.90%. One homozygous mutation in exon 7, R147W, co-segregated with the synonymous SNP 2196 (homozygote) of the PC gene, resulting in decreased PC activity and antigenic levels. The PS gene revealed three haplotypes with two frequent dimorphisms in exon 15 and the 3'-untranslated region. The most frequent haplotype in the PS gene was H3 (wild type). There was no correlation between the haplotypes of PC and PS genes with functional and antigenic levels of PC and PS.     

The evaluation of left ventricular systolic and diastolic functions in patients with Friedreich ataxia. A pulse tissue Doppler study

Friedreich's ataxia (FRDA), the most common subtype of early onset hereditary ataxia, is an autosomal recessive neurodegenerative disorder caused by unstable GAA expansions. Two-dimensional, pulse, and pulse tissue Doppler echocardiographic examinations were performed on 21 patients with GAA expansion. There was no association between left ventricle ejection fraction, tissue Doppler systolic s wave, and left ventricle diastolic functions examined by pulse and tissue Doppler. The septum thickness of patients with Friedreich's ataxia was significantly increased when compared with that of the control group and wall thickness was found to be associated with GAA repeats. In patients with FRDA, despite a correlation between genetic abnormality with left ventricular early and late diastolic parameters, global diastolic functions were preserved when examined by tissue Doppler.     

Lipoprotein lipase D9N, N291S and S447X polymorphisms: their influence on premature coronary heart disease and plasma lipids.

Lipoprotein lipase (LPL) plays a pivotal role in lipoprotein metabolism. Three recently described exonic polymorphisms of the gene, D9N, N291S and S447X, have been variably found to influence plasma lipids while effects on coronary heart disease (CHD) are less well documented. Two predominantly Caucasian groups were studied: CHD patients <50 years of age, with angiographically documented CHD; and a randomly recruited community control group without a history of heart disease. The 9N allele of the D9N polymorphism was present in 25 of 428 (5.8%) of Caucasian males with CHD and in seven of 291 (2.4%) of corresponding community subjects (odds ratio, 2.5; 95% confidence interval (CI), 1.1-5.9; P=0.03) and was also significantly over-represented in the Caucasian males with myocardial infarction (MI) (21 of 308 or 6.8%; odds ratio, 2.6; 95% CI, 1.1-5.9; P=0.01). The distributions of the other two polymorphisms were similar in the CHD and community groups. In multivariate models adjusted for age, sex, diabetes, body mass index, smoking, lipid levels and race, the D9N polymorphism remained significantly related to both CHD and MI, with an odds ratio >2. There were, generally, trends to more adverse fasting plasma high-density lipoprotein (HDL) cholesterol and triglycerides in carriers of the 291S and 9N alleles, and the opposite trends for triglycerides in 447X carriers. In the community group, male carriers of 291S (n=13) had significantly (20%) lower HDL cholesterol than corresponding non-carriers (n=323), 0.98+/-0.07 mmol/l (mean+/-S.E.) versus 1.22+/-0.02 mmol/l (P<0.005), while HDL cholesterol was not different in male carriers (n=8) and non-carriers (n=296) of 9N (1.23+/-0.13 mmol/l versus 1.22+/-0.02 mmol/l). Multivariate analysis confirmed that the 291S allele carrier status conferred a significantly lower HDL cholesterol (P=0.001) and the 447X allele lower triglyceride (P<0.01) in the community group. In conclusion, LPL 9N carrier status was unequivocally related to premature CHD and to MI in males, strongly supporting recent results in older aged males. The somewhat different effects of the D9N and N291S polymorphisms on plasma lipids, and the absence of a clear effect of the N291S on CHD, raise the possibility that the effect of 9N carrier status might be mediated through effects on LPL function in addition to those influencing fasting plasma lipids.     

Relationship between the microsatellite D2S388‐5 and D2S2232 polymorphisms and chronic obstructive pulmonary disease in the Chinese Kazakh population

Background and objective: Chronic obstructive pulmonary disease (COPD) is influenced by multiple genetic and environmental factors. The role of genetic susceptibility in the pathogenesis of COPD has recently gained more attention. The surface lung surfactant protein B plays an important role in COPD pathogenesis. Microsatellite DNA has been characterized in the surfactant protein B alleles D2S388‐5 and D2S2232. The aim of this research was to investigate the distribution of the D2S388‐5 and D2S2232 microsatellite polymorphisms in smokers of the Kazakh ethnic group in Xinjiang, China, with and without COPD to assess whether such polymorphisms are associated with COPD susceptibility. Methods: DNA was extracted from the blood of 197 smokers with COPD and 236 control smokers of Kazakh ethnicity. The smokers diagnosed with COPD were registered at the Department of Respiratory Medicine from four different hospitals. The control group was recruited at the medical examination centre from the same area. The polymorphisms of the D2S388‐5 and D2S2232 microsatellite loci were measured by multiple short tandem repeat amplification using fluorescence‐labelled polymerase chain reaction and capillary electrophoresis. Results: Nine alleles and 32 genotypes were identified in D2S388‐5, while 9 alleles and 31 genotypes were identified in D2S2232. Both genotype distributions in control smokers were in accordance with Hardy–Weinberg equilibrium. The frequency of the 254 bp allele from the D2S388‐5 locus was significantly higher in the COPD group versus the control (P < 0.001, odds ratio = 5.942). Conclusions: D2S388‐5 microsatellite polymorphism may be associated with susceptibility to COPD in Xinjiang Kazakhs.     

Restriction fragment length polymorphisms at the GLUT4 and GLUT1 gene loci in type 2 diabetes.

Inherited abnormalities of the glucose transporters could explain many of the pathophysiological features of Type 2 diabetes including the strong familial predisposition to the disease. Previous studies have suggested a possible association between an allele of an Xba1 restriction fragment length polymorphism (RFLP) at the GLUT1 gene locus and Type 2 diabetes in Caucasian and Japanese subjects. In order to test this hypothesis further, population association studies were performed at the Xba1/GLUT1 and Kpn1/GLUT4 gene loci employing a group of diabetic patients with a strong family history for the disease. The frequencies of the two alleles at the GLUT1 locus were 0.28 and 0.72 in diabetic patients and 0.31 and 0.69 in control subjects. At the GLUT4 locus, the two alleles had frequencies of 0.24 and 0.76 in diabetic patients and 0.25 and 0.75 in control subjects. These differences were not statistically significant. The present study does not support the hypothesis that genetic variation within the GLUT1 or GLUT4 gene loci may be responsible for familial susceptibility to Type 2 diabetes.     

Role of CARD15, DLG5 and OCTN genes polymorphisms in children with inflammatory bowel diseases

AIM: To investigate the contribution of variants of CARD15, OCTN1/2 and DLG5 genes in disease predispo- sition and phenotypes in a large Italian cohort of pediatric patients with inflammatory bowel diseases (IBD). METHODS: Two hundred patients with Crohn’s disease (CD), 186 ulcerative colitis (UC) patients, 434 par- ents (217 trios), and 347 healthy controls (HC) were studied. Polymorphisms of the three major variants of CARD15, 1672C/T and -207G/C SNPs for OCTN genes, IGR2096a_1 and IGR2198a_1 SNPs for the IBD5 locus, and 113G/A variant of the DLG5 gene were evaluated. Potential correlations with clinical sub-phenotypes were investigated. RESULTS: Polymorphisms of CARD15 were significantly associated with CD, and at least one variant was found in 38% of patients (15% in HC, OR = 2.7, P < 0.001). Homozygosis for both OCTN1/2 variants was more com- mon in CD patients (1672TT 24%, -207CC 29%) than in HC (16% and 21%, respectively; P = 0.03), with an in- creased frequency of the TC haplotype (44.8% vs 38.3% in HC, P = 0.04). No association with the DLG5 variant was found. CD carriers of OCTN1/2 and DLG5 variants more frequently had penetrating disease (P = 0.04 and P = 0.01), while carriers of CARD15 more frequently had ileal localization (P = 0.03). No gene-gene interaction was found. In UC patients, the TC haplotype was morefrequent (45.4%, P = 0.03), but no genotype/phenotype correlation was observed. CONCLUSION: Polymorphisms of CARD15 and OCTN genes, but not DLG5 are associated with pediatric on- set of CD. Polymorphisms of CARD15, OCTN, and DLG5 genes exert a weak influence on CD phenotype.     

D2S388 D2S2232微卫星多态性与新疆维吾尔族吸烟者慢性阻塞性肺疾病易感性研究

目的研究D2S388、D2S2232微卫星多态性在新疆维吾尔族正常人群及慢性阻塞性肺疾病(COPD)患者中的分布并探讨D2S388、D2S2232微卫星多态性与新疆维吾尔族COPD易感性关系。方法提取石河子大学医学院第一附属医院呼吸科、新疆维吾尔族自治区人民医院呼吸科、新疆阿克苏农一师医院呼吸科及新疆喀什地区第一人民医院呼吸科2009年3月至2010年9月住院的维吾尔族吸烟COPD患者118例和吸烟健康体检者110名(对照组)外周血基因组DNA。采用荧光标记的多重聚合酶链式反应扩增短串联重复序列(STR-PCR)结合毛细管电泳检测方法检测D2S388、D2S2232多态性。结果 D2S388位点共检测到9种等位基因和26种基因型,D2S2232位点共检测到9种等位基因和24种基因型。2个位点对照组基因型分布符合Hardy-Weinberg定律。D2S388位点254 bp等位基因频率在COPD组显著高于对照组(P<0.05);D2S2232位点204 bp等位基因频率在COPD组显著低于对照组(P<0.05)。结论 D2S388和D2S2232微卫星多态性可能与新疆维吾尔族吸烟者COPD易感性有关。     

Diverse effects of the CARD15 and IBD5 loci on clinical phenotype in 630 patients with Crohn's disease

OBJECTIVES: Genetic variants at the CARD15 and IBD5 loci are strongly associated with Crohn's disease (CD), but evidence of the effect of these variants on the clinical expression of CD is conflicting and has often been hampered by small sample sizes. We studied 630 well-characterized patients to clarify the genotype/phenotype relationship in CD. METHODS: Patients and healthy controls were genotyped for three common mutations in CARD15 and a marker of the IBD5 risk haplotype. Allele frequencies were compared between phenotypic subgroups using chi2 or Fisher's exact tests. Genotype/phenotype analysis was carried out using multinomial logistic regression modelling allowing for adjustment for correlated or confounding factors. RESULTS: The mean age at diagnosis was significantly lower in carriers of the CARD15 or IBD5 risk alleles. After correction for age and smoking, CARD15 mutations were strongly associated with both ileal disease (P=8.8 x 10(-6)) and stenotic disease (P=0.003), but the association with stenotic disease appeared to be due to a confounding effect with ileal disease. CARD15 mutations were also associated with the presence of granulomas (P=5.7 x 10(-5)), which remained significant after adjustment for age at diagnosis and disease location (P=0.0047). The IBD5 risk haplotype frequency was significantly elevated in cases with perianal disease (P=0.028) and axial spondyloarthropathy (P=0.012). CONCLUSION: Genetic variants at the CARD15 and IBD5 loci have diverse effects on clinical expression in CD. CARD15 mutations are significantly correlated with the presence of granulomas.     

DNA hypermethylation at the D17S5 locus and reduced HIC-1 mRNA expression are associated with hepatocarcinogenesis

To examine the significance of aberrant DNA methylation in hepatocarcinogenesis, the DNA methylation status at the D17S5 locus and mRNA expression of a candidate tumor suppressor gene, HIC-1 (hypermethylated-in-cancer), which was identified at the D17S5 locus, in primary hepatocellular carcinomas (HCCs) and their corresponding noncancerous liver tissues were assessed. DNA hypermethylation at the D17S5 locus was detected in 44% of the noncancerous liver tissues showing chronic hepatitis or cirrhosis, which are widely considered to be precancerous conditions, but was not observed in noncancerous liver tissues showing no remarkable histological findings. The incidence of DNA hypermethylation at this locus was significantly higher in HCCs (90%) than noncancerous liver tissues (P <.001). Loss of heterozygosity at the D17S5 locus, which was preceded by DNA hypermethylation at the same locus, was detected in 54% of HCCs. The HIC-1 mRNA expression level of noncancerous liver tissues showing chronic hepatitis or cirrhosis was significantly lower than that of noncancerous liver tissues showing no remarkable histological findings (P <.01), and that of HCCs was even lower than that of noncancerous liver tissues (P <.05). Poorly differentiated HCCs showed lower expression levels than well- to moderately differentiated HCCs. Mutation of the p53 gene may be involved in HIC-1 inactivation. Moreover, wild-type p53 did not overcome DNA hypermethylation at the D17S5 locus to activate HIC-1 in HCCs. These data suggest that aberrant DNA methylation at this locus and reduced HIC-1 mRNA expression participate in hepatocarcinogenesis during both early developmental stages and malignant progression of HCCs.     

Longitudinal analysis of haplotypes and polymorphisms of the APOA5 and APOC3 genes associated with variation in serum triglyceride levels: the Bogalusa Heart Study

Polymorphisms in the APOC3 and APOA5 genes, from the APOA1/APOC3/APOA4/APOA5 gene cluster on chromosome 11q23, have been associated with interindividual variation in plasma triglycerides. APOA5 polymorphisms implicated include 2 in the promoter region (-1131 T/C and -3 A/G) and 1 in exon 2 (+56 C/G). APOC3 polymorphisms implicated include 1 (SstI) in the 3' untranslated region and 1 (-2854 G/T) in the APOC3-APOA4 intergenic region. We analyzed the associations of haplotypes and multilocus genotypes of these polymorphisms on longitudinal serum triglyceride profiles in 360 African American and 823 white subjects from the Bogalusa Heart Study. Subjects were examined from 2 to 8 times (mean +/- SD, 5.4 +/- 1.3) between 1973 and 1996, at ages ranging from 4 to 38 years, with 1978 observations in African Americans and 4465 in whites. Serum triglycerides were significantly higher among whites across all ages. Allele frequencies differed significantly between African Americans and whites at all but the APOA5 +56 C/G locus. Linkage disequilibrium among the loci was higher in whites and haplotype diversity lower: 6 haplotypes had estimated frequencies of more than 1% in African Americans, 5 in whites. Individually, all polymorphisms except APOC3 -2854 G/T showed significant associations with triglyceride levels in the full sample. However, genotype models including all 5 loci showed significant triglyceride associations for only 3 (APOC3 SstI, APOA5 -1131 T/C, and APOA5 +56 C/G); significant interactions among them indicated their effects were not independent. Neither APOC3 -2854 G/T nor APOA5 -3 A/G had significant effects when the other 3 loci were in the models. The EM algorithm was used to estimate haplotype frequencies and assign haplotype probabilities to individuals, which is conditional on their genotypes; individuals' haplotype probability vectors were then used as predictors in multilevel mixed models of longitudinal triglyceride profiles. Of haplotypes comprising, in order, APOC3 SstI and -2854 G/T and APOA5 -1131 T/C, -3 A/G, and +56 C/G, 3 were significantly associated with higher triglycerides, even after adjusting for multiple tests: GGTAG (P = .002), GTTAG (P < .0001), and CGCGC (P = .0002). Each GGTAG haplotype carried would be expected to raise triglyceride levels (relative to those of GTTAC homozygotes) by approximately 19 mg/dL, each GTTAG haplotype by approximately 15 mg/dL, and each CGCGC haplotype by approximately 7 mg/dL. Haplotypes comprising the 3 loci implicated by genotype analyses (SstI, -1131 T/C, and +56 C/G) were also tested: haplotypes C_C_C and G_T_G significantly raised triglycerides, even after adjustment for multiple comparisons (P < .002 for both), with each copy of C_C_C expected to raise triglycerides by approximately 7 mg/dL and each copy of G_T_G by approximately 15 mg/dL. Overall, our findings support those of others in associating specific polymorphisms and haplotypes in the APOA1/C3/A4/A5 gene cluster with higher serum triglyceride levels. However, the degree to which polymorphisms in the APOC3 and APOA5 genes may be independently associated with triglyceride levels remains to be determined.     

Certain mutations observed in the 5' sequences of the G gamma- and A gamma-globin genes of beta S chromosomes are specific for chromosomes with major haplotypes.

In this paper we describe the distribution of some specific sequence differences in the 5' flanking regions of the A gamma- and G gamma-globin genes from 100 Black adult and 57 newborn SS patients from the southeastern United States, from 76 individuals with AS, S-beta-thal, SC, AC, or A-beta-thal, and from 31 normal individuals. Haplotypes for all adult individuals have been previously determined using various restriction endonucleases. The DNA samples were amplified, dot blotted, and hybridized with 32P-labeled specific oligonucleotide probes. All 134 chromosomes with haplotype 19 were positive for the G----T substitution at position -657 (A gamma), while 132 were also positive for the C----G mutation at -369 (G gamma). The three specific changes for the chromosome with haplotype 20 were found on all 54 chromosomes with this haplotype. The C----T mutation at -158 5' to G gamma was present on all 41 chromosomes with haplotype 3, and on two chromosomes with a related atypical haplotype. Normal and beta-thal chromosomes with each of these substitutions had the same 5' subhaplotype as beta S haplotypes 19 or 20, respectively. The close relationship between the occurrence of specific mutations and the haplotype of beta S chromosomes makes the determination of these haplotypes with specific oligonucleotide probes attractive with respect to time and expense.     

Loss of heterozygosity at D14S62 and D14S51 detected by a simple and non-radioactive method in plasma DNA is a potential marker of metastasis and recurrence after curative hepatic resection in hepatocellular carcinoma

BACKGROUND/AIMS: Recurrence and metastasis in hepatocellular carcinoma remains a major challenge to further improve survival. High frequency of loss of heterozygosity at D14S62 and D14S51 in tumor tissue has been shown to be closely related to metastasis and recurrence in breast cancer. But, loss of heterozygosity on 14q in plasma and tumor tissue DNA of hepatocellular carcinoma patients has not been investigated. To establish a way to predict metastasis and recurrence after curative hepatic resection, we analyzed loss of heterozygosity on 14 q in plasma and tumor tissue DNA of hepatocellular carcinoma patients with curative resection. METHODOLOGY: We used a simple, rapid and non-radioactive method to analyze loss of heterozygosity at D14S62 and D14S51 in paired plasma, lymphocyte and tumor tissue DNA of 85 hepatocellular carcinoma patients with curative resection. RESULTS: From 79 cases informative for D14S62 and 78 cases informative for D14S51 of 85 hepatocellular carcinoma tissue DNA, loss of heterozygosity at D14S62 and D14S51 was present in 45 (57.0%) and 41 (52.6%) cases respectively. And in 96.0% of the tissues which showed loss of heterozygosity we were able to detect loss of heterozygosity in their matched plasma. In matched 85 cases of hepatocellular carcinoma plasma DNA, we detected loss of heterozygosity at D14S62 in 55.7% and at D14S51 in 50.0% of the respective informative DNA samples. The loss of heterozygosity patterns of plasma DNA were almost identical to their corresponding tumor tissues. A comparison of these genetic changes with clinicopathological data of these checked hepatocellular carcinoma patients showed that loss of heterozygosity at D14S62 and D14S51 was adversely correlated significantly with the presence of tumor size, with 35.4% at both the D14S62 and D14S51 locus in the HTMR (high-tendency to metastasis and recurrence) group compared with 72.9% and 59.4% in the LTMR (low-tendency to metastasis and recurrence) group at D14S62 and D14S51, respectively (P = 0.001 and P = 0.027, respectively). CONCLUSION: Our results suggest that loss of heterozygosity at D14S62 and D14S51 plays an important role in the metastasis and recurrence of hepatocellular carcinoma patients following curative resection. Loss of heterozygosity at D14S62 and D14S51 in the plasma DNA of hepatocellular carcinoma patients detected by a simple and non-radioactive method has great potentials to be clinically used to predicate metastasis and recurrence after curative hepatic resection.     

New insights into the origin of the Gaucher disease-causing mutation N370S: extended haplotype analysis using the 5GC3.2, 5470 G/A, and ITG6.2 polymorphisms.

Gaucher disease is a lysosomal storage disorder inherited as an autosomal recessive trait. It is highly prevalent among Ashkenazi Jews but also present in other populations. Mutations in the glucocerebrosidase gene are the main cause of the disorder. One of these gene defects, N370S, is the most prevalent disease allele in the Ashkenazi Jewish patient population and also frequent in others, such as the Spanish and Portuguese Gaucher disease populations. Previous results based on haplotype analysis support the hypothesis of a single origin for this mutation. We have extended the haplotype analysis to include three newly described polymorphisms, 5GC3.2, ITG6.2 (very close to the gene), and 5470 G/A (in intron 7 of the GBA gene) in a sample of Spanish and Ashkenazi Jewish patients. The results confirm the single origin of the mutation in these two populations. The 5470A allele is only found in N370S chromosomes and was believed to be limited to the Portuguese population. Here we describe that it is also present with a similar frequency in Spain. Moreover, most of the 5470A alleles are found within particular haplotypes, which have some differences from the common N370S haplotype.     

Sequence variations in the 5' flanking and IVS-II regions of the G gamma- and A gamma-globin genes of beta S chromosomes with five different haplotypes

We have amplified and sequenced the 5' flanking and the second intervening sequence (IVS-II) regions of both the G gamma- and A gamma-globin genes of the beta S chromosomes from sickle cell anemia (SS) patients with homozygosities for five different haplotypes. The sequencing data, compared with previously published sequences for the normal chromosomes A and B, show many similarities to chromosome B for haplotypes 19, 20, and 17, while haplotypes 3 and 31 are remarkably similar to chromosome A and also similar to each other. Several unique mutations were found in the 5' flanking regions (G gamma and A gamma) of haplotypes 19 and 20 and in the IVS-II segments of the same genes of haplotypes 19, 20, and 17; the IVS-II of haplotypes 3 and 31 were identical to those of chromosome A. Dot-blot analyses of amplified DNA from additional SS patients with specific probes have confirmed that these mutations are unique for each haplotype. The two general patterns that have been observed among the five haplotypes have most probably arisen by gene conversion events between the A and B type chromosomes in the African population. These patterns correlate with high and low fetal hemoglobin expression, and it is speculated that these and other yet unknown gene conversions may contribute to the variations in hemoglobin F and G gamma levels observed among SS patients. In vitro expression experiments involving the approximately 1.3-kb 5' flanking regions of the G gamma- and A gamma-globin genes of the beta S chromosomes with the five different haplotypes failed to detect differences between the levels of expression, suggesting that the sequence variations observed between these segments of DNA are not the primary cause of the differences in hemoglobin F levels among the SS patients.     

Vitamin D receptor gene polymorphisms and association with type 2 diabetes mellitus in a Polish population.

Vitamin D plays an important role in insulin secretion. There is also evidence that this steroid may influence the insulin sensitivity. Thus genes involved in its metabolic pathway have been regarded as good candidates for type 2 diabetes mellitus (T2DM). One of them is vitamin D receptor gene (VDR). Its multiple polymorphisms have been examined for the association with T2DM in several populations. Those studies did not provide clear answers about the role of VDR in this disease. The aim of the study was to search for the association of FokI, ApaI, BsmI, and TaqI polymorphisms of VDR gene with T2DM in a Polish population using a case-control study design. Overall, 548 individuals were examined: 308 T2DM patients and 240 control individuals. The study groups were genotyped for VDR FokI, ApaI, BsmI, and TaqI variants using the restriction fragment length polymorphism (RFLP) method. Since variants of ApaI, BsmI, and TaqI polymorphisms were in very strong linkage disequilibrium, three loci haplotypes could be assigned to phase-unknown individuals with a high degree of confidence. Differences in allele, genotype, haplotype, and haplotype combination distribution between the groups were examined by chi2 test. The VDR allele frequencies for T2DM patients and controls were as follows: FokI-F/f - 53.4 %/46.6 % vs. 55.2 %/44.8 %, BsmI-B/b - 34.4 %/65.6 % vs. 37.5 %/62.5 %, ApaI-A/a - 47.9 %/52.1 % vs 50.9 %/49.1 %, TaqI-T/t - 67.6 %/32.4 % vs. 62.7 %/37.3 %, respectively. There was no difference between the groups in allele frequency. Similarly, distribution of genotypes, three locus BsmI/ApaI/TaqI haplotypes and their combinations were similar in the groups. In conclusion, our study did not provide evidence for the association of four examined VDR polymorphisms with T2DM in a Polish population. We postulate that to fully determine whether the sequence differences in VDR gene are susceptibility variants for T2DM, additional studies in different populations are required in a large study group.