NcoI Restriction Fragment Length Polymorphism Research Articles

Migraine and tumour necrosis factor gene polymorphism

To assess the possibility of an association between TNF gene polymorphisms and migraine without aura, a case-control study was performed in a Sardinian sample. Migraine without aura is a complex genetic disease in which susceptibility and environmental factors contribute towards its development. Several studies suggest that tumour necrosis factors (TNF) (TNF-alpha and lymphotoxin-alpha or TNF-ss) may be involved in the pathophysiology of migraine. The TNF-alpha and TNF-ss genes are located on chromosome 6p21.3 in the human leukocyte antigene (HLA) class III region. We evaluated 299 patients affected by migraine without aura (I.H.S. criteria 2004) and 278 migraine-free controls. The polymorphisms G308A of the TNF- alpha gene, and G252A of TNF-beta gene were determined by NcoI restriction fragment length polymorphism analysis. We found a statistically significant difference in allele (p = 0.018; OR = 1.46 95 % CI: 1.066 to 2.023) and genotype (trend chi2 = 5.46, df = 1, p = 0.019) frequencies of TNF-beta gene, between cases and controls. Allele and genotype frequencies of TNF-alpha polymorphism did not differ significantly between the two groups. These data suggest that subjects with the TNFB2 allele have a low risk of developing migraine without aura and/or that the polymorphism of the TNF-beta gene is in linkage disequilibrium with other migraine responsible genes in the HLA region.

The caregene study: muscle-specific creatine kinase gene and aerobic power in coronary artery disease

In 927 biologically unrelated Caucasian patients with coronary artery disease it was investigated whether the NcoI restriction fragment length polymorphism of the muscle-specific creatine kinase (CKMM) gene is associated with aerobic power and with the response to physical training. Physical training significantly (P<0.001) increased peak oxygen consumption in the GG, AG and AA NcoI genotypes. Covariate-adjusted peak oxygen consumption at baseline, after training and the response to training were not different across CKMM NcoI genotypes.

TNF-α, IL-8 and CD14 gene polymorphisms in Helicobacter pylori-positive duodenal ulcer patients

Background: The activation of inflammatory cytokines plays an important role in the pathogenesis of the development of Helicobacter pylori (HP)-positive duodenal ulcer (DU). Cytokine production is determined in part by the nucleotide polymorphisms of cytokine genes. The aim was to evaluate the frequency of TNF-α, IL-8 and CD14 gene polymorphisms in HP-positive DU patients. Patients. 69 patients with HP-positive DU (mean age 46.8 years) and 47 HP- positive healthy blood donors (mean age 42.6 years) were included in the study. Methods: The TNFα-308A (G to A) gene polymorphism was determined by NcoI RFLP (restriction fragment length polymorphism), the IL-8–251A (T to A) gene polymorphisms by ARMS (amplification refractory mutation system) methods and the CD14–159T (C to T) polymorphism by melting point analysis.

Are postoperative complications genetically determined by TNF-β NcoI gene polymorphism?

Background Postoperative infectious complications are the leading causes for postoperative sepsis. In severe sepsis, tumor necrosis factor-beta (TNF-β) NcoI polymorphism was associated with increased mortality. Therefore, the aim of this study was to determine whether the biallelic NcoI polymorphism within the TNF locus is associated with the development of postoperative complications. Methods One hundred sixty patients were included in this prospective observation study. Patients undergoing major gastrointestinal surgery, such as esophagectomy, gastrectomy, Whipple operation, major liver resection, or colon resection were included. Patients were monitored during the clinical course, and postoperative complications, divided into severe and minor complications, were documented. The NcoI restriction fragment length polymorphism of the TNF-β gene was determined by polymerase chain reaction; gene expression as well as complications were correlated. Results The patients' genotype distribution and demographic characteristics were comparable within the different groups of operations. Patients with the heterozygous genotype TNF-β1/β2 had a 1.6-fold higher relative risk for developing complications. If patients with the homozygous genotype TNF-β2 developed a complication, they had a 1.5-fold higher relative risk for severe complications. Furthermore, the mortality of patients with postoperative sepsis who were homozygous for the genotype TNF-β2 was significantly elevated. Conclusions The TNF-β NcoI polymorphism influences the development of postoperative complications. While the genotype TNF-β1/β2 has a higher risk for developing complications in general, the TNF-β2/β2 genotype is associated with more severe complications and mortality from sepsis.

Gene polymorphisms in tumor necrosis factor locus and waist–hip ratio in obese Koreans

Background: The study was designed to investigate the association among tumor necrosis factor-beta (TNFβ)+252A/G, TNF-alpha (TNFα)-308G/A polymorphisms and anthropometric parameters related to obesity in Korean obese subjects. Methods: The study included 152 obese healthy subjects (BMI≥25 kg/m 2, range 25.0–40.4, age range 15–40 years) and 82 non-obese controls (BMI<25 kg/m 2, age range 15–40 years). Total fat mass and percent body fat were determined by dual-energy X-ray absorptiometry (DEXA). Genomic DNA was extracted and used for NcoI restriction fragment length polymorphism (RFLP)-based genotyping of TNF. Results: No differences were observed for allelic and genotype frequencies between obese and non-obese subjects. Also, no association of TNF polymorphisms was observed with body mass index (BMI) for genotype in obese subjects. In addition, age, percent body fat, BMI and cholesterol concentrations did not differ from TNF genotypes. However, waist-to-hip ratio (WHR) was significantly decreased in subjects with TNFα A/TNFβ G haplotype compared with other haplotypes carriers (0.92±0.03 vs. 0.94±0.06, P=0.005). Conclusions: These results suggest that TNF polymorphisms at position −308 and +252 are not a significant factor for BMI, but affect the WHR in obese Koreans.

Polymorphism in exon 6 of the dopamine D2 receptor gene (DRD2) is associated with elevated blood pressure and personality disorders in men

A deficient dopamine D(2) receptor (DA2) formation or action may contribute to hypertension via an increase of catecholamine release. In addition, Axis II personality disorders that appears odd or eccentric (cluster A) is associated with a low density of DA2. This study sought to examine if a NcoI restriction fragment length polymorphism (C to T transition) in exon 6 of the dopamine D(2) receptor gene (DRD2) was associated with these characteristics. The genotypes (CC, CT and TT) were compared in anthropometric, endocrine, metabolic and haemodynamic variables as well as estimates of personality disorders in 284 randomly selected 51-year-old men. Homozygotes for the C allele constituted 49% of the men and homozygotes for the T allele 9%, while heterozygotes were 41%. The TT genotype was associated with elevated systolic and diastolic blood pressure, independent of obesity and endocrine abnormalities, including the hypothalamic-pituitary-adrenal axis regulation. Moreover, the TT genotype was significantly more frequent among subjects with grade 1 (mild) hypertension (>140/90 mm Hg) compared to normotensive subjects (<130/85 mm Hg). The polymorphism in exon 6 of the DRD2 was also significantly associated with cluster A personality disorders. These results suggest that a polymorphism in exon 6 of the DRD2examined with the restriction enzyme NcoI is associated with an elevated blood pressure, independent of obesity. Paranoid or schizoid personality disorders is also associated with a polymorphism of the DRD2, which might be associated with a previously demonstrated low density of this receptor.

Relation of the bi-allelic NcoI restriction fragment length polymorphism within the tumour necrosis factor B gene to the development of mediastinitis.

During recent years the dual role of endogenous inflammatory mediators such as tumour necrosis factor (TNF) has become evident. While TNF has been recognised to possess a great detrimental potential, for example in the case of sepsis, it is on the other hand an integral component of an adequate immune response to bacterial invasion. These different properties of TNF and others seem to be dependent mainly on the quantitative extent of their formation. Some recent findings indicate that this extent may in part be determined genetically. The classification of patients according to polymorphic cytokine genes might, therefore, predict some of their reactions to septic challenges.

Muscle-specific creatine kinase gene polymorphisms in elite endurance athletes and sedentary controls.

The purpose of this study was to investigate the association between elite endurance athlete (EEA) status and two restriction fragment length polymorphisms (RFLPs) at the muscle-specific creatine kinase (CKMM) gene locus. Genomic DNA was extracted from white blood cells or lymphoblastoid cell lines of 124 unrelated Caucasian male EEA (VO2max > 73 mL.kg-1.min-1) and 115 unrelated Caucasian sedentary male controls (SCON). The genetic polymorphism at the CKMM locus was detected by the polymerase chain reaction and DNA digestion with the NcoI and TaqI restriction endonucleases. The allelic frequencies for the NcoI and TaqI RFLPs were not different (P > 0.05) between EEA and SCON subjects. The three expected genotypes for CKMM-NcoI (1170/1170 bp, 1170/985 + 185 bp, and 985 + 185/985 + 185 bp) and CKMM-TaqI (1170/1170 bp, 1170/1020 + 150 bp, and 1020 + 50/1020 + 150 bp) were observed in the EEA and SCON groups. These genotype frequencies were in Hardy-Weinberg equilibrium, but they were not significantly (P > 0.05) different between the EEA and SCON. A strong (P < 0.001) linkage disequilibrium was detected among the NcoI and TaqI RFLPs in both EEA and SCON. These findings indicate that the skeletal muscle CK-NcoI and CK-TaqI gene polymorphisms are not associated with the elite endurance athlete status.

Decreased tumour necrosis factor-beta production in TNFB*2 homozygote: an important predisposing factor of lupus nephritis in Koreans.

Low TNF production and its association with TNF gene restriction fragment length polymorphism (RFLP) was demonstrated in (NZW/NZB) F1 mice. However, little is known about the significance of TNF production in association with TNF gene polymorphism in human SLE. This study was designed to evaluate the role of TNF production of peripheral blood mononuclear cells (PBMC) and its association with TNFB gene polymorphism in SLE, particularly lupus nephritis. TNFB gene polymorphism was defined by PCR-NcoI RFLP. TNF productions of phytohemagglutinin (PHA)-stimulated PBMC and T cells were examined by bioassay using L929 cell line and ELISA. The PBMC stimulated by PHA from patients with SLE (n = 60) tended to secrete less amounts of TNF by bioassay (1032 +/- 184 pg/ml vs 1524 +/- 224 pg/ml, P = 0.094), and TNF-beta by ELISA (P = 0.0082) than that from normal controls (n = 38). The low TNF-alpha producer was more frequent in nephritis than non-nephritis (34.4% vs 7.1% respectively, P < 0.01). TNF-beta also revealed similar results (53.1% vs 21.4%, P < 0.05). In SLE, mean production of TNF-beta was decreased in TNFB*2 homozygote (n = 18) than that in TNFB*1 homozygote (n = 9) (1126.3 +/- 145 pg/ml) vs 642 +/- 118.4 pg/ml, respectively, P = 0.021), whereas TNF-alpha production showed little difference between the two groups (710.1 +/- 56.4 vs 542.4 +/- 71.1 pg/ml, respectively, P = 0.149). Our results demonstrate that decreased TNF production of PBMC, which was significantly associated with TNFB*2 homozygosity, could be an important predisposing factor of lupus nephritis in Koreans.

NcoI restriction fragment length polymorphism at -308 of the tumor necrosis factor alpha (TNFA) promoter region in Korean.

Tumor necrosis factor alpha (TNFA) is a cytokine, which is secreted from activated macrophage, with a broad range of biological activities. The gene encoding TNFA is located in tandem with the TNFB gene within the HLA complex on chromosome 6p21.3. We detected a single base polymorphism in the human TNFA gene promoter region in 300 unrelated Korean individuals. The TNFA promoter region which showed a G to A transition at position of -308 was investigated by NcoI restriction fragment length polymorphism analysis. A biallelic polymorphism of TNFA gene showed fragments of 87/20 bp and 107 bp acting as TNFA*1 allele and TNFA*2 allele, respectively. The allele frequencies of TNFA*1 and TNFA*2 were 0.8783 and 0.1217, respectively. The 21.7% of heterozygosity was observed. No association between promoter region phenotypes of TNFA and the first intron phenotypes of TNFB was observed in Korean. Allele frequencies of Koreans were compared with that of Europeans.

10.5-kb homozygote of tumor necrosis factor-beta gene is associated with a better prognosis in gastric cancer patients.

In NcoI restriction fragment length polymorphism analysis of tumor necrosis factor-beta (TNF-beta) gene, the frequency of 10.5-kb homozygote is low in patients with lung cancer and is associated with a better prognosis. These results should be examined in other malignancies. Using polymerase chain reaction, the authors performed NcoI restriction fragment length polymorphism analysis in 152 patients with gastric cancer, in 69 patients with benign gastric lesion, and in 141 healthy volunteers. In 3-year survival, the 10.5-kb homozygote showed a better prognosis (87.1%) than other alleles (5.5-kb homozygote, 52.5%; heterozygote, 79.1%), and there was a statistically significant difference between the 10.5-kb homozygote and the 5.5-kb homozygote. In 3-year survival for Stages III and IV, the 10.5-kb homozygote also showed a better prognosis (64.9%) than other alleles (5.5-kb homozygote, 16.7%; heterozygote, 41.4%). There were statistically significant differences (10.5-kb homozygote vs. 5.5-kb homozygote, P < 0.01; heterozygote vs. 5.5-kb homozygote, P < 0.05). There was a statistical difference between all patients and Stages III and IV (P < 0.05). The 10.5-kb homozygote of TNF-beta gene is associated with a prolonged survival in patients with gastric cancer, as has been shown in the patients with lung cancer.

TNF Nco-I RFLP is not an independent risk factor in rheumatoid arthritis.

The human TNF genes are located within the MHC class-III region on chromosome 6. The presence or absence of an Nco-I restriction site in the 5' non-coding sequence of the TNF beta gene defines two alleles (TNFB*1 and TNFB*2). The segregation of these alleles has been associated with levels of TNF alpha or TNF beta production in systemic lupus erythematosis (SLE), insulin-dependent diabetes mellitus (IDDM) and in healthy control individuals. Rheumatoid arthritis (RA) is characterized by high levels of TNF alpha within the synovial fluid and to address the question of whether this could be brought about by a genetic predisposition to high TNF production by RA individuals, we examined the distribution of this Nco-I polymorphism in 98 healthy volunteers and 123 patients with active rheumatoid arthritis. No difference was observed between the normal and RA groups with respect to haplotype segregation or allelic frequency. Furthermore, no difference was observed between DR4+ or DR4- individuals in the control or RA groups. These data demonstrate that the high level of TNF alpha seen in the joints of RA patients is unlikely to be due to a genetic predisposition of these patients to high TNF alpha production, as defined by the TNF Nco-I restriction fragment length polymorphism (RFLP).

The human serum amyloid A protein (SAA) superfamily gene cluster: mapping to chromosome 11p15.1 by physical and genetic linkage analysis.

The human serum amyloid A protein (SAA) family comprises a number of small, hepatically produced, differentially expressed apolipoproteins encoded by genes localized on the short arm of chromosome 11.SAA1 and SAA2 are highly related genes that together encode the acute-phase SAAs; SAA3 is a pseudogene; and SAA4 is a low-level constitutively expressed gene encoding constitutive SAA. We have used a combination of physical and genetic mapping techniques to provide evidence that the SAA gene superfamily comprises a cluster of closely linked genes localized to 11p15.1. Pulsed-field gel electrophoresis placed SAA1 to within 350 kb of the previously linked SAA2 and SAA4 genes. SAA locus-specific polymerase chain reaction amplification from a panel of somatic cell hybrids carrying defined regions of chromosome 11p mapped all four loci to 11p15.1-pter. Fluorescence in situ hybridization analysis using a cosmid probe carrying the SAA2 and SAA4 genes refined the localization of these genes (and SAA1) to 11p15.1. To order SAA3 on the genetic map, a highly polymorphic (CA)n dinucleotide repeat within SAA3 was typed through the CEPH reference families. In accordance with the physical localization of SAAs 1, 2, and 4, SAA3 maps to the 11p15.1 region proximal to the parathyroid hormone (PTH) locus (theta = 0.02; lod = 12.020) and distal to D11S455 (theta = 0.058, lod = 8.274). To provide further evidence of an SAA superfamily gene cluster, an NcoI restriction fragment length polymorphism in the SAA2 gene was also typed through the CEPH reference panel.(ABSTRACT TRUNCATED AT 250 WORDS)

DXS539, a polymorphic DNA marker proximal of the fragile-X gene.

We report a new polymorphic DNA marker (pJH89, DXS539) proximal to the fragile-X site. The pJH89 probe identifies a TaqI and a NcoI restriction fragment length polymorphism (combined heterozygosity of 42%) and is linked to the fragile-X locus with a maximal LOD score of 12 at 4 cM. Multipoint linkage analysis and physical mapping studies indicate that the pJH89 probe is located within in the interval defined by the markers DXS369 and DXS548.

Association of tumor necrosis factor (TNF) and class II major histocompatibility complex alleles with the secretion of TNF-alpha and TNF-beta by human mononuclear cells: a possible link to insulin-dependent diabetes mellitus.

We have investigated the correlation between different tumor necrosis factor (TNF) and class II major histocompatibility complex alleles in the lipopolysaccharide- or phytohemagglutinin-induced secretion of TNF-alpha and TNF-beta by human monocytes and peripheral blood mononuclear cells in 87 unrelated Danish male individuals. Significant differences in TNF-alpha secretory capacity between TNF NcoI restriction fragment length polymorphisms, TNFa and TNFc microsatellite alleles and DR alleles were identified. No correlation with TNF-beta secretory capacity was found for any of the markers studied. TNF genotyping allowed us to define four extended HLA haplotypes which correlate with TNF-alpha secretory capacity. Two of these are DR4 positive: DQw8, DR4, TNFB*1, TNFa6, B44, A2 and DQw8, DR4, TNFB*2, TNFa2, B15, A2. Individuals carrying the TNFB*2, TNFa2 haplotype had a higher TNF-alpha secretory capacity than those carrying the TNFB*1, TNFa6 haplotype. In a group of DR3/DR4 heterozygous patients with insulin-dependent diabetes mellitus (IDDM), the frequency of the TNFa2 allele was higher than in HLA-DR matched controls, whereas the TNFa6 allele was more frequent in control individuals. In the DR3/DR4 heterozygous diabetic group 12/26 had the alleles combination DQw8, DR4 (Dw4), C4A3, TNFB*2, TNFa2, B15, whereas only 1/18 controls had this haplotype. This diabetogenic haplotype is identical to the DR4 haplotype which correlates with a higher TNF-alpha response. These observations suggest a direct role for the TNF locus in the pathogenesis of IDDM.

Highly polymorphic region of the human prothrombin (F2) gene.

We have found a highly polymorphic region in the human prothrombin gene. Our sequence differed from that previously reported at as many as 6 positions in a 225-bp stretch spanning exon 6 and its flanking regions; four of these positions were related to endonuclease restriction sites for AluI, HpaII(MspI), MboII, and NcoI. AluI and HpaII digested all alleles of the Japanese tested. MboII and NcoI restriction fragment length polymorphisms are highly heterozygous and not in linkage disequilibrium; they thus serve as good human DNA markers.

Tumour necrosis factor B gene polymorphism in relation to complotype in couples with spontaneous abortions and in control families.

NcoI restriction fragment length polymorphism (RFLP) of the tumour necrosis factor B (TNFB) gene gives two allelic fragments of 5.5 and 10.5 kb, corresponding to the TNFB*1 and TNFB*2 alleles, respectively. The frequencies of these alleles were analysed in 121 healthy Finns and 56 Finnish couples suffering from recurrent spontaneous abortions (RSA). In the healthy Finns the frequency of TNFB*1 was 37% and that of TNFB*2 63%, of which the frequency of TNFB*1 was significantly increased compared with the Danish population. No deviation was seen between the RSA couples and the Finnish controls. TNF genes are located in major histocompatibility complex class III region close to complement (BF, C4A and C4B) genes. Some complotypes associated most often with the TNFB*1 (S01, S30, S02) and some (S31, F320) with the TNFB*2 allele in the healthy Finns. The combination of the TNFB and the C4 'null' allele differed between the RSA couples and the Finnish controls.

NCOI restriction fragment length polymorphism of the tumour necrosis factor region in systemic lupus erythematosus

NCOI restriction fragment length polymorphism of the tumour necrosis factor region in systemic lupus erythematosus

Polymorphic structure of the tumor necrosis factor (TNF) locus: an NcoI polymorphism in the first intron of the human TNF-beta gene correlates with a variant amino acid in position 26 and a reduced level of TNF-beta production.

Since a dysregulated synthesis of tumor necrosis factor alpha (TNF-alpha) may be involved in the pathogenesis of autoimmune diseases, it was of interest to precisely locate the recently reported NcoI restriction fragment length polymorphism (RFLP) of the TNF-alpha region. However, by mapping of 56.8 kb of overlapping cosmid clones and direct sequencing, we could localize the polymorphic NcoI restriction site within the first intron of the TNF-beta gene and not in the TNF-alpha gene. To study whether regulatory mechanisms are affected by this polymorphism, we analyzed the TNF-alpha/TNF-beta production of phytohemagglutinin-stimulated peripheral blood mononuclear cells of individuals homozygous for the TNF-beta NcoI RFLP by ELISA and concomitant Northern blot analysis. On days 2-4 after stimulation with mitogen, the TNFB*1 allele corresponding to a 5.3-kb NcoI fragment presented with a significantly higher TNF-beta response. A mRNA analysis demonstrated that higher protein levels of TNF-beta correlate also with increased amounts of TNF-beta transcripts. No allelic association was found in respect to TNF-alpha production. To further investigate a possible allelic influence on transcription, we determined the DNA sequence of 2 kb of the 5' portion of our cloned TNFB*2 allele and compared it with the available TNF-beta sequences. By computer-aided recognition motif search of DNA binding factors, we report putative binding sites conserved between mouse and man in the 5' flanking region as well as in intron 1 of the TNF-beta gene, found also in other cytokine promoter sequences. In addition, by polymerase chain reaction amplification and sequencing of 740 bp of the 5' part of TNF-beta of individuals typed homozygously for the NcoI RFLP, we could show that amino acid position 26 is conserved as asparagine in the TNFB*1 and as threonine in the TNFB*2 sequence. A previously reported, EcoRI RFLP in the 3' untranslated region of TNF-beta does not segregate with either of the two alleles. Thus, four TNFB alleles can be defined at the DNA level.

Genomic Organization, Chromosomal Localization, and Developmentally Regulated Expression of the Glycosyl-Phosphatidylinositol-Specific Phospholipase C of Trypanosoma brucei

The surface of the bloodstream form of the African trypanosome, Trypansoma brucei, is covered with about 10(7) molecules of the variant surface glycoprotein (VSG), a protein tethered to the plasma membrane by a glycosyl-phosphatidylinositol (GPI) membrane anchor. This anchor is cleavable by an endogenous GPI-specific phospholipase C (GPI-PLC). GPI-PLC activity is down regulated when trypanosomes differentiate from the bloodstream form to the procyclic form found in the tsetse fly vector. We have mapped the GPI-PLC locus in the trypanosome genome and have examined the mechanism for this developmental regulation in T. brucei. Southern blot analysis indicates a single-copy gene for GPI-PLC, with two allelic variants distinguishable by two NcoI restriction fragment length polymorphisms. The gene was localized solely to a chromosome in the two-megabase compression region by contour-clamped homogeneous electric field gel electrophoresis. No rearrangement of the GPI-PLC gene occurs during differentiation to procyclic forms, which could potentially silence GPI-PLC gene expression. Enzymological studies give no indication of a diffusible inhibitor of GPI-PLC activity in procyclic forms, and Western immunoblot analysis reveals no detectable GPI-PLC polypeptide in these forms. Therefore, it is highly unlikely that the absence of GPI-PLC activity in procyclic forms is due to posttranslational control. Northern (RNA) blot analysis reveals barely detectable levels of GPI-PLC mRNA in procyclic forms; therefore, regulation of GPI-PLC activity in these forms correlates with the steady-state mRNA level.