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PubMedDate not supplied

Evaluation of a polymorphism in intron 2 of the p53 gene in ovarian cancer patients. From the Danish "Malova" Ovarian Cancer Study.

BACKGROUND: The p53 gene is frequently mutated in various human tumours. In addition, single nucleotide polymorphisms are often observed in exons and introns of the p53 gene in normal tissues and tumours. MATERIALS AND METHODS: A total of 210 blood and tissue samples from 182 ovarian cancers (OC) and 28 ovarian borderline tumours, in addition to blood samples from 72 healthy women, were analysed. The used analyses were PCR and SSCP. The distinguishable SSCP patterns were confirmed by DNA sequencing. RESULTS: A polymorphism located at position 38 in intron 2 of the p53 gene was studied in blood and tumour tissues from Danish ovarian tumour patients and in blood from controls. Significant differences were found between the distributions of the genotypes in blood samples compared to the corresponding tissue samples (p = 0.0002). A tendency towards a significant difference in survival was observed between OC stage II patients with a shift from one genotype in the blood to another genotype in the tissue and patients with no shift (p = 0.05). In multivariate COX regression analysis restricted to stage III OC patients, the only independent factors found were shift, serum-tetranectin and age. CONCLUSION: A shift from one p53 intron 2 genotype in the blood to another genotype in the tissue may be a prognostic factor in ovarian cancer patients.

Adult↗
PubMed1994

The random amplification of polymorphic DNA can discriminate species and strains of Echinococcus.

The random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), also called arbitrary priming PCR (AP-PCR), is a DNA polymorphism assay based on the amplification of genomic DNA using a single oligonucleotide primer of arbitrary nucleotide sequence. Using carefully controlled conditions, the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) proved useful for distinguishing Echinococcus species and genetically distinct strains of Echinococcus granulosus. Amongst twenty random 10 mer oligonucleotide primers tested, 4 (5'-GGGAATTCGG-3', 5'-GGCTGCAGAA-3', 5'-GGAGTACTGG-3', 5'-CCTCTAGACC-3') were most suitable for producing complex but characteristic patterns for discrimination purposes. Although the method amplifies vertebrate DNA, the resulting patterns do not interfere with the identification of Echinococcus isolates. Consequently, the technique can still be used effectively to distinguish Echinococcus species and strains even if host contamination occurs during the course of parasite collection. The approach complements several other methods, based on direct DNA examination, recently developed in our laboratory, which also allow unambiguous discrimination of Echinococcus genotypes.

Animals↗
PubMed2003

On selecting markers for association studies: patterns of linkage disequilibrium between two and three diallelic loci.

Association studies depend on linkage disequilibrium (LD) between a causative mutation and linked marker loci. Selecting markers that give the best chance of showing useful levels of LD with the causative mutation will increase the chances of successfully detecting an association. This report examines the variation in the extent of LD between a disease locus and one or two diallelic marker loci (termed single nucleotide polymorphisms or SNPs). We use a simulation method based on the neutral coalescent in a population of variable size to find the distribution of LD as a function of allele frequencies, the recombination rate, and the population history. Given that LD exists, the allele frequencies determine if a site will be useful for detecting an association with the disease mutation. We show that there is extensive variation in LD even for closely linked loci, implying that several markers may be needed to detect a disease locus. The distribution of LD between common variants is strongly influenced by ancestral population size. We show that in general, best results will be obtained if the frequencies of marker alleles are at least as large as the frequency of the causative mutation. Haplotypes of two or more SNPs generally have a higher probability than individual SNPs of showing useful LD with a disease mutation, although exceptions are described.

Alleles↗
PubMed1996

Simultaneous detection and screening of T833C and G919A mutations of the cystathionine beta-synthase gene by single-strand conformational polymorphism.

OBJECTIVE: We used single-strand conformational polymorphism (SSCP) to screen for mutations at nucleotides 833 and 919 of the cystathionine beta-synthase (CBS) gene in 13 patients with homocystinuria and 11 of their relatives. METHODS: Exon 8 of genomic DNA was selectively amplified by PCR using primers derived from intronic sequences of the human CBS gene. SSCP analysis was performed on the amplified products. Genotypes identified by SSCP were confirmed by DNA sequencing and an allele-specific PCR method. RESULTS: SSCP identified 5 patterns corresponding to five genotypes. We confirmed that the different genotypes result from mutations at nucleotides 833 and 919 of the CBS gene, and that these 2 mutations account for approximately 50% of affected alleles in homocystinuria patients. CONCLUSION: Our recent elucidation of intron-exon borders and intronic sequences of the CBS gene has made possible the use of SSCP to screen for known/unknown mutations in the CBS gene. Because T833C and G919A represent the two most common mutations and both are located within exon 8 of the CBS gene, SSCP of exon 8 allows screening of the heterozygous carrier state of these mutations in a large population, to determine the importance of heterozygosity of CBS mutations as the cause of mild hyperhomocyst(e)inemia associated with premature vascular diseases.

Alleles↗
PubMed2006

Genetic polymorphism of the binding domain of surfactant protein-A2 increases susceptibility to meningococcal disease.

BACKGROUND: Meningococcal disease occurs after colonization of the nasopharynx with Neisseria meningitidis. Surfactant protein (SP)-A and SP-D are pattern-recognition molecules of the respiratory tract that activate inflammatory and phagocytic defences after binding to microbial sugars. Variation in the genes of the surfactant proteins affects the expression and function of these molecules. METHODS: Allele frequencies of SP-A1, SP-A2, and SP-D were determined by polymerase chain reaction in 303 patients with microbiologically proven meningococcal disease, including 18 patients who died, and 222 healthy control subjects. RESULTS: Homozygosity of allele 1A1 of SP-A2 increased the risk of meningococcal disease (odds ratio [OR], 7.4; 95% confidence interval [CI], 1.3-42.4); carriage of 1A5 reduced the risk (OR, 0.3; 95% CI, 0.1-0.97). An analysis of the multiple single-nucleotide polymorphisms in SP-A demonstrated that homozygosity for alleles encoding lysine (in 1A1) rather than glutamine (in 1A5) at amino acid 223 in the carbohydrate recognition domain was associated with an increased risk of meningococcal disease (OR, 6.7; 95% CI, 1.4-31.5). Carriage of alleles encoding lysine at residue 223 was found in 61% of patients who died, compared with 35% of those who survived (OR adjusted for age, 2.9; 95% CI, 1.1-7.7). Genetic variation of SP-A1 and SP-D was not associated with meningococcal disease. CONCLUSIONS: Gene polymorphism resulting in the substitution of glutamine with lysine at residue 223 in the carbohydrate recognition domain of SP-A2 increases susceptibility to meningococcal disease, as well as the risk of death.

Adult↗
PubMed2004

Genetic variation in DLG5 is associated with inflammatory bowel disease.

Crohn disease and ulcerative colitis are two subphenotypes of inflammatory bowel disease (IBD), a complex disorder resulting from gene-environment interaction. We refined our previously defined linkage region for IBD on chromosome 10q23 and used positional cloning to identify genetic variants in DLG5 associated with IBD. DLG5 encodes a scaffolding protein involved in the maintenance of epithelial integrity. We identified two distinct haplotypes with a replicable distortion in transmission (P = 0.000023 and P = 0.004 for association with IBD, P = 0.00012 and P = 0.04 for association with Crohn disease). One of the risk-associated DLG5 haplotypes is distinguished from the common haplotype by a nonsynonymous single-nucleotide polymorphism 113G-->A, resulting in the amino acid substitution R30Q in the DUF622 domain of DLG5. This mutation probably impedes scaffolding of DLG5. We stratified the study sample according to the presence of risk-associated CARD15 variants to study potential gene-gene interaction. We found a significant difference in association of the 113A DLG5 variant with Crohn disease in affected individuals carrying the risk-associated CARD15 alleles versus those carrying non-risk-associated CARD15 alleles. This is suggestive of a complex pattern of gene-gene interaction between DLG5 and CARD15, reflecting the complex nature of polygenic diseases. Further functional studies will evaluate the biological significance of DLG5 variants.

Alleles↗
PubMed2004

Human controlled ovarian hyperstimulation outcome is a polygenic trait.

This study aimed to evaluate the association between follicle-stimulating hormone (FSH) hormone efficacy and FSHR, CYP19, ESR1 and ESR2 genes using single nucleotide polymorphism analyses. One hundred and seventy women with conserved ovarian function undergoing controlled ovarian stimulation (COS) with daily exogenous recombinant FSH administration. Women were categorized as poor responders to FSH (three or less ovarian follicles observed at the end of cycle) or normal responders (more than three follicles). The outcome is the number of normal/poor responders as defined by the number of follicles obtained during COS. The DNA markers studied are located in genes related to the FSH mechanism of action (FSH receptor, CYP19 aromatase and oestrogen receptors alpha and beta genes). We conducted an association study between the COS outcome and selected DNA markers using two-point and multi-locus genetic association studies. Genotype pattern tracking in extreme phenotypes and multi-locus analysis using Sumstat and PM algorithms provided significant evidences of genetic interaction between FSHR, ESR1 and ESR2 markers in relation to COS outcome (P = 0.0015). Our results support the hypothesis that a discrete set of genes, related to the FSH hormone mechanism of action, controls the ovarian response to FSH in humans. An oligogenic model including specific FSHR, ESR1 and ESR2 genotype patterns may partially explain the poor response to FSH hormone during controlled ovarian stimulation treatments. The existence of genetic heterogeneity is also suspected.

Adult↗
PubMed2006

Genetic variability at the leptin receptor (LEPR) locus is a determinant of plasma fibrinogen and C-reactive protein levels.

OBJECTIVE: Cellular and animal studies suggest that leptin has proinflammatory and prothrombotic effects that could link increased adipose mass directly to atherogenesis. To investigate this hypothesis, we examined the effect of genetic variability at the leptin receptor (LEPR) locus on the plasma levels of fibrinogen and CRP--two markers of inflammation and susceptibility to atherosclerosis. METHODS AND RESULTS: Linkage disequilibrium analysis of 71 single-nucleotide polymorphisms (SNPs) spanning the LEPR locus revealed four haplotype blocks that could be tagged by 11 SNPs. In 630 healthy Caucasian individuals, variability in block #4 was significantly associated with plasma fibrinogen (p=0.005), accounting for 3% of its variance (r2=0.030). The same block was also associated with CRP levels (p=0.049, r2=0.022). The effect was strongest for two of the SNPs in this block. At rs3790432, fibrinogen was 10% higher in minor allele homozygotes than in major allele homozygotes and intermediate in heterozygotes (p=0.015). At rs1805096, it was 5% higher (p=0.007) and CRP 32% higher (p=0.011) in major allele homozygotes than in minor allele carriers. This pattern of association was also evident in the haplotype analysis. CONCLUSIONS: Association of leptin receptor variability with inflammatory traits supports the hypothesis that leptin may play a role in atherogenesis.

Adipose Tissue↗
PubMed2006

Lack of association between the protein tyrosine phosphatase non-receptor 22 (PTPN22)*620W allele and systemic sclerosis in the French Caucasian population.

The minor allele of the R620W missense single-nucleotide polymorphism (SNP; rs2476601) in the PTPN22 (protein tyrosine phosphatase non-receptor 22) gene has been reported to be associated with multiple autoimmune diseases, including type 1 diabetes, systemic lupus erythematosus, rheumatoid arthritis, juvenile idiopathic arthritis, autoimmune thyroiditis and vitiligo. Systemic sclerosis (SSc) is a connective tissue disease with some autoimmune abnormalities. The aim of our study was to test for association of the PTPN22*620W allele with SSc in a French Caucasian cohort with a case-control study of 121 patients with SSc and 103 controls. All patients and controls were genotyped for the PTPN22*R620W SNP. No association was found between the PTPN22*620W allele and SSc (7% v 9.2%, p = 0.39). The frequency of genotypes carrying at least one 620W allele was similar in both groups (13% v 17%, p = 0.38). The PTPN22*620W allele was also not associated with autoantibody patterns. Thus, the PTPN22*R620W polymorphism cannot be regarded as a genetic susceptibility factor for SSc in the French Caucasian population.

Adult↗
PubMed2006

TGF-beta1 gene polymorphisms influence the course of the disease in non-Hodgkin's lymphoma patients.

Non-Hodgkin's lymphomas (NHL) constitute a heterogenous group of mainly B-cell lymphoproliferative diseases with different patterns of clinical behaviour. Biological mechanisms leading to development of NHL are not clearly understood. Transforming growth factor-beta1 (TGF-beta1) influences B cell growth and development. The present study aimed to determine whether there is an association between the polymorphic features located within the TGF-beta1 gene in NHL patients and progression of the disease. Two single nucleotide polymorphisms at positions 869 T/C (Leu10Pro) and 915 G/C (Arg25Pro) in the precursor region of the TGF-beta1 gene were determined in 55 NHL patients and 50 healthy individuals by PCR-SSP technique using commercial primers. In univariate analysis the presence of TGF-beta1 high producer genotypes (T/T G/G or T/C G/G) was found to significantly associate with an increased number of extranodal sites (11/30 vs 3/25, p=0.035 for two or more extranodal sites in patients having or lacking the TGF-beta1 high producer genotype, respectively). TGF-beta1 high producer genotype together with other clinical and biological factors (patient sex and age, stage and aggressiveness of the disease, presence of B symptoms, serum LDH level) were subjected to multivariate logistic regression analyses for the number of extranodal sites. Multivariate analysis confirmed the role of TGF-beta1 high producer genotype as a risk factor of NHL manifestation in two or more extranodal sites (OR=7.217, p=0.043) in addition to histological aggressiveness of the disease (OR=4.302, p=0.057). TGF-beta1 gene polymorphisms were found to associate with the course of the disease in NHL patients. TGF-beta1 high producer genotype appeared as an independent risk factor of extranodal manifestation of the disease.

Alleles↗
PubMed2004

Association of the homeobox transcription factor, ENGRAILED 2, 3, with autism spectrum disorder.

Mouse mutants of the homeobox transcription factor Engrailed2 (En2) and autistic individuals display similar cerebellar morphological abnormalities, which include hypoplasia and a decrease in the number of Purkinje cells. Human EN2 maps to 7q36, a chromosomal region that has demonstrated suggestive linkage to autism spectrum disorder (ASD). To investigate EN2 for evidence of association with ASD, four single-nucleotide polymorphisms (SNPs) (rs3735653, rs1861972, rs1861973, rs2361689) that span the majority of the 8.0 kb gene were assessed by the transmission/disequilibrium test. Initially, 138 triads of autistic individuals and their parents were tested. Two intronic SNPs (rs1861972 and rs1861973) demonstrated significant association with autism (rs1861972, P=0.0018; rs1861973, P=0.0003; haplotype, P=0.000005). Flanking exonic SNPs (rs3735653 and rs2361689) did not display association. This analysis was then extended to include 167 small nuclear ASD pedigrees and significant association was again only observed for rs1861972 and rs1861973 under both the narrow and broad diagnostic criteria (narrow: rs1861972 P=0.0290, rs1861973 P=0.0073, haplotype P=0.0009; broad: rs1861972 P=0.0175, rs1861973 P=0.0107, haplotype P=0.0024). These data demonstrate association between a cerebellar patterning gene and ASD, suggesting a role for EN2 as a susceptibility locus and supporting a neurodevelopmental defect hypothesis in the etiology of autism.

Animals↗
PubMed1997

Phylogeography and pleistocene evolution in the North American black bear.

To determine the extent of phylogeographic structuring in North American black bear (Ursus americanus) populations, we examined mitochondrial DNA sequences (n = 118) and restriction fragment length polymorphism profiles (n = 258) in individuals from 16 localities. Among the bears examined, 19 lineages falling into two highly divergent clades were identified. The clades differ at 5.0% of nucleotide positions, a distance consistent with an origin 1.8 MYA, and have different but overlapping geographical distributions. Areas of clade cooccurrence show that eastern and western populations are currently mixing, but regional differences in lineage distribution suggest that mixing has begun only recently. The long-term population history of black bears appears to be characterized predominantly by long-term regional isolation followed by recent contact and hybridization. Congruence between the pattern of diversity observed in black bears and patterns of forest refuge formation during the Pleistocene supports earlier speculation that Pleistocene forest fragmentations underlie a common pattern in the phylogeography of North American forest taxa.

Animals↗
PubMed2002

Microevolution of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data.

The direct repeat (DR) region has been determined to be an important chromosomal domain for studying the evolution of Mycobacterium tuberculosis. Despite this, very little is known about microevolutionary events associated with clonal expansion and how such events influence the interpretation of both restriction fragment length polymorphism (RFLP) and spoligotype data. This study examined the structure of the DR region in three independently evolving lineages of M. tuberculosis with a combination of DR-RFLP, spoligotyping, and partial DNA sequencing. The results show that the duplication of direct variable repeat (DVR) sequences and single-nucleotide polymorphisms is rare; conversely, the deletion of DVR sequences and IS6110-mediated mutation is observed frequently. Deletion of either single or contiguous DVR sequences was observed. The deletion of adjacent DVR sequences occurred in a dependent manner rather than as an accumulation of independent events. Insertion of IS6110 into either the direct repeat or spacer sequences influenced the spoligotype pattern, resulting in apparent deletion of DVR sequences. Homologous recombination between adjacent IS6110 elements led to extensive deletion in the DR region, again demonstrating a dependent evolutionary mechanism. Different isolates from the same strain family and isolates from different strain families were observed to converge to the same spoligotype pattern. In conclusion, the binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of M. tuberculosis. This has important implications for molecular epidemiologic strain tracking and for the application of spoligotype data to phylogenetic analysis of M. tuberculosis isolates.

Bacterial Typing Techniques↗
PubMed2005

TLR signaling in the gut in health and disease.

The human intestine has evolved in the presence of diverse enteric microflora. TLRs convert the recognition of pathogen-associated molecules in the gut into signals for anti-microbial peptide expression, barrier fortification, and proliferation of epithelial cells. Healing of injured intestinal epithelium and clearance of intramucosal bacteria require the presence of intact TLR signaling. Nucleotide oligomerization domain (Nod)1 and Nod2 are additional pattern recognition receptors that are required for defense against invasive enteric pathogens. Through spatial and functional localization of TLR and Nod molecules, the normal gut maintains a state of controlled inflammation. By contrast, patients with inflammatory bowel disease demonstrate inflammation in response to the normal flora. A subset of these patients carry polymorphisms in TLR and CARD15/NOD2 genes. A better understanding of the delicate regulation of TLR and Nod molecules in the gut may lead to improved treatment for enteric infections and idiopathic inflammatory bowel diseases.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Detection of allelic imbalance in ascitic supernatant by digital single nucleotide polymorphism analysis.

PURPOSE: Cytological examination of ascitic fluid is critical for clinical management of patients with peritoneal or pelvic diseases. Such morphological examination can only achieve a sensitivity of <62%, and thus a molecular test that is able to distinguish benign versus malignant ascites could be clinically useful. In this study we determined the presence of allelic imbalance (AI) in tumor-released DNA in ascitic supernatant by directly counting the alleles using a newly developed technology, digital single nucleotide polymorphism (SNP) analysis. EXPERIMENTAL DESIGN: Allelic status was assessed using a total of seven SNP markers that commonly demonstrated AI in ovarian, colorectal, and pancreatic cancers. RESULTS: With digital SNP analysis, AI in at least one SNP marker was found in 19 of 20 (95%) ascitic fluid DNA samples obtained from patients with cytologically proven carcinomas in ascitic fluid. In contrast, AI was detected in only 1 of 20 patients with negative cytology. This latter patient with AI in her ascites had known stage III ovarian carcinoma at the time of cytology sampling. The ascitic specimen of this patient demonstrated the presence of carcinoma cells in culture with an identical AI pattern found in the ascitic supernatant and surgical specimen. CONCLUSIONS: These findings suggest that detection of AI using digital SNP analysis can be a useful adjunct for the detection of ovarian and other types of cancer in ascitic fluid.

Alleles↗
PubMed2005

Cosmopolitan linkage disequilibrium maps.

Linkage maps have been invaluable for the positional cloning of many genes involved in severe human diseases. Standard genetic linkage maps have been constructed for this purpose from the Centre d'Etude du Polymorphisme Humain and other panels, and have been widely used. Now that attention has shifted towards identifying genes predisposing to common disorders using linkage disequilibrium (LD) and maps of single nucleotide polymorphisms (SNPs), it is of interest to consider a standard LD map which is somewhat analogous to the corresponding map for linkage. We have constructed and evaluated a cosmopolitan LD map by combining samples from a small number of populations using published data from a 10-megabase region on chromosome 20. In support of a pilot study, which examined a number of small genomic regions with a lower density of markers, we have found that a cosmopolitan map, which serves all populations when appropriately scaled, recovers 91 to 95 per cent of the information within population-specific maps. Recombination hot spots appear to have a dominant role in shaping patterns of LD. The success of the cosmopolitan map might be attributed to the co-localisation of hot spots in all populations. Although there must be finer scale differences between populations due to other processes (mutation, drift, selection), the results suggest that a whole-genome standard LD map would indeed be a useful resource for disease gene mapping.

Chromosome Mapping↗
PubMed1990

Crystallographic characterization of wild-type and mutant ribonuclease T1 complexes with several ribonucleotides.

Ribonuclease T1 and the mutant enzymes were cocrystallized with several ribonucleotides, including non-hydrolyzable substrate analogs of di- and triribonucleotides, which have a novel guanylate in which the 2'-hydroxyl group of the ribose is replaced by a fluorine atom. One of the mutant enzymes has a tryptophan residue, instead of Tyr45 of the wild-type enzyme, to enhance the binding of ribonucleotides to the enzyme and the other mutant enzyme has histidine and aspartate residues, instead of Asn43 and Asn44, respectively, to reproduce the natural substitutions found in ribonuclease Ms. Polymorphism of the crystals was observed for wild-type and mutant enzymes. However, orthorhombic crystals, which are virtually all isomorphous to each other, were successfully obtained from wild-type and mutant (Y45W) enzymes by the macroscopic seeding technique using mother crystals of the wild-type ribonuclease T1 complexed with 2'GMP or 3'GMP. The diffraction patterns of these crystals extend beyond 2.5 A resolution and the diffraction data were collected from some of the crystals on a diffractometer up to a range of 2.5 to 1.8 A resolution.

Aspergillus oryzae↗
PubMed2006

Analysis of high-resolution HapMap of DTNBP1 (Dysbindin) suggests no consistency between reported common variant associations and schizophrenia.

DTNBP1 was first identified as a putative schizophrenia-susceptibility gene in Irish pedigrees, with a report of association to common genetic variation. Several replication studies have reported confirmation of an association to DTNBP1 in independent European samples; however, reported risk alleles and haplotypes appear to differ between studies, and comparison among studies has been confounded because different marker sets were employed by each group. To facilitate evaluation of existing evidence of association and further work, we supplemented the extensive genotype data, available through the International HapMap Project (HapMap), about DTNBP1 by specifically typing all associated single-nucleotide polymorphisms reported in each of the studies of the Centre d'Etude du Polymorphisme Humain (CEPH)-derived HapMap sample (CEU). Using this high-density reference map, we compared the putative disease-associated haplotype from each study and found that the association studies are inconsistent with regard to the identity of the disease-associated haplotype at DTNBP1. Specifically, all five "replication" studies define a positively associated haplotype that is different from the association originally reported. We further demonstrate that, in all six studies, the European-derived populations studied have haplotype patterns and frequencies that are consistent with HapMap CEU samples (and each other). Thus, it is unlikely that population differences are creating the inconsistency of the association studies. Evidence of association is, at present, equivocal and unsatisfactory. The new dense map of the region may be valuable in more-comprehensive follow-up studies.

Alleles↗