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A novel common single nucleotide polymorphism in the promoter region of the C-reactive protein gene associated with the plasma concentration of C-reactive protein.

The plasma CRP concentration has consistently been shown to be associated with the risk of future coronary heart disease (CHD) and recent studies have suggested that CRP has a pathogenic role in CHD. Family studies and genotype-phenotype association studies of known polymorphisms in the intron, second exon and 3'-untranslated region (UTR) have suggested that plasma CRP concentrations are under genetic control. However, no functional polymorphisms have so far been reported in the promoter region of the CRP gene. Screening of 1600 base pair (bp) of the promoter region of the CRP gene, using denaturing high performance liquid chromatography, revealed two novel common single nucleotide polymorphisms (SNPs). One of them, a three allelic SNP located at position -286 from the transcription start, was strongly associated with the plasma CRP concentration, predominantly in patients with CHD. No difference in allele frequency was seen between middle-aged post-infarction patients and population-based controls. The prognostic role and therapeutic implications in CHD and the functionality of this polymorphism remain to be determined.

Adenine↗

Progress in concurrent analysis of loss of heterozygosity and comparative genomic hybridization utilizing high density single nucleotide polymorphism arrays.

Genetic aberrations, such as deletions and amplifications are among the major pathogenetic mechanisms underlying many medical disorders. Analysis of chromosomal aberrations is particularly important in cancer research, where amplifications of oncogenes and deletions of tumor suppressor genes are major steps in the "multi-hit" process of tumorigenesis. Genome-wide molecular biological analyses, such as loss of heterozygosity (LOH) profiling and comparative genomic hybridization (CGH) have significantly enhanced our ability to detect chromosomal aberrations in cancer cells and assess their role in tumorigenesis. The recent introduction of high-density oligonucleotide arrays for measuring single nucleotide polymorphisms (SNP) has sparked a new wave of high-resolution genetic mapping studies, including LOH and CGH applications on various cancer types. This review highlights recent progress on concurrent LOH and CGH analyses utilizing high density SNP arrays and their application in cancer research.

Genome, Human↗

Single-nucleotide polymorphisms of mismatch repair genes in healthy Chinese individuals and sporadic colorectal cancer patients.

Mismatch repair (MMR) genes are among of the most important genes associated with colorectal cancer (CRC). Single-nucleotide polymorphisms (SNPs) are generally thought to provide important information across a wide spectrum of life sciences; however, no study of association between SNPs of MMR genes and Chinese sporadic colorectal cancer (SCRC) is available. We chose 29 reported single-nucleotide variants that have rarely been verified in a population-based study. We identified SNPs and the genotype-phenotype association in Chinese populations of 150 healthy individuals and 160 SCRC patients. We extracted the genomic DNA from the blood of these individuals and used sequencing to determine these SNPs. Three SNPs (MLH1 394G-->C, 655A-->G, 1151T-->A) occurred with a frequency of 8.8-11.2% in the Chinese population. These SNPs formed a series with combined effects. The haplotype of concurrent MLH1 655 and 1151 SNPs and the haplotype combinations of MLH1 1151, MLH1 394 occurred exclusively in SCRC. None of the other 26 variants were detected in the Chinese population.

Adaptor Proteins, Signal Transducing↗

Single nucleotide polymorphisms in an STS region linked to the Ncc-tmp1A locus are informative for characterizing the differentiation of chromosome 1A in wheat.

Homoeoalleles of Ncc confer nucleus-cytoplasm (NC) compatibility on NC hybrids of wheat with the D plasmon of Aegilops squarrosa. To dissect the chromosomal region containing Ncc, a RAPD marker linked to the Ncc-tmplA locus, which is located on chromosome 1A of T timopheevi, was sequenced and converted to a PCR-based sequence-tagged-site (STS) marker. Five single nucleotide polymorphisms (SNPs) between T timopheevi and T turgidum. were detected in a 509-bp genomic DNA fragment. Based on the SNPs, the STS alleles in 164 accessions from emmer wheat, timopheevi wheat and two einkorn wheats, T. urartu and T. boeoticum were surveyed by PCR-RFLP analysis. The sequence comparisons and PCR-RFLP analyses revealed nine alleles based on six SNPs. These SNPs were highly conserved within each group of wheat, and all groups could be distinguished by particular combinations of the SNPs. All accessions of T. urartu had one unique STS allele as compared with the others. Our results indicate that the SNPs in the STS marker linked to the Ncc-tmplA locus would be informative for studies of the differentiation of chromosome 1A in wheat.

Alleles↗

The MCP-1 -2518 (A to G) single nucleotide polymorphism is not associated with myocardial infarction in the Czech population.

Monocyte chemoattractant protein (MCP)-1 is the key chemokine in the process of atheroslerotic vascular inflammation. Examining already reported association between coronary artery disease (CAD) and the SNP A/G in the MCP-1 gene (position -2518), 139 Czech patients with CAD manifested as myocardial infarction (MI) and 359 unrelated healthy control (C) subjects were genotyped by PCR-SSP. Genotype and allele frequencies were not different in MI and C groups (allele G: MI, 20.5%; C, 23.8%, OR = 0.8, P > 0.05). No differences were detected when the patients were subdivided based on sex or the age of MI first occurrence. Further, no relationship was observed between circulating MCP-1 levels and carriage of the G allele. The data do not support a role for the MCP-1 -2518 single nucleotide polymorphism in susceptibility to CAD manifested by myocardial infarction.

Alleles↗

Analysis of single-nucleotide polymorphisms in the interleukin-4 receptor gene for association with inflammatory bowel disease.

Genetic linkage analysis in families with multiple cases of inflammatory bowel disease (IBD) has mapped a gene which confers susceptibility to IBD to the pericentromeric region of chromosome 16 (IBD1). The linked region includes the interleukin(IL)-4 receptor gene (IL4R). Since IL-4 regulation and expression are abnormal in IBD, the IL4R gene is thus both a positional and functional candidate for IBD1. We screened the gene for single-nucleotide polymorphisms (SNPs) by fluorescent chemical cleavage analysis, and tested a subset of known and novel SNPs for allelic association with IBD in 355 families, which included 435 cases of Crohn's disease and 329 cases of ulcerative colitis. No association was observed between a haplotype of four SNPs (val50ile, gln576arg, A3044G, G3289A) and either the Crohn's disease or ulcerative colitis phenotypes using the transmission disequilibrium test. There was also no evidence for association when the four markers were analyzed individually. The results indicate that these variants are not significant genetic determinants of IBD, and that the IL4R gene is unlikely to be IBD1. Linkage disequilibrium analyses showed that the val50ile and gln576arg variants are in complete equilibrium with each other, although they are separated by only about 21 kilobases of genomic DNA. This suggests that a very dense SNP map may be required to exclude or detect disease associations with some candidate genes.

Alleles↗

Novel single nucleotide polymorphisms in the 3'-UTR of the TGFbetaRI and TGFbetaRIII genes.

Transforming growth factor beta (TGFbeta) family members are multifunctional cytokines that play a key role in cellular growth, proliferation and differentiation. Transmembrane signalling by TGFbeta occurs via a complex of the serine/threonine kinases TGFbeta type 1 (TGFbetaRI), type 2 (TGFbetaRII), and type 3 (TGFbetaRIII) receptors. Previous studies have implicated TGFbeta receptors (TGFbetaR) in a variety of important hereditary clinical disorders. Mutations of the TGFbetaR genes have been observed in several human cancers. The aim of this study was to identify and confirm novel single nucleotide polymorphisms (SNPs) in TGFbetaRI and RIII and to determine the relative allele and genotype frequencies of these SNPs. SNPs were identified from the examination of sequence alignments held in databases and were confirmed by DNA sequencing. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was devised for genotyping TGFbeta receptor polymorphisms. DNA samples from 91 controls were examined. The observed heterozygosities of TGFbetaRI and TGFbetaRIII gene polymorphisms in the control population were 43 and 33%, respectively, suggesting these SNPs could be useful markers in disease association studies.

3' Untranslated Regions↗

Coding single nucleotide polymorphism in the high-affinity immunoglobulin E receptor b chain (FcepsilonRI-beta) gene is associated with immunoglobulin E receptor-mediated histamine release from basophils.

BACKGROUND: Our previous work on linkage analysis showed that histamine release from basophils to anti-IgE stimuli was linked to the gene marker of chromosome 11q13, where the beta chain of the high-affinity receptor for IgE (FcepsilonRI-beta) is located. OBJECTIVE: To evaluate the association between FcepsilonRI-mediated histamine release from basophils and four bi-allelic single nucleotide polymorphisms of the FcepsilonRI-beta gene. METHODS: Phenotypes of asthma, such as maximal histamine release from basophils and atopy, were measured from 80 randomly recruited asthmatic children. Polymorphisms of the FcepsilonRI-beta gene were determined by PCR-based methods. RESULTS: The polymorphism in exon 7, resulting in Glu to Gly substitution, was significantly associated with histamine release from basophils to anti-IgE stimuli, but not with total IgE levels and skin test responses to aeroallergens. CONCLUSION: This study supports a role for the FcepsilonRI-beta gene in the expression of high affinity IgE receptor-mediated histamine release from basophils.

Adolescent↗

Russell-Silver syndrome: molecular diagnosis of maternal uniparental disomy of chromosome 7 using methylation-specific polymerase chain reaction assay and single nucleotide polymorphisms genotyping.

Russell-Silver syndrome (RSS) should be suspected in patients with prenatal and postnatal growth retardation. Because there is no clinical feature specific for RSS, molecular analysis is necessary to confirm the diagnosis. Recently, maternal uniparental disomy of chromosome 7 (mUPD7) has been reported in approximately 10% of RSS patients. We describe a 10-year-old Taiwanese RSS girl with prenatal and postnatal growth retardation, relative macrocephaly, a triangular face, frontal bossing, and mild fifth finger clinodactyly. Molecular diagnosis of mUPD7 was confirmed by use of methylation-specific polymerase chain reaction and haplotype analysis with single nucleotide polymorphisms (SNPs) genotyping. Analyzing the methylation status of the PEG1/MEST gene is a cost-effective screening method for mUPD7 molecular diagnosis. However, positive cases should be subsequently confirmed by haplotype analysis using SNPs genotyping or short tandem repeat markers.

Child↗

Association of single nucleotide polymorphisms of the insulin gene with chicken early growth and fat deposition.

Growth rate, body composition, and fat deposition are important traits in chickens. Insulin plays important roles in hepatic cells, muscle cells, and adipose tissue cells. The purpose of the present study was to analyze association of the insulin (INS) gene with chicken growth and body composition traits. Using a F2 design resource population constructed with the crossing of Chinese native Xinghua chickens and White Recessive Rock chickens, the association of 4 single nucleotide polymorphisms (SNP; A+428G, C+1549T, T+3737C, and A+3971G) of INS gene with 13 growth and body composition traits was studied. The T+3737C genotypes were significantly associated with small intestine length (P = 0.0002), and the A+3971G genotypes were significantly associated with early growth (hatch weight and BW at 28 d of age) (P < 0.0001), breast angle (P = 0.0002), and small intestine length (P < 0.0001). None of the 4 SNP was significantly associated with abdominal fat pad weight (P > 0.05). The haplotypes based on the 4 SNP were also significantly associated with early growth (hatch weight and BW at 28 d of age; P < 0.0001) and breast angle (P < 0.0001) but not with small intestine length (P = 0.0505). These results suggested that variation of the insulin gene was significantly associated with chicken early growth but not with fat deposition. In addition, the data from the present study supported the inference that both the one-SNP-at-a-time and the haplotype-based approaches have their own advantages and disadvantages when association analysis of one SNP and haplotypes with chicken complex traits was conducted.

Animals↗

Effects of single nucleotide polymorphisms in human N-acetyltransferase 2 on metabolic activation (O-acetylation) of heterocyclic amine carcinogens.

N-Acetyltransferase 2 (NAT2) catalyzes the O-acetylation of N-hydroxy heterocyclic amines such as N-hydroxy-2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (N--OH--MeIQx) and N-hydroxy-2-amino-1-methyl-6-phenylimidazo[4,5-b] pyridine (N--OH --PhIP) to DNA binding metabolites that initiate mutagenesis and carcinogenesis. NAT2 acetylator phenotype is associated with increased cancer risk. Single nucleotide polymorphisms (SNPs) have been identified in the NAT2 coding region. Although the effects of these SNPs on N-acetyltransferase activity have been reported, very little is known regarding their effects on O-acetylation activity. To investigate the functional consequences of SNPs in the NAT2 coding region on the O-acetylation of N-hydroxy heterocyclic amines, reference NAT2*4 and NAT2 variant alleles possessing one were cloned and expressed in yeast (Schizosaccaromyces pombe). T111C, C282T, C481T, C759T, and A803G (K268R) SNPs did not significantly (p > 0.05) modify O-acetylation catalysis with N--OH--PhIP or N--OH--MeIQx. C190T (R64W), G191A (R64Q), T341C (I114T), A434C (E145P), G590A (R197Q) and A845C (K282T) significantly (p < 0.01) reduced the O-acetylation of both N--OH--PhIP and N--OH--MeIQx, whereas G857A (G286E) significantly (p < 0.05) decreased catalytic activity towards the O-acetylation of N--OH--MeIQx but not N--OH--PhIP. These results have important implications towards the interpretation of molecular epidemiological studies of NAT2 genotype and cancer risk.

Acetylation↗

Lack of association between single nucleotide polymorphisms in the corticotropin releasing hormone receptor 1 (CRHR1) gene and alcohol dependence.

While the physiological mechanisms that contribute to the development of alcohol dependence remain unclear, a number of recent studies have indicated a role for the corticotropin releasing hormone receptor 1 (CRHR 1) in modulating the response of the central nervous system to ethanol. Based on these data, the present study aims to identify associations between variations in the CRHR 1 gene and alcohol dependence in a population of individuals of European ancestry. In order to identify such putative associations, five single nucleotide polymorphisms (SNPs) in the CRHR 1 gene were analyzed in 120 alcohol dependent and 180 control subjects. In comparing both allele and genotype frequencies at these five loci between alcohol dependent and control populations, no significant associations between variations in the CRHR 1 gene and alcohol dependence were detected. The results of this study suggest that polymorphisms in the CRHR 1 gene are not major risk factors for the development of alcohol dependence in persons of European ancestry.

Alcoholism↗

Single nucleotide polymorphisms in the gene encoding Krüppel-like factor 7 are associated with type 2 diabetes.

AIMS/HYPOTHESIS: Although genetic susceptibility plays an important role in the pathogenesis of type 2 diabetes, most of the genes that influence susceptibility to type 2 diabetes have yet to be identified. Krüppel-like transcription factors are known to play important roles in development and cell differentiation, and have recently been implicated in the pathogenesis of type 2 diabetes. The present study aimed to examine the associations of single nucleotide polymorphisms (SNPs) in genes encoding members of the Krüppel-like-factor (KLF) family with type 2 diabetes in a large cohort of Japanese subjects. METHODS: We genotyped 33 SNP loci found in 12 KLF genes in subjects with type 2 diabetes and in subjects from the general population using the PCR-Invader assay. We also examined the effects of the overexpression of KLF7 on adipogenesis in 3T3-L1 cells. RESULTS: We identified a significant association between an SNP in KLF7 and type 2 diabetes (A vs C: p=0.004 after Bonferroni's correction, odds ratio=1.59, 95% CI 1.27-2.00). The expression of Klf7 decreased in response to the differentiation of 3T3-L1 adipocytes, and the overexpression of KLF7 resulted in significant inhibition of adipogenesis in 3T3-L1 cells. CONCLUSIONS/INTERPRETATION: These results indicate that the gene encoding KLF7 is a novel candidate for conferring genetic susceptibility to type 2 diabetes.

3T3 Cells↗

Linkage and association studies of discoidin domain receptor 1 (DDR1) single nucleotide polymorphisms (SNPs) in juvenile oligoarthritis.

OBJECTIVES: Multiple independent juvenile oligoarthritis susceptibility loci have been identified within the major histocompatibility complex (MHC), including HLA-A, HLA-DRB1 and an as yet unlocalized effect in the centromeric class I region. The discoidin domain receptor 1 (DDR1) gene resides within this region and codes for a receptor tyrosine kinase that plays an important role in regulating cell attachment to collagen, chemotaxis, proliferation and matrix metalloproteinase (MMP) production. DDR1 expression in chondrocytes has not been investigated. The objectives of this study were to investigate expression of DDR1 in healthy chondrocytes and to identify linkage and association of this candidate gene with juvenile oligoarthritis. METHODS: A set of 135 simplex juvenile idiopathic arthritis families consisting of one affected child and healthy parent(s) and 199 healthy unrelated individuals were genotyped for six single nucleotide polymorphisms (SNPs) within the DDR1 gene using the primer extension SNaPshot trade mark method. Single-point and multipoint transmission disequilibrium tests were carried out with the ETDT and TDTPHASE packages. Allele frequency comparisons between cases and controls were carried out with the chi(2) test. DDR1 expression was investigated in normal articular cartilage by RT-PCR and immunofluorescence methods. RESULTS: No linkage and association with any of the six SNPs or their haplotypic combinations were observed in the families studied. No significant differences were observed in allele frequencies between patients and controls. DDR1 expression was found in normal articular cartilage by RT-PCR and by immunofluorescence. CONCLUSIONS: The DDR1 SNPs examined are not involved in susceptibility to juvenile oligoarthritis.

Arthritis, Juvenile↗

Single nucleotide polymorphisms of the resistin (RSTN) gene.

Type 2 diabetes mellitus is a complex phenotype that is frequently associated with central obesity and insulin resistance. Recently, a protein named resistin, encoded by RSTN (OMIM #605565), was identified in adipose tissue. Serum resistin was elevated in obese and diabetic mice, and administration of resistin to normal mice was found to interfere with glucose tolerance and insulin action. Because of these functions, resistin is a candidate gene for diabetes and obesity. Through the use of DNA sequencing, we thus developed amplification primers for rapid screening of the RSTN gene that encodes resistin. No putative mutations were found, but two noncoding single-nucleotide polymorphisms (SNPs) were identified, and these were found to vary in frequency across various ethnic groups. The identification of amplification primers and SNPs provides tools to investigate resistin for association with other phenotypes.

Base Sequence↗

Lack of association between a single nucleotide polymorphism within the choline acetyltransferase gene and patients with Alzheimer's disease.

Alterations of the cholinergic system may account for typical clinical and pathophysiological disturbances of Alzheimer's disease (AD). In particular, a marked decline of choline acetyltransferase activity (CHAT) and as a consequence of acetylcholine during the course of the disease has been described. Due to the chromosomal localization of CHAT at 10q11.23 and its possible role in the pathophysiology of AD, CHAT may represent an appropriate candidate gene conferring risk to AD. In fact, a recent study identified a functional single nucleotide polymorphism (SNP) within the first common exon of CHAT, which was associated with AD giving an odds ratio of 3.8 (Neurosci. Lett. 333 (2002) 9). Because of the potential importance of this finding we analyzed this SNP and another functional SNP within exon 9 (rs868749) of the CHAT gene using a German case control sample consisting of 242 patients with AD and 143 cognitively healthy controls. No statistically significant differences were obtained for the previously described polymorphism. In addition, the exon 9 SNP (rs868749) was not polymorphic in the studied population. We conclude that the previously identified polymorphism is not associated with AD.

Aged↗

Extended single nucleotide polymorphism and haplotype analysis of the elastin gene in Caucasians with intracranial aneurysms provides evidence for racially/ethnically based differences.

BACKGROUND: There is growing evidence that genetic variants have an impact on the pathogenesis of intracranial aneurysm (IA). Recently, the genetic locus around the elastin gene (7q11) has been identified as linked to IA in a Japanese population. Our aim was to confirm these results in Caucasian populations. METHODS: We conducted a case-control study in 120 Caucasian patients with IA and 172 controls to investigate 8 single nucleotide polymorphisms (SNPs) and various haplotypes within the elastin gene, which were frequently found and associated with the phenotype in the Japanese populations. Real-time PCR and melting curve analysis were used for the detection of genotypes. RESULTS: Allele frequencies and genotypes were equally distributed between Caucasian cases and controls. We failed to identify haplotypes that are associated with the phenotype in our population, which is in contrast to the Japanese study. However, allele frequencies in control populations differ between Caucasians and Japanese. CONCLUSIONS: We found no association between SNPs and haplotypes of the elastin gene and the occurrence of IA in our Caucasian populations. However, our data provide strong evidence for racial/ethnic differences in the association of SNP and specific haplotypes of the elastin gene with the phenotype. There might be other genetic variants of the elastin gene associated with IA in Caucasians.

Adult↗

ABCA1 single nucleotide polymorphisms on high-density lipoprotein-cholesterol and overweight: the D.E.S.I.R. study.

The adenosine triphosphate-binding cassette A1 (ABCA1) gene plays a key role in reverse cholesterol transport. Some ABCA1 gene polymorphisms have been associated with high-density lipoprotein-cholesterol (HDL-C) concentrations. The aim of this study was to assess the effect of three polymorphisms, C69T, G378C, and G1051A (R219K), on HDL-C levels and their interaction with BMI in more than 5000 French whites from the D.E.S.I.R. (Data from an Epidemiological Study on the Insulin Resistance syndrome) cohort study. The T allele of the C69T single nucleotide polymorphism (SNP) was associated with higher HDL-C levels in normal-weight men (BMI <25 kg/m(2)). The C allele of the G378C SNP was associated with lower HDL-C in overweight subjects (BMI > or =25 kg/m(2)). For the G1051A SNP, in the normal-weight group, the minor A allele was significantly associated with higher HDL-C levels. In contrast, in overweight people, the minor allele was associated with lower HDL-C levels. After accounting for multiple testing, empiric p values remained significant for the associations between G378C SNP and HDL-C in the overweight group and between G1051A SNP and HDL-C in the normal-weight group. This study suggests that ABCA1 gene polymorphisms modulate HDL-C concentrations, in interaction with BMI, and, thus, they might influence cardiovascular risk in the general population.

ATP Binding Cassette Transporter 1↗