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PubMed2004

Automated solid-phase extraction for purification of single nucleotide polymorphism genotyping products prior to matrix-assisted laser desorption/ionisation time-of-flight mass spectrometric analysis.

In this article, we describe the application of a novel micro elution solid-phase extraction method for purification of short stretches of DNA products of single nucleotide polymorphisms (SNPs) prior to MALDI mass spectrometry analysis. An important feature of our method is that the purification columns containing a copolymer of divinylbenzene and N-vinylpyrrolidone can be used several times thereby significantly reducing costs. We implemented this DNA purification technology into a fully automated procedure including molecular biology, MALDI sample preparation, automated mass spectrometric analysis and SNP allele calling by software. Due to the facile purification protocol, the methodology shown could furthermore be used for other applications where efficient medium to high-throughput purification of nucleic acids is required.

Alkaline Phosphatase↗

PubMed2004

[Single nucleotide polymorphism in SCN5A and the distribution in Chinese Han ethnic group].

Mutations in voltage-gated sodium channel type (SCN5A) may evoke severe, life-threatening disturbances in cardiac rhythm, including long QT syndrome, idiopathic ventricular fibrillation (Brugada Syndrome), and isolated cardiac conduction disease. There is increasing awareness of the role of common polymorphisms in altering gene function and in susceptibility to diseases. The aim of the present study was to investigate single nucleotide polymorphism (SNP) in SCN5A gene and the distribution of these identified SNPs in Chinese Han nationality. SCN5A gene was sequenced by fluorescent labeling automatic sequencing method in 120 unrelated samples from Han nationality in South China. Allele frequency distribution was tested by Hardy-Weinberg equilibrium. The results showed that a total of 5 SNPs were identified in SCN5A gene, including three SNPs in code region, one SNP in regulatory region and the other in intron 23 adjacent to donor splicing site. The distribution of the SNPs in SCN5A gene was uneven. These allele frequencies in Han population of South China were as follows: G87A (A29A) 27.5%, A1673G (H588R) 10.4%, 4245+82A>G 32.8%, C5457T (D1819D) 41.3% and G6174A 44.9% respectively. The SNPs G87A (A29A), 4245+82A>G and G6174A were reported for the first time. There was no significant difference in the allele frequency of A1673G (H558R) within different ethical populations (P>0.05). C5457T (D1819D) allele frequency of Han population in South China was similar to that observed in Japanese (P>0.5), but higher than that in American (p<0.005). There was no significant difference in the distribution of the SNPs between male group and female group (all p>0.05). S1102Y and other 10 SNPs identified in other ethnic populations have not been detected in Chinese Han population. The allele distribution of SNPs was in good unity with the Hardy-Weinberg equilibrium. It is suggested that the SNP distribution of SCN5A gene varies within different nationalities. These data will be of use for genetic association studies of acquired arrythmias and investigation of sensitivity to drug therapy.

Arrhythmias, Cardiac↗

PubMed2004

Novel single nucleotide polymorphisms of organic cation transporter 1 (SLC22A1) affecting transport functions.

Organic cation transporter OCT1 (SLC22A1) plays an essential role in absorption, distribution, and excretion of various xenobiotics including therapeutically important drugs. In the present study, we analyzed the functional properties of the single nucleotide polymorphisms (SNPs) in SLC22A1 gene found in Japanese control individuals. Four mutations resulting in the amino acid changes (F160L, P283L, R287G, and P341L) were functionally characterized in Xenopus oocyte expression system. Two new SNPs, identified in Japanese population, P283L and R287G exhibited no uptake of both [14C]TEA and [3H]MPP+, although their protein expressions were detected in the plasma membrane of the oocytes injected with their cRNAs. Uptake of [14C]TEA by P341L was reduced to 65.1% compared to wild type, whereas F160L showed no significant change in its transport activity. This study suggests that the newly found OCT1 variants will contribute to inter-individual variations leading to the differences in cationic drug disposition and perhaps certain disease processes.

Animals↗

PubMed2006

Association of the BTNL2 rs2076530 single nucleotide polymorphism with Graves' disease appears to be secondary to DRB1 exon 2 position beta74.

OBJECTIVE: The HLA region encodes numerous immune response genes, with the DR/DQ molecules consistently associated with autoimmune disease (AID). Recent studies in sarcoidosis have identified association of a single nucleotide polymorphism (SNP) rs2076530 within BTNL2, a potential T-cell inhibitor, independent of the known DRB1 association. The aim of this study was to investigate the association rs2076530 with disease in a large UK Caucasian Graves' disease (GD) dataset. DESIGN: A case control association study of the rs2076530 polymorphism. PATIENTS: Eight hundred sixty-four Graves' disease patients and 864 controls. MEASUREMENTS: Tests for association with disease. RESULTS: We detected association of rs2076530 within a large GD dataset [OR = 1.32 (95% CI = 1.14-1.52)], however, linkage disequilibrium (LD) analysis revealed association of rs2076530 to be secondary to the previously established DRB1 exon 2 encoded position beta74 effect although a rare haplotype effect, including both loci, cannot be excluded. CONCLUSIONS: BTNL2 may be a sarcoidosis-specific susceptibility loci, although only extensive examination of the whole HLA region in different inflammatory/AIDs will enable DR/DQ independent HLA effects to be determined.

Butyrophilins↗

PubMed2004

Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22.

We performed a linkage analysis on 25 extended multiplex Portuguese families segregating for bipolar disorder, by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay, the GeneChip Human Mapping 10K Array (HMA10K). Of these families, 12 were used for a direct comparison of the HMA10K with the traditional 10-cM microsatellite marker set and the more dense 4-cM marker set. This comparative analysis indicated the presence of significant linkage peaks in the SNP assay in chromosomal regions characterized by poor coverage and low information content on the microsatellite assays. The HMA10K provided consistently high information and enhanced coverage throughout these regions. Across the entire genome, the HMA10K had an average information content of 0.842 with 0.21-Mb intermarker spacing. In the 12-family set, the HMA10K-based analysis detected two chromosomal regions with genomewide significant linkage on chromosomes 6q22 and 11p11; both regions had failed to meet this strict threshold with the microsatellite assays. The full 25-family collection further strengthened the findings on chromosome 6q22, achieving genomewide significance with a maximum nonparametric linkage (NPL) score of 4.20 and a maximum LOD score of 3.56 at position 125.8 Mb. In addition to this highly significant finding, several other regions of suggestive linkage have also been identified in the 25-family data set, including two regions on chromosome 2 (57 Mb, NPL = 2.98; 145 Mb, NPL = 3.09), as well as regions on chromosomes 4 (91 Mb, NPL = 2.97), 16 (20 Mb, NPL = 2.89), and 20 (60 Mb, NPL = 2.99). We conclude that at least some of the linkage peaks we have identified may have been largely undetected in previous whole-genome scans for bipolar disorder because of insufficient coverage or information content, particularly on chromosomes 6q22 and 11p11.

Bipolar Disorder↗

PubMed2005

A single nucleotide polymorphism in the carboxylesterase gene is associated with the responsiveness to imidapril medication and the promoter activity.

Imidapril is an angiotensin-converting enzyme inhibitor that is widely used in treating hypertension, although the responses vary among individuals. We investigated whether a single nucleotide polymorphism at position -816 of the carboxylesterase 1 (CES1) gene, which activates imidapril in the liver, is involved in the responsiveness to imidapril medication. A total of 105 Japanese hypertensives with systolic/diastolic blood pressures (SBP/DBP) of 140/90 mmHg or higher were prescribed 5-10 mg/day of imidapril. At baseline, blood pressure levels were not different between patients with and those without the -816C allele (AA vs. AC+ CC groups). After 8 weeks of treatment, we classified the responders and non-responders based on the decline in their blood pressures, and found that the responder rate was significantly higher in the AC+CC group than in the AA group (p=0.0331). Also, the reduction in SBP was significantly greater in the AC+CC group than in the AA group (24.7+/-11.8 vs. 17.6+/-16.8 mmHg, p=0.0184). Furthermore, an in vitro reporter assay revealed that the -816C construct had significantly higher promoter activity (p<0.0001). These findings suggest that the A(-816)C polymorphism affects the transcriptional activity, and that this may account for the responsiveness to imidapril.

Adult↗

PubMed2001

Molecular modelling of disease-causing single-nucleotide polymorphisms in collagen.

The purpose of the work was to investigate at the molecular structural and energy levels the consequence of amino acid substitutions in collagen that cause systemic diseases. The data have been systematized on defects in human collagen III, and the patterns of single-nucleotide polymorphisms collected. Then molecular mechanics calculations were performed for native and mutant collagen molecule fragments. The observed energy components and structural alterations that accompany particular amino acid substitutions were used to propose an interpretation of negative consequences in terms of stability and hydration of the macromolecule.

Amino Acid Substitution↗

PubMed2001

Thirteen single-nucleotide polymorphisms in the human osteopontin gene identified by sequencing of the entire gene in Japanese individuals.

Osteopontin (OPN) is one of the major noncollagenous bone matrix proteins produced by osteoblasts and osteoclasts. We systematically surveyed the entire structure of the OPN gene for single-nucleotide polymorphisms (SNPs) by directly sequencing 48 alleles derived from 24 unrelated Japanese individuals. We identified 13 SNPs in the OPN gene. Ten polymorphisms were identified in introns 1, 3, and 5; 2 in the coding region of exons 6 and 7; and 1 in the 3' untranslated region of exon 7. Allele frequencies for some of the polymorphisms were significantly different from those reported in the United States National Center for Biotechnology Information (NCBI) dbSNP database. These polymorphisms will be useful in genetic studies to evaluate the role of OPN proteins in bone metabolism.

Asian People↗

PubMed2001

Allelic frequencies and patterns of single-nucleotide polymorphisms in candidate genes for asthma and atopy in Iceland.

Numerous asthma and atopy loci have been reported in studies demonstrating associations of the asthma-related phenotypes atopy, elevated IgE levels, and bronchial hyperresponsiveness with alleles of microsatellite markers and single-nucleotide polymorphisms (SNPs) within specific cytokine/chemokine and IgE-regulating genes. Although the studies reporting these observations are compelling, most of them lack statistical power. We assessed the nature, pattern, and frequency of SNPs in 24 candidate genes in Iceland and looked for associations with asthma and atopy. We identified 42 SNPs with an average minor allele frequency of 20.3% (asthma) and 20.7% (control). Twenty SNPs (48%) were within coding sequences and 90% of those led to a predicted change in protein sequence. No differences were detected in the allelic frequencies of SNPs in any of these candidate genes between control subjects and the patients with atopic asthma. Moreover, linkage analysis that included 269 patients with atopic asthma uncovered no evidence of linkage to markers associated with these genes. We conclude that this study has failed to produce evidence in support of the notion that variations within these 24 candidate atopy and asthma genes significantly influence the expression of the atopic asthmatic phenotype or contribute to the susceptibility of atopic asthma.

Adolescent↗

PubMed2002

Catalog of 86 single-nucleotide polymorphisms (SNPs) in three uridine diphosphate glycosyltransferase genes: UGT2A1, UGT2B15, and UGT8.

We report here three high-density maps of variations found among 48 Japanese individuals in three uridine diphosphate glycosyltransferase (UGT) genes, UGT2A1, UGT2B15, and UGT8. A total of 86 single-nucleotide polymorphisms (SNPs) were identified through systematic screening of genomic regions containing these genes: 8 in 5' flanking regions, 7 in coding regions, 67 in introns, 3 in 3' untranslated regions, and 1 in a 3' flanking region. We also discovered 14 variations of other types. Of the 86 SNPs, 63 (73%) were considered to be novel on the basis of comparison of our data with the Database of SNPs (dbSNP) of the National Center for Biotechnology Information. Among the seven SNPs identified in exonic sequences, five were non-synonymous changes that would result in amino-acid substitutions. The collection of SNPs derived from this study will serve as an additional resource for studies of complex genetic diseases and responsiveness to drug therapy.

Chromosome Mapping↗

PubMed2002

Single nucleotide polymorphism (G994-->T) in the plasma platelet-activating factor-acetylhydrolase gene is associated with graft patency of femoropopliteal bypass.

BACKGROUND: Plasma platelet-activating factor-acetylhydrolase (PAF-AH) is known to catalyze platelet-activating factor (PAF). The single nucleotide polymorphism (SNP) of plasma PAF-AH gene (G994 -->T in exon 9) is associated with a decreased level of plasma PAF-AH activity. This study analyzed the risk of the SNP on graft occlusion of femoropopliteal bypass in patients with atherosclerotic occlusive disease. METHODS: We retrospectively assessed the patency of 50 above-knee femoropopliteal bypass grafting in 50 patients. Genomic DNA was analyzed for the mutant allele. Plasma PAF-AH activity was measured by radioimmunoassay. RESULTS: The 10-year cumulative primary patency of the bypass was 78.5% in GG (normal genotype) and 50.0% in GT (heterozygous) or TT (homozygous deficient) (P <.05, Kaplan-Meier method). The relative risk of graft failure in GT or TT genotypes was 1.68 (P =.08, Cox proportional hazards model). PAF-AH activity (nmol/min/50 microL) was 1.92 +/- 0.82 in patients with patent grafts and 1.42 +/- 0.47 in those with occluded grafts (mean +/- standard deviation; P <.05, unpaired t test). CONCLUSIONS: The SNP of plasma PAF-AH was associated with a decreased primary graft patency of above-knee femoropopliteal bypass. The risk of graft failure may increase when patients have the SNP. To confirm the independent risk of graft failure by the SNP, further study is necessary and prospective study should be performed.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed2006

A functional single nucleotide polymorphism in the vitamin-K-dependent gamma-glutamyl carboxylase gene (Arg325Gln) is associated with bone mineral density in elderly Japanese women.

The vitamin-K-dependent gamma-glutamyl carboxylase (GGCX) carboxylates vitamin-K-dependent proteins including bone Gla protein (osteocalcin) and matrix Gla protein, which play important roles in bone metabolism. Therefore, GGCX polymorphism might explain in part individual susceptibility to osteoporosis. In the present study, polymorphisms in the exons of this gene were screened in Japanese elderly women and a non-synonymous single nucleotide polymorphisms (SNP) were found; c.8762 G>A; (Arg325Gln). When the kinetic parameters of GGCX325-Gln and GGCX325-Arg were compared in vitro, Vmax/Km was significantly higher for GGCX325-Gln (944.4+/-9.21 pmol/30 min/mg/mM FLEEL) than for GGCX325-Arg (671.9+10.79 pmol/30 min/mg/mM FLEEL) (p=0.018). Then, association study of this polymorphism with forearm bone mineral density (BMD) of Japanese postmenopausal women (n=500, age 73.6+/-5.74) was conducted. As a result, the body mass index (BMI)-adjusted Z score in the subpopulation older than 75 years (n=207) was higher in those with 325-Gln (0.650+/-0.883, mean+/-SD) than those with 325-Arg/Gln or 325-Arg (0.133+/-0.650) (p=0.0383). This is the first report to demonstrate the different activities of GGCX between the common genotypes and their association with BMD.

Aged↗

PubMed2006

SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms.

Inherited genetic variation plays a critical but largely uncharacterized role in human differentiation. The completion of the International HapMap Project makes it possible to identify loci that may cause human differentiation. We have devised an approach to find such ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database. We selected ESNPs using the nearest shrunken centroid method (NSCM), and performed multiple tests for genetic heterogeneity and frequency spectrum on genes having ESNPs. The function and disease association of the selected SNPs were also annotated. This resulted in the identification of 100 736 SNPs that appeared uniquely in each ethnic group. Of these SNPs, 1009 were within disease-associated genes, and 85 were predicted as damaging using the Sorting Intolerant From Tolerant system. This study resulted in the creation of the SNP@Ethnos database, which is designed to make this type of detailed genetic variation approach available to a wider range of researchers. SNP@Ethnos is a public database of ESNPs with annotation information that currently contains 100 736 ESNPs from 10 138 genes, and can be accessed at http://variome.net and http://bioportal.net/ or directly at http://bioportal.kobic.re.kr/SNPatETHNIC/.

Chromosome Mapping↗

PubMed2005

IL-10 promoter single nucleotide polymorphisms are significantly associated with resistance to leprosy.

The minor haplotype -3575A/-2849G/-2763C in IL-10 promoter has been defined as a marker of disease resistance to leprosy and its severity in Brazilian population. Our investigation of six single-nucleotide polymorphisms (SNPs) in IL-10 promoter in 282 Indian leprosy patients and 266 healthy controls by direct PCR sequencing, however, showed that the extended haplotype: -3575T/-2849G/-2763C/-1082A/-819C/-592C was associated with resistance to leprosy per se and to the development of severe form of leprosy, using either a binomial (controls vs cases, P=0.01, OR=0.58, CI=0.37-0.89) or ordinal (controls vs paucibacillary vs multibacillary, P=0.004) model. Whereas, IL-10 haplotype -3575T/-2849G/-2763C/-1082A/-819T/-592A was associated with the risk of development of severe form of leprosy (P=0.0002) in contrast to the minor risk haplotype -3575T/-2849A/-2763C in the Brazilian population. The role of IL-10 promoter SNPs in Brazilian and Indian population strongly suggests the involvement of IL-10 locus in the outcome of leprosy.

Brazil↗

PubMed2004

Functional characterization of human organic cation transporter OCTN1 single nucleotide polymorphisms in the Japanese population.

The organic cation transporter OCTN1 (SLC22A4) is expressed ubiquitously, with strong expression in kidney, trachea, bone marrow, and fetal liver, and it mediates transport of organic cations in a pH-dependent manner. Recent studies have identified single nucleotide polymorphisms (SNPs) of OCTN1 in the Japanese population. Two SNPs present in the exon regions, c1063t and g1531a, cause amino acid mutation, Thr306Ile (T306I) and Gly462Glu (G462E), respectively. We examined the influence of these SNPs on the intracellular localization, protein expression, and transport activity of OCTN1. Immunocytochemical analysis showed similar localizations of OCTN1 in cellular membranes of HEK293 cells transiently transfected with an expression plasmid DNA for OCTN1 or its SNP allelic variants. The Km and Vmax values for tetraethylammonium (TEA) uptake by T306I were similar to those of the wild-type even when the Vmax value was normalized for the expression level of OCTN1 protein. In contrast, G462E had almost negligible transport activity, although the protein expression level of G462E was equivalent to that of the wild-type. We conclude that the SNP that causes the single amino acid mutation T306I does not affect TEA transport activity, whereas the mutation G462E abrogates the TEA transport activity, presumably affecting the physiological function of OCTN1 and/or the pharmacological characteristics of its substrates.

Asian People↗

PubMed2006

Molecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays.

Genomic amplification of oncogenes and inactivation of suppressor genes are critical in the pathogenesis of human cancer. To identify chromosomal alterations associated with hepatocarcinogenesis, we performed allelic gene dosage analysis on 36 hepatocellular carcinomas (HCCs). Data from high-density single-nucleotide polymorphism arrays were analysed using the Genome Imbalance Map (GIM) algorithm, which simultaneously detects DNA copy number alterations and loss of heterozygosity (LOH) events. Genome Imbalance Map analysis identified allelic imbalance regions, including uniparental disomy, and predicted the coexistence of a heterozygous population of cancer cells. We observed that gains of 1q, 5p, 5q, 6p, 7q, 8q, 17q and 20q, and LOH of 1p, 4q, 6q, 8p, 10q, 13q, 16p, 16q and 17p were significantly associated with HCC. On 6q24-25, which contains imprinting gene clusters, we observed reduced levels of PLAGL1 expression owing to loss of the unmethylated allele. Finally, we integrated the copy number data with gene expression intensity, and found that genome dosage is correlated with alteration in gene expression. These observations indicated that high-resolution GIM analysis can accurately determine the localizations of genomic regions with allelic imbalance, and when integrated with epigenetic information, a mechanistic basis for inactivation of a tumor suppressor gene in HCC was elucidated.

Algorithms↗

PubMed2003

Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device.

A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.

Alleles↗

PubMed2006

Racial or ethnic differences in allele frequencies of single-nucleotide polymorphisms in the methylenetetrahydrofolate reductase gene and their influence on response to methotrexate in rheumatoid arthritis.

BACKGROUND: The anti-folate drug methotrexate (MTX) is commonly used to treat rheumatoid arthritis. OBJECTIVE: To determine the allele frequencies of five common coding single-nucleotide polymorphisms (SNPs) in the methylenetetrahydrofolate reductase (MTHFR) gene in African-Americans and Caucasians with rheumatoid arthritis and controls to assess whether there are differences in allele frequencies among these ethnic or racial groups and whether these SNPs differentially affect the efficacy or toxicity of MTX. METHODS: Allele frequencies in the 677, 1298 and 3 additional SNPs in the MTHFR coding region in 223 (193 Caucasians and 30 African-Americans) patients with rheumatoid arthritis who previously participated in one of two prospective clinical trials were characterised, and genotypes were correlated with the efficacy and toxicity of MTX. Another 308 subjects with rheumatoid arthritis who participated in observational studies, one group predominantly Caucasian and the other African-American, as well as 103 normal controls (53 African-Americans and 50 Caucasians) were used to characterise allele frequencies of these SNPs and their associated haplotypes. RESULTS: Significantly different allele frequencies were seen in three of the five SNPs and haplotype frequencies between Caucasians and African-Americans. Allele frequencies were similar between patients with rheumatoid arthritis and controls of the same racial or ethnic group. Frequencies of the rs4846051C, 677T and 1298C alleles were 0.33, 0.11 and 0.13, respectively, among African-Americans with rheumatoid arthritis. Among Caucasians with rheumatoid arthritis, these allele frequencies were 0.08 (p<0.001 compared with African-Americans with rheumatoid arthritis), 0.30 (p = 0.002) and 0.34 (p<0.001), respectively. There was no association between SNP alleles or haplotypes and response to MTX as measured by the mean change in the 28-joint Disease Activity Score from baseline values. In Caucasians, the 1298 A (major) allele was associated with a significant increase in MTX-related adverse events characteristic of a recessive genetic effect (odds ratio 15.86, 95% confidence interval 1.51 to 167.01; p = 0.021), confirming previous reports. There was an association between scores of MTX toxicity and the rs4846051 C allele, and haplotypes containing this allele, in African-Americans, but not in Caucasians. CONCLUSIONS: : These results, although preliminary, highlight racial or ethnic differences in frequencies of common MTHFR SNPs. The MTHFR 1298 A and the rs4846051 C alleles were associated with MTX-related adverse events in Caucasians and African-Americans, respectively, but these findings should be replicated in larger studies. The rs4846051 SNP, which is far more common in African-Americans than in Caucasians, can also be proved to be a useful ancestry informative marker in future studies on genetic admixture.

Black or African American↗