Multiplex single base extension method for simultaneous genotyping of non‐synonymous SNP in the three human SOD genes

Iida, Reiko; Tsubota, Etsuko; Takeshita, Hitoshi; Yasuda, Toshihiro

doi:10.1002/elps.200800332

Cited by 32 publications

(11 citation statements)

References 36 publications

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“…[3] For SNP genotyping, single-base-extended primers and unextended primers labeled with fluorescent dyes [4] are separated by using high-performance liquid chromatography [5] or capillary electrophoresis. [6] Alternatively, the extension products are directly subjected to SNP genotyping with mass spectrometry [7] or microarray technology. [8] Such enzymatic reaction-based SNP genotyping is quite accurate, especially with recombinant DNA polymerases that exhibit elevated fidelity.…”

Section: Introductionmentioning

confidence: 99%

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

Akiyama

Shikagawa

Kanayama

et al. 2014

Chemistry A European J

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A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

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Section: Introductionmentioning

confidence: 99%

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

Akiyama

Shikagawa

Kanayama

et al. 2014

Chemistry A European J

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“…The details of multiplex single base extension procedure were described in a previous study [13]. In brief, primers for single base extension were designed to have a melting temperature of 55–60°C and a length of 30–67 bp, to terminate on base 5′ of the SNP and avoid dimer formation between primers.…”

Section: Methodsmentioning

confidence: 99%

“…Five templates containing the five substituted sites of interest were amplified from genomic DNA using a 2X PCR Master Mix (Fermentas Inc., Hanover, Md., USA) by multiple PCR procedures [13]. The primers used in the PCR are summarized in table 1.…”

Section: Methodsmentioning

confidence: 99%

Association of RS2200733 but Not RS10033464 on 4q25 with Atrial Fibrillation Based on the Recessive Model in a Taiwanese Population

Lee¹,

Yeh

Tung

et al. 2010

Cardiology

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Objectives: To determine the association between genetic variants on chromosome 4q25 and atrial fibrillation (AF) in a Taiwanese population. Methods: We enrolled 200 patients with AF (mean age: 67 ± 13 years) and 158 controls (mean age: 63 ± 10 years). The genotypes of five SNPs, RS2634073, RS2200733, RS13143308, RS2220427 and RS10033464, were determined using multiplex single base extension methods. Results: The distribution of the RS2200733 and RS10033464 genotypes did not significantly deviate from the Hardy-Weinberg equilibrium in the control group. The distribution of the RS2200733 genotypes differed significantly between the AF group and the controls (p = 0.03), whereas the distribution of the RS10033464 genotypes did not (p = 0.49). At RS2200733, patients with the CC genotype exhibited a 0.45 times higher risk of developing AF than those with the TT genotype (p = 0.02) and a recessive model was suggested (p = 0.01). After adjusting for various covariates, patients with the CC genotype remained recessively associated with a lower risk of developing AF than those with the TT genotype (odds ratio: 0.27, 95% confidence interval: 0.11–0.65; p < 0.01). Conclusions: In the Taiwanese, there is an association between SNP RS2200733 – but not RS10033464 – and the development of AF. Based on a recessive model of inheritance, individuals with SNP RS2200733 genotype CC are at a lesser risk of developing AF.

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“…The Ala/Ala homozygote carriers were found to have decreased SOD activity levels when compared with the Thr allele carriers. However, no difference between this polymorphism and SOD activity was found in a Japanese population (28). This difference may be caused by the different study populations.…”

Section: Discussionmentioning

confidence: 83%

SOD3 and eNOS genotypes are associated with SOD activity and NOx

Dong

Liu

et al. 2014

Experimental and Therapeutic Medicine

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Oxidative stress, characterized by increased reactive oxygen species production and/or decreased antioxidant enzyme activity, plays an important role in the pathogenesis of hypertension. The identification of molecular markers corresponding to the oxidative stress status of hypertension may assist in the antioxidant therapy of hypertension. In the present study, superoxide dismutase (SOD) and endothelial nitric oxide synthase (eNOS) were analyzed as markers of hypertension responding to oxidative stress. The plasma SOD activity and mononitrogen oxides (NOx) concentration were measured, and the SOD3 Ala58Thr and eNOS Glu298Asp polymorphisms were genotyped in hypertensive patients and normotensive controls. Further association experiments were replicated in an extended population, including 343 hypertensive patients and 290 controls. The results demonstrated that no statistically significant differences in the total SOD activity and NOx concentration were identified between the hypertensive patients and controls. However, the plasma SOD activity levels in the SOD3 Ala/Ala homozygote carriers (80.51±27.68 U/ml) were significantly lower compared with the Thr allele carriers (92.18±16.37 U/ml; P=0.031). In addition, the plasma NOx concentration in the eNOS Glu/Glu homozygote carriers (129.66±59.15 μmol/l) was significantly lower compared with the Asp allele carriers (169.84± 55.18 μmol/l; P=0.010). Notably, the altered SOD activity levels and NOx concentration were in concordance in 56.3% of the 80 participants. Therefore, the concordance of decreased SOD activity and NOx concentration, combined with genotypes of SOD3 Ala/Ala and/or eNOS Glu/Glu in hypertensive patients, may be useful in directing the antioxidant therapy of hypertension.

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Multiplex single base extension method for simultaneous genotyping of non‐synonymous SNP in the three human SOD genes

Cited by 32 publications

References 36 publications

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

Association of RS2200733 but Not RS10033464 on 4q25 with Atrial Fibrillation Based on the Recessive Model in a Taiwanese Population

SOD3 and eNOS genotypes are associated with SOD activity and NOx

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