Typing of multiple single nucleotide polymorphisms in cytokine and receptor genes using sNaPshot

Turner, David M.; Choudhury, Farhana Murtaza; Reynard, Mark; Railton, Dawn; Navarrete, Cristina

doi:10.1016/s0198-8859(02)00392-0

Cited by 41 publications

(26 citation statements)

References 13 publications

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“…The fluorescently labeled extension primers can then be visualized by electrophoresis on an capillary PRISM 310 automated sequencer (Applied Biosystems). Turner et al (Turner et al, 2002) provides a good overview about this method. Detailed information on PCR primers and extension primer sequences as well as reaction PCR conditions can be obtained on request.…”

Section: Genotypingmentioning

confidence: 99%

SNP- and Haplotype Analysis of the Tryptophan Hydroxylase 2 Gene in Alcohol-Dependent Patients and Alcohol-Related Suicide

Zill

Preuss

Koller

et al. 2007

Neuropsychopharmacol

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Several lines of evidence indicate that disturbances of the central serotonergic system are involved in the pathophysiology of alcohol dependence and suicidal behavior. Recent studies have indicated that a newly identified second isoform of the tryptophan hydroxylase gene (TPH2) is preferentially involved in the rate limiting synthesis of neuronal serotonin. Genetic variations in the TPH2 gene have been associated with an increased risk for major depression and suicidal behavior. We performed single SNP (single nucleotide polymorphism), linkage disequilibrium and haplotype studies on 353 alcohol-dependent patients of whom 102 individuals had a history of at least one suicide attempt and 305 healthy controls with 20 SNPs covering the entire gene region of TPH2. Neither single SNP-, nor haplotype analysis could detect significant associations with alcohol dependence and/or suicidal behavior among alcohol-dependent patients. One major haplotype block of strong linkage disequilibrium between introns 5 and 8 of the TPH2 gene has been found in alcoholics and controls, which is in concordance with recent reports. In conclusion, our results suggest that single SNPs, respectively, haplotypes of the TPH2 gene are unlikely to play a major role in the pathophysiology of alcohol dependence or the alcoholism-related phenotype suicidal behavior. Further analysis are needed to confirm these results.

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Section: Genotypingmentioning

confidence: 99%

SNP- and Haplotype Analysis of the Tryptophan Hydroxylase 2 Gene in Alcohol-Dependent Patients and Alcohol-Related Suicide

Zill

Preuss

Koller

et al. 2007

Neuropsychopharmacol

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“…The primers were extended by adding a single fluorescently labeled ddNTP to its 3Ј-end. [22][23][24][25] Fluorescent dyes attached to each ddNTP are as follows: dR6G (green) for A, dTAMRA (yellow, which appears black on the electropherogram) for C, dR110 (blue) for G, and dROX (red) for T. The reactions were cycled with the following conditions: 25 cycles at 96°C for 10 seconds, 50°C for 5 seconds, and 60°C for 30 seconds. Samples were treated with one unit of shrimp alkaline phosphatase at 37°C for 45 minutes, followed by heat inactivation of enzyme at 80°C for 15 minutes.…”

Section: Allele-specific Oligodeoxyribonucleotide Single Nucleotide Ementioning

confidence: 99%

Simultaneous Amplification, Detection, and Analysis of Common Mutations in the Galactose-1-Phosphate Uridyl Transferase Gene

Jama

Nelson²,

Mao

et al. 2007

The Journal of Molecular Diagnostics

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Classic galactosemia is an autosomal recessive inherited error of galactose metabolism. It is caused by lack of galactose-1-phosphate uridyl transferase, an enzyme that is required to metabolize galactose-1-phosphate to uridine diphosphate galactose. The build up of galactose-1-phosphate is toxic at high levels and can damage the liver, brain, eyes, and other vital organs. Over 200 mutations have been identified in affected individuals. We describe an assay to identify nine target mutations or variants in the galactose-1-phosphate uridyl transferase gene, namely p.Q188R, p.S135L, p.K285N, p.L195P, p.T138M, p.Y209C, IVS2-2 A>G, p.L218L, and p.N314D. A single long-range PCR is followed by a multiplexed nucleotide extension assay (single nucleotide extension) and capillary electrophoresis to detect simultaneously all nine target mutations/variants. Fiftyfour previously characterized samples (47 clinical samples and seven controls) gave a 100% concordance. We also report a nontarget novel mutation, p.L192X, and its profile using single nucleotide extension. This assay can complement the enzyme activity assay and identify familial mutations for testing additional family members. (J Mol Diagn 2007, 9:618 -623;

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“…The fi rst group included individuals characterized by relatively low secretion of TNF-· , IFN-Á , RANTES, IL-10, and other cytokines related to a Th2 type of immune response . Obviously, it is only speculative and premature at this point to suggest that different individuals may respond differently to IL-2 stimulation in relation to polymorphism of their IL-2 receptor [Khani-Hanjani et al, 2001] or polymorphism(s) of the promoter region of different cytokines [Keen, 2002a[Keen, , 2002bTurner et al, 2002]. Considering, however, the extreme variability in the response of individual patients to systemic IL-2 administration in terms of toxicity and therapeutic response, it is tempting to postulate that, perhaps, such differences, if confi rmed, may be on the basis of such disparity.…”

Section: A Proteomics Approach Using Protein-based Platformsmentioning

confidence: 99%

“…As these cytokines have disparate and possibly opposite effects, it is possible that toxicity and anti-tumor effects are independently related to the sum of the effect of the various cytokines secreted by various individuals in the context of an eclectic tumor microenvironment [Marincola et al, 2003]. Considering the polymorphism of the IL-2 receptor [Khani-Hanjani et al, 2001] and of the down-stream regulatory regions of various cytokines [Turner et al, 2002], it is possible that individual differences are genetically predetermined.…”

Section: A Proteomics Approach Using Protein-based Platformsmentioning

confidence: 99%

A Genomic- and Proteomic-Based Hypothesis on the Eclectic Effects of Systemic Interleukin-2 Administration in the Context of Melanoma-Specific Immunization

Panelli

Martin

Nagorsen

et al. 2004

Cells Tissues Organs

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Among human cancers, melanoma is characterized by an almost unique predisposition to regress in response to immune therapy. Recent clinical studies suggest that the frequency of this favorable event is enhanced by combining T-cell-directed active specific immunization with the systemic administration of interleukin (IL)-2. While waiting for additional clinical experience to confirm this observation, we embraced the working hypothesis that this combination provides superior response rates than either treatment alone. In particular, we have focused our interest on the paradoxical observation that active specific immunization consistently induces circulating CD8+ T cells capable of recognizing in ex vivo assays tumor cells, but cannot induce tumor regression alone. In these settings, it appears that combining the systemic administration of IL-2 is almost an absolute requirement for the induction of clinical responses. Here, we will expand on previous speculations on the postulated mechanism(s) of action of systemic IL-2 administration and, based on original data recently derived through high-throughput transcriptional and post-translational analysis, we will suggest an explanation for the eclectic effects of IL-2 administration in the context of active specific immunization.

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Typing of multiple single nucleotide polymorphisms in cytokine and receptor genes using sNaPshot

Cited by 41 publications

References 13 publications

SNP- and Haplotype Analysis of the Tryptophan Hydroxylase 2 Gene in Alcohol-Dependent Patients and Alcohol-Related Suicide

SNP- and Haplotype Analysis of the Tryptophan Hydroxylase 2 Gene in Alcohol-Dependent Patients and Alcohol-Related Suicide

Simultaneous Amplification, Detection, and Analysis of Common Mutations in the Galactose-1-Phosphate Uridyl Transferase Gene

A Genomic- and Proteomic-Based Hypothesis on the Eclectic Effects of Systemic Interleukin-2 Administration in the Context of Melanoma-Specific Immunization

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