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TaqMan Allelic Discrimination (taqman + allelic_discrimination)
Selected AbstractsNovel PlexorÔ SNP genotyping technology: comparisons with TaqMan® and homogenous MassEXTENDÔ MALDI-TOF mass spectrometry,HUMAN MUTATION, Issue 9 2007E.A. Tindall Abstract Analysis of SNPs for association, linkage, haplotype, and pharmacogenetic studies has led to a dramatic increase in the number and evolution of medium- to high-throughput genotyping technologies. This study introduces PlexorÔ as a new method for medium-throughput (single SNP) genotyping. We compare this fluorescent-based chemistry for call rate, accuracy, affordability, throughput, and overall efficiency against two commonly used technologies. These include fluorescent-based TaqMan® allelic discrimination for single SNP analysis (medium-throughput) and the homogenous MassEXTENDÔ (hMEÔ) chemistry using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for multiple SNP analysis (high-throughput). Analysis of 11 SNPs, including all six possible nucleotide substitutions, showed PlexorÔ to be highly comparable for both call rate (94.7%) and accuracy (99.2%) to the TaqMan® (94.6% and 99.8%, respectively) and hMEÔ (91.9% and 98.1%, respectively) chemistries. We demonstrate that this novel method is an efficient, cost-effective alternative to TaqMan® genotyping commonly used in diagnostic settings. Hum Mutat 28(9), 922,927, 2007. © 2007 Wiley-Liss, Inc. [source] Replication of the tumor necrosis factor receptor,associated factor 1/complement component 5 region as a susceptibility locus for rheumatoid arthritis in a European family-based studyARTHRITIS & RHEUMATISM, Issue 9 2008F. A. S. Kurreeman Objective We recently showed, using a candidate gene approach in a case,control association study, that a 65-kb block encompassing tumor necrosis factor receptor,associated factor 1 (TRAF1) and C5 is strongly associated with rheumatoid arthritis (RA). Compared with case,control association studies, family-based studies have the added advantage of controlling potential differences in population structure and are not likely to be hampered by variation in population allele frequencies, as is seen for many genetic polymorphisms, including the TRAF1/C5 locus. The aim of this study was to confirm this association in populations of European origin by using a family-based approach. Methods A total of 1,356 western European white individuals from 452 "trio" families were genotyped for the rs10818488 polymorphism, using the TaqMan allelic discrimination assay. Results We observed evidence for association, demonstrating departure from Mendel's law, with an overtransmission of the rs10818488 A allele (A = 55%; P = 0.036). By taking into consideration parental phenotypes, we also observed an increased A allele frequency in affected versus unaffected parents (A = 64%; combined P = 0.015). Individuals carrying the A allele had a 1.2-fold increased risk of developing RA (allelic odds ratio 1.24, 95% confidence interval 1.04,1.50). Conclusion Using a family-based study that is robust against population stratification, we provide evidence for the association of the TRAF1/C5 rs10818488 A allele and RA in populations of European descent, further substantiating our previous findings. Future functional studies should yield insight into the biologic relevance of this locus to the pathways involved in RA. [source] Gefitinib,phenytoin interaction is not correlated with the 14C-erythromycin breath test in healthy male volunteersBRITISH JOURNAL OF CLINICAL PHARMACOLOGY, Issue 2 2009Stephanie Chhun WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT , The response to gefitinib is variable and could be explained partly by the interindividual variability in gefitinib exposure. , Gefitinib is mainly metabolized by CYP3A4 and CYP2D6, and is to a lesser extent a P-glycoprotein (P-gp) substrate. , Patients with cancer are at high risk of drug,drug interactions, such as with phenytoin, a potent CYP3A4 inducer. WHAT THIS STUDY ADDS , The reduced systemic exposure of gefitinib with multiple-dose phenytoin treatment. , An effect attributed to the possible induction of intestinal CYP3A4 because of the lack of correlation between changes in gefitinib disposition and the erythromycin breath test and the lack of association between allelic variant in the ABCB1 gene and baseline and induced oral gefitinib clearance. , The CYP2D6 extensive metabolizer seems to be less sensitive to the interaction with phenytoin, as the magnitude of induction of gefitinib clearance was greater in CYP2D6 poor metabolizers than in CYP2D6 extensive metabolizers. AIMS We aimed to describe the pharmacokinetic interaction between phenytoin, a potent CYP3A4 and P-glycoprotein (P-gp) (ABCB1) inducer, and gefitinib, a CYP3A4, CYP2D6 and P-gp substrate. METHODS An open-label, randomized, two-phase crossover study was conducted. Eighteen healthy male volunteers (nine homozygous CC and nine homozygous TT as determined by their ABCB1 C3435T polymorphism in exon 26) received a single oral dose of 250 mg gefitinib alone or after 5 days treatment with phenytoin (5 mg kg,1 daily). Gefitinib plasma concentrations were determined by high-performance liquid chromatography. Hepatic CYP3A4 activity was evaluated by the 14C-erythromycin breath test (ERMBT) and the ABCB1 and CYP2D6 genetic polymorphisms were determined by the TaqMan allelic discrimination assay and long polymerase chain reaction, respectively. RESULTS Following treatment with phenytoin, mean gefitinib Cmax and AUC0,, decreased by 26 ± 44% [95% confidence interval (CI) for the difference 5,48%, P= 0.005] and 47 ± 26% (95% CI for the difference 34,60%, P= 0.001), respectively, and apparent oral clearance increased by 126 ± 93% (95% CI for the difference 80,172%, P= 0.004). Concomitantly, phenytoin increased the mean ERMBT by 91 ± 44% (95% CI 75,105%, P < 0.001) from baseline, but the extent of liver CYP3A4 induction was not correlated to the extent of interaction. Furthermore, this interaction was independent of ABCB1 genetic polymorphism. The CYP2D6 genotype was slightly but significantly related to gefitinib clearance (P= 0.04) during the control phase. CONCLUSIONS The significant interaction between gefitinib and phenytoin was not correlated with the erythromycin breath test and was independent of ABCB1 polymorphism, but may involve presystemic CYP3A-mediated intestinal first-pass. [source] Sex-specific association between leptin receptor polymorphisms and leptin levels and BMI in healthy adolescents,ACTA PAEDIATRICA, Issue 10 2010P Riestra Abstract Aim:, To examine the relationship of three common polymorphisms in the leptin receptor (LEPR) gene, implicated in the regulation of body weight, with leptin levels and obesity-related phenotypes in a population-based sample of healthy pubertal children in Spain. Methods:, The study included 806 boys and girls aged 12,16 whose anthropometrical data and body composition were recorded. Serum leptin levels were determined by ELISA. The LEPR Q223R, K109R and K656N polymorphisms were determined by TaqMan® allelic discrimination assays. Results:, When analysing the Q223R polymorphism, we observed that female carriers of the RR genotype had significantly higher plasma leptin levels (18.2 vs. 15.1 ng/mL p = 0.016) and significantly higher mean BMI values (22.5 vs. 21.3 Kg/m2 p = 0.032) than QR carriers. Furthermore, the frequency of the RR genotype in overweight-obese girls was significantly higher than that found in normal-weight girls. No significant differences were observed in boys. Neither boys nor girls showed significant differences when comparing leptin levels, anthropometric variables or body composition by K109R or K656N genotype. Conclusion:, The fact, that the Q223R polymorphism in the LEPR gene is significantly associated with leptin levels and BMI only in girls, suggests a sex-specific influence of this polymorphism on these variables. [source] | ||||||||||