Assessment of two flexible and compatible SNP genotyping platforms: TaqMan® SNP Genotyping Assays and the SNPlex™ Genotyping System

Vega, Francisco; Lazaruk, Katherine; Rhodes, Michael D.; Wenz, Michael

doi:10.1016/j.mrfmmm.2005.01.008

Cited by 212 publications

(48 citation statements)

References 42 publications

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“…TaqMan Genotyping Assay Reagent kits for allelic discrimination (Applied Biosystems, Foster City, CA, USA) were used to genotype all candidate variants, following the manufacturer’s instructions. A full description of this method can be found elsewhere [16, 17]. High platelet reactivity was defined as P2Y12 reaction unit (PRU) values ≤230.…”

Section: Methodsmentioning

confidence: 99%

Effect of cilostazol on platelet reactivity among patients with peripheral artery disease on clopidogrel therapy

Hernández-Suárez

Nuñez-Medina

Scott

et al. 2018

Drug Metabolism and Personalized Therapy

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Background Antiplatelet therapy with clopidogrel is recommended to reduce cardiovascular events in patients with peripheral artery disease (PAD); however, clopidogrel efficacy has not been adequately studied in this patient population. Therefore, we aimed to determine the effects of cilostazol therapy on platelet reactivity among PAD patients on clopidogrel. Methods We performed a cross-sectional pilot study of 46 Puerto Rican patients diagnosed with PAD. The cohort was divided based on use of clopidogrel and cilostazol (n = 24) or clopidogrel alone (n = 22). Platelet function was measured ex vivo using the VerifyNow P2Y12 assay. Genomic DNA was extracted from peripheral blood samples using the QIAamp DNA Blood Midi Kit, which was subjected to candidate variant genotyping (CYP2C19, ABCB1, PON1 and P2RY12) using TaqMan quantitative polymerase chain reaction assays. All analyses were performed using SAS version 9.4 (SAS Institute). Results Among all enrolled patients, 18 (39%) had high on-treatment platelet reactivity (HTPR). The mean platelet reactivity was 207 ± 53 (range, 78–325) with higher P2Y12 reaction units in the non-cilostazol group, 224 ± 45 vs. 191 ± 55 on the cilostazol group (p = 0.03). No significant differences were observed in the clinical or genetic variables between the two groups. A multiple regression analysis determined that history of diabetes mellitus (p= 0.03), use of cilostazol (p = 0.03) and hematocrit (p = 0.02) were independent predictors of platelet reactivity. Conclusions In Puerto Rican PAD patients on clopidogrel therapy, history of diabetes mellitus, use of cilostazol and hematocrit are independent predictors of platelet reactivity. Adjunctive cilostazol therapy may enhance clopidogrel efficacy among PAD patients with HTPR.

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Section: Methodsmentioning

confidence: 99%

Effect of cilostazol on platelet reactivity among patients with peripheral artery disease on clopidogrel therapy

Hernández-Suárez

Nuñez-Medina

Scott

et al. 2018

Drug Metabolism and Personalized Therapy

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“…Genomic DNA extraction was performed maximally 48 h after sample collection, as previously described [13]. Samples were then genotyped on amplified DNA by the real-time allele-specific polymerase chain reaction (PCR) technique, using the TaqMan® SNP Genotyping Assays platform (Applied Biosystems, Foster City, Calif., USA) [14]. The assays were performed according to the manufacturer's specifications and then run on a thermocycler IQ5™ Real-Time PCR Detection System from BIO-RAD (online suppl.…”

Section: Methodsmentioning

confidence: 99%

Association Study of GWAS-Derived Loci with Height in Brazilian Children: Importance of MAP3K3, MMP24 and IGF1R Polymorphisms for Height Variation

Fontenele¹,

Moraes²,

d’Alva³

et al. 2015

Horm Res Paediatr

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Background/Aim: The single nucleotide polymorphisms (SNPs) rs2282978 (CDK6), rs2425019 (MMP24), rs8081612 (MAP3K3), rs2871865 (IGF1R) and rs3782415 (SOCS2) were among the SNPs most strongly associated with height in a meta-analysis of 47 genome-wide association studies (GWAS) involving 114,223 adults from six ethnic groups. The present study aimed to examine associations between these SNPs and height in Brazilian children. Methods: Cross-sectional heights of 1,008 healthy unrelated 4.4- to 9.7-year-old children were evaluated. All genotypes were determined by allele-specific polymerase chain reactions. Height standard deviation scores (SDS) were generated for this population and regressed on allele counts. Linear regressions were performed to estimate the effect of individual SNPs or a polygenic allelic score on height. Results: The T allele of rs8081612 (MAP3K3), the C allele of rs2871865 (IGF1R) and the G allele of rs2425019 (MMP24) were significantly associated with a 0.091-SDS greater height (95% CI 0.089-0.093, p = 0.001) by polygenic analysis. The mean height SDS difference between children with 2 ‘tall' alleles and children with 4 ‘tall' alleles was 0.24 SDS (95% CI 0.05-0.43, p = 0.01). The observed allelic effect is consistent with that found in previous GWAS. Conclusions: Polymorphisms in MAP3K3, MMP24 and IGF1R act additively on height in children of an admixed population. These results demonstrate the importance of these loci for children's height.

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“…The single nucleotide polymorphism (SNP) R381Q was genotyped in these samples using the SNPlex Genotyping System (Applied Biosystems), which is based on oligonucleotide ligation/PCR, as described previously [12,35,36]. In brief, 100 ng of genome DNA was dried overnight at room temperature in TwinTec 384well plates (Eppendorf, Hamburg, Germany) and used for genotyping with the SNPlex chemistry system (Applied Biosystems) on an automated platform with TECAN Freedom EVO and 384well TEMO liquid handling robots (TECAN, Männe-dorf, Switzerland).…”

Section: Genotype Analysismentioning

confidence: 99%

Genetic Association of Nonsynonymous Variants of the IL23R with Familial and Sporadic Inflammatory Bowel Disease in Women

et al. 2009

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We replicated the association of IL23R R381Q with CD but not UC, and we observed an association of L310P with UC, but not CD, in a central Pennsylvania population. Further analysis of the distribution of IL23R variants revealed that these effects were largely female-specific. The results suggest that IL23R R381Q confers protection against CD and that L310P confers protection against UC in females.

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Assessment of two flexible and compatible SNP genotyping platforms: TaqMan® SNP Genotyping Assays and the SNPlex™ Genotyping System

Cited by 212 publications

References 42 publications

Effect of cilostazol on platelet reactivity among patients with peripheral artery disease on clopidogrel therapy

Effect of cilostazol on platelet reactivity among patients with peripheral artery disease on clopidogrel therapy

Association Study of GWAS-Derived Loci with Height in Brazilian Children: Importance of <b><i>MAP3K3, MMP24</i></b> and <b><i>IGF1R</i></b> Polymorphisms for Height Variation

Genetic Association of Nonsynonymous Variants of the IL23R with Familial and Sporadic Inflammatory Bowel Disease in Women

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