Development of a TaqMan allelic discrimination assay for the distinction of two major subtypes of the grapevine yellows phytoplasma Bois noir

2009 ◽  
Vol 124 (3) ◽  
pp. 521-526 ◽  
Author(s):  
Jennifer Berger ◽  
Josef Dalla Via ◽  
Sanja Baric
Keyword(s):  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Bois Noir ◽  
Taqman Allelic Discrimination Assay ◽  
Taqman Allelic Discrimination ◽  
Grapevine Yellows

scholarly journals Lack of association between miR-218 rs11134527 A>G and Kawasaki disease susceptibility

2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Lei Pi ◽  
Lanyan Fu ◽  
Yufen Xu ◽  
Di Che ◽  
Qiulian Deng ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
Disease Susceptibility ◽  
Coronary Artery Lesions ◽  
Cancer Risks ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Taqman Allelic Discrimination Assay ◽  
Taqman Allelic Discrimination ◽  
Age Related ◽  
The Relationship

Kawasaki disease (KD) is a type of disease that includes the development of a fever that lasts at least 5 days and involves the clinical manifestation of multicellular vasculitis. KD has become one of the most common pediatric cardiovascular diseases. Previous studies have reported that miR-218 rs11134527 A>G is associated with susceptibility to various cancer risks. However, there is a lack of evidence regarding the relationship between this polymorphism and KD risk. The present study explored the correlation between the miR-218 rs11134527 A>G polymorphism and the risk of KD. We recruited 532 patients with KD and 623 controls to genotype the miR-218 rs11134527 A>G polymorphism with a TaqMan allelic discrimination assay. Our results illustrated that the miR-218 rs11134527 A>G polymorphism was not associated with KD risk. In an analysis stratified by age, sex, and coronary artery lesions, we found only that the risk of KD was significantly decreased for children older than 5 years (GG vs. AA/AG: adjusted OR = 0.26, 95% CI = 0.07–0.94, P=0.041). The present study demonstrated that the miR-218 rs1113452 A>G polymorphism may have an age-related relationship with KD susceptibility that has not previously been revealed.

Association between rs4149056 variant in SLCO1B1 and early discontinuation of statin after acute myocardial infarction

2020 ◽  
Vol 21 (3) ◽  
pp. 163-172
Author(s):  
Abdallah Al-Salameh ◽  
Nicolas Danchin ◽  
Céline Verstuyft ◽  
Salma Kotti ◽  
Etienne Puymirat ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Acute Myocardial Infarction ◽  
Wild Type Allele ◽  
Wild Type ◽  
Early Discontinuation ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Taqman Allelic Discrimination Assay ◽  
Taqman Allelic Discrimination ◽  
Increased Risk

Data from two French surveys were used to analyze the association between in-hospital statin discontinuation and SLCO1B1 polymorphism (rs4149056) in patients with acute myocardial infarction. Using TaqMan allelic discrimination assay, 1674 and 1708 patients were genotyped for SLCO1B1 in 2005 and 2010, respectively. The association with in-hospital statin discontinuation was assessed after adjusting for confounding factors. In 2005, homozygosity for the reduced-function allele was associated with an increased risk of in-hospital statin discontinuation (OR: 3.68; p = 0.004) compared with the wild-type allele but this association disappeared in 2010. However, statin type and intensity-dose differed significantly between the surveys. SLCO1B1 polymorphism (rs4149056) does not seem to be a major determinant of early ‘in-hospital’ statin discontinuation after acute myocardial infarction.

scholarly journals Molecular Typing of Bois Noir Phytoplasma Strains in the Chianti Classico Area (Tuscany, Central Italy) and Their Association with Symptom Severity in Vitis vinifera ‘Sangiovese’

2018 ◽  
Vol 108 (3) ◽  
pp. 362-373 ◽  
Author(s):  
R. Pierro ◽  
A. Passera ◽  
A. Panattoni ◽  
P. Casati ◽  
A. Luvisi ◽  
...  
Keyword(s):  
Symptom Severity ◽  
Central Italy ◽  
Mediterranean Area ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Bois Noir ◽  
Field Surveys ◽  
Eastern Pyrenees ◽  
Polyphagous Insect ◽  
First Time

Bois noir (BN) is the most widespread disease of the grapevine yellows complex in the Euro-Mediterranean area. BN is caused by ‘Candidatus Phytoplasma solani’ (BNp), transmitted from herbaceous plants to grapevine by polyphagous insect vectors. In this study, genetic diversity among BNp strains and their prevalence and possible association with grapevine symptom severity were investigated in a Sangiovese clone organic vineyard in the Chianti Classico area (Tuscany). Field surveys over 2 years revealed a range of symptom severity on grapevine and an increase of BN incidence. A TaqMan allelic discrimination assay detected only tufB type b among BNp strains, suggesting the prevalence of the bindweed-related ecology. Nucleotide sequence analyses of vmp1 and stamp genes identified 12 vmp1 and 16 stamp sequence variants, showing an overall positive selection for such genes. The prevalent genotype was Vm43/St10, reported for the first time in this study and closely related to strains identified only in the French Eastern Pyrenees. BNp strains identified in the examined vineyard and mostly grouped in separate bindweed-related phylogenetic clusters showed statistically significant differences in their distribution in grapevines exhibiting distinct symptom severity. These results suggest the possible occurrence of a range of virulence within BNp strain populations in the Chianti Classico area.

scholarly journals The miRNA-608 rs4919510 G>C polymorphism confers reduce coronary injury of Kawasaki disease in a Southern Chinese population

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Yanfei Wang ◽  
Zhaoliang Lu ◽  
Lanyan Fu ◽  
Yaqian Tan ◽  
Di Che ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
Systemic Vasculitis ◽  
Mucocutaneous Lymph Node Syndrome ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Taqman Allelic Discrimination ◽  
Southern Chinese ◽  
Immune Mediated ◽  
Single Locus Analysis ◽  
The Relationship

Abstract Kawasaki disease (KD) is also called mucocutaneous lymph node syndrome and is an acute febrile pediatric disease characterized by systemic vasculitis. KD typically occurs in children 5 years old or younger and occurs more often in males than in females. miRNA-608 has been reported to interact with interleukin-6 and affect innate immunity. The immune-mediated inflammation could induce the occurrence of KD; however, there is no previous research focused on the relationship between miRNA-608 polymorphism and the KD risk. The present study explored the correlation between the miRNA-608 rs4919510 G>C polymorphism and the risk for KD. We recruited 532 patients with KD and 623 controls to genotype the miRNA-608 rs4919510 G>C polymorphism with a TaqMan allelic discrimination assay. Single-locus analysis showed no significant association between miRNA rs4919510 G>C polymorphism and KD susceptibility. However in an analysis stratified by age, gender, and coronary artery lesion (CAL), we found a relationship between the miRNA-608 rs4919510 G>C polymorphism and KD susceptibility. When KD patients were stratified by coronary injury, the CG/CC genotypes of the miRNA-608 rs4919510 G>C polymorphism contributed to a higher occurrence of KD than that was found in the GG genotype patients (adjusted odds ratio = 0.74, 95% CI = 0.56–0.98, P = 0.033). The present study demonstrated that the miRNA-608 rs4919510 G>C polymorphism may have a CAL-related relationship with KD susceptibility that has not been previously revealed.

scholarly journals TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene

2010 ◽  
Vol 55 (No. 8) ◽  
pp. 307-312 ◽  
Author(s):  
I. Manga ◽  
J. Dvořák
Keyword(s):  
Large Scale ◽  
Nucleotide Substitution ◽  
Bos Taurus ◽  
Single Nucleotide Substitution ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Single Nucleotide ◽  
Taqman Allelic Discrimination ◽  
Fluorogenic Probes ◽  
Genotype And Allele Frequencies

Alleles A1 and A2 of the Bos taurus CSN2 gene are the most frequent in a number of dairy cattle breeds. In this study, a new allelic discrimination assay using TaqMan fluorogenic probes was developed to detect single nucleotide substitution characterizing the A1/A2 alleles of the CSN2 gene. The method was validated using DNA samples of known genotypes with different concentrations and the results were compared with those for the commonly used problematic ACRS-PCR. We found the TaqMan method to be more effective, 100% reliable and hundred times more sensitive for testing the CSN2 genetic marker in cattle than the ACRS-PCR. As it enabled a rapid analysis of a large number of DNA samples in uniform format without previous DNA quality assessment and without the requirement for post-amplification manipulations, it presents an effective tool for the analysis of large-scale sample sets. The method was applied for testing on a sample of 120 Czech Holstein dairy cows. The observed relative genotype and allele frequencies were as follows: A1A1–0.20, A1A2–0.51, A2A2–0.29; A1–0.45, A2–0.55.

scholarly journals Assessment of the myostatin Q204X allele using an allelic discrimination assay

2006 ◽  
Vol 29 (3) ◽  
pp. 496-497
Author(s):  
Ana M. Sifuentes-Rincón ◽  
Herlinda E. Puentes-Montiel ◽  
Víctor R. Moreno-Medina ◽  
Xóchitl F. de la Rosa-Reyna
Keyword(s):  
Allelic Discrimination Assay ◽  
Allelic Discrimination

scholarly journals Single Nucleotide Polymorphisms of Indoleamine 2,3-Dioxygenase 1 Influenced the Age Onset of Parkinson’s Disease

2020 ◽  
Author(s):  
Nóra Török ◽  
Rita Maszlag-Török ◽  
Kinga Molnár ◽  
Zoltán Szolnoki ◽  
Ferenc Somogyvári ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Subgroup Analysis ◽  
Snp Analysis ◽  
Healthy Controls ◽  
Nucleotide Polymorphisms ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Single Nucleotide ◽  
Indoleamine 2,3 Dioxygenase ◽  
Tryptophan Dioxygenase

Earlier studies reported alterations of the kynurenine (KYN) pathway of tryptophan (TRP) metabolism in Parkinson’s disease (PD). The first rate-limiting enzymes indoleamine 2,3-dioxygenase (IDO) and tryptophan dioxygenase were observed upregulated, resulting elevated KYN/TRP ratios in the serum and cerebrospinal fluid samples of patients with PD. An increasing number of single nucleotide polymorphisms (SNPs) have been identified in a population of PD. However, little is known if genetic variations of the IDO contribute to disturbance of the KYN metabolism in and the pathogenesis of PD. SNP analysis of IDO1 was performed by allelic discrimination assay with fluorescently labelled TaqMan probes and a subgroup analysis was conducted according to the age of PD onset. The frame shifts variant rs34155785, intronic variant rs7820268, and promotor region variant rs9657182 SNPs of 105 PD patients without comorbidity were analyzed and compared to 129 healthy controls. No significant correlation was found in three SNPs between PD patients and healthy controls. However, the subgroup analysis revealed that A alleles of rs7820268 SNP or rs9657182 SNP carriers contribute to later onset of PD than non-carriers. The study suggested that SNPs of IDO1 influenced the age onset of PD and genotyping of SNPs in certain alleles potentially serves as a risk biomarker of PD.

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