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Добірка наукової літератури з теми "T-ARMS-PCR"

Автор: Grafiati

Опубліковано: 9 лютого 2024

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Статті в журналах з теми "T-ARMS-PCR"

Piccioli, Patrizia, Martina Serra, Viviana Gismondi, Simona Pedemonte, Fabrizio Loiacono, Sonia Lastraioli, Lucio Bertario, Maria De Angioletti, Liliana Varesco, and Rosario Notaro. "Multiplex Tetra-Primer Amplification Refractory Mutation System PCR to Detect 6 Common Germline Mutations of the MUTYH Gene Associated with Polyposis and Colorectal Cancer." Clinical Chemistry 52, no. 4 (April 1, 2006): 739–43. http://dx.doi.org/10.1373/clinchem.2005.060137.

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Abstract Background: We describe a simple tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) for detecting MUTYH mutations, which are associated with colorectal adenomas and colorectal cancer. Methods: We designed specific T-ARMS-PCR assays for 6 mutations (Y165C, G382D, 1395_7delGGA, Y90X, 1103delC, and R231H) selected on the basis of the frequency of their occurrence. We also designed a set of 3 multiplex T-ARMS PCR assays, each for detection of 2 mutations. We tested DNA samples from patients with attenuated or classic adenomatous polyposis coli and no detectable APC germline mutations. Results: All mutations were easily detected with both the specific and multiplex T-ARMS-PCR assays. Results were confirmed by DNA HPLC analysis in all 54 patients, and each mutation was confirmed by direct DNA sequencing. Conclusions: T-ARMS-PCR does not require any special equipment, and it provides rapid, reproducible, and cost-effective detection of common MUTYH mutations. Multiplex T-ARMS-PCR allows the detection of 6 common MUTYH mutations with use of as few as 3 single tube PCR reactions. It could be useful to carry out large population-based epidemiologic studies.

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Paul, Saikat, Rajneesh Dadwal, Shreya Singh, Dipika Shaw, Arunaloke Chakrabarti, Shivaprakash M. Rudramurthy, and Anup K. Ghosh. "Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis." PLOS ONE 16, no. 1 (January 13, 2021): e0245160. http://dx.doi.org/10.1371/journal.pone.0245160.

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Increasing reports of azole resistance inCandida tropicalis, highlight the development of rapid resistance detection techniques. Nonsynonymous mutations in the lanosterol C14 alpha-demethylase (ERG11) gene is one of the predominant mechanisms of azole resistance inC.tropicalis. We evaluated the tetra primer-amplification refractory mutation system-PCR (T-ARMS-PCR), restriction site mutation (RSM), and high-resolution melt (HRM) analysis methods for rapid resistance detection based onERG11polymorphism inC.tropicalis. Twelve azole-resistant and 19 susceptible isolates ofC.tropicaliswere included. DNA sequencing of the isolates was performed to check theERG11polymorphism status among resistant and susceptible isolates. Three approaches T-ARMS-PCR, RSM, and HRM were evaluated and validated for the rapid detection ofERG11mutation. The fluconazole MICs for the 12 resistant and 19 susceptible isolates were 32–256 mg/L and 0.5–1 mg/L, respectively. The resistant isolates showed A339T and C461T mutations in theERG11gene. The T-ARMS-PCR and RSM approaches discriminated all the resistant and susceptible isolates, whereas HRM analysis differentiated all except one susceptible isolate. The sensitivity, specificity, analytical sensitivity, time, and cost of analysis suggests that these three methods can be utilized for the rapid detection ofERG11mutations inC.tropicalis. Additionally, an excellent concordance with DNA sequencing was noted for all three methods. The rapid, sensitive, and inexpensive T-ARMS-PCR, RSM, and HRM approaches are suitable for the detection of azole resistance based onERG11polymorphism inC.tropicalisand can be implemented in clinical setups for batter patient management.

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Pua, Jing Yit, Ang Lee, Vienna Zi Wei Khor, Thanaseelan Pushpanathan, Abdul Aziz Mohamed Yusoff, Zamzuri Idris, and Azim Patar. "Development of a sensitive, specific and cost-effective T-ARMS PCR assay for the genotyping of R132H of IDH1 gene in glioma patients." Asian Journal of Medicine and Biomedicine 6, S1 (November 9, 2022): 61–63. http://dx.doi.org/10.37231/ajmb.2022.6.s1.528.

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The discovery of isocitrate dehydrogenase isoform 1 (IDH1) mutation as a key molecular marker has resulted in a change in glial tumour classification [1]. IDH1 mutations are commonly in gliomas, particularly in low-grade gliomas and secondary glioblastoma [2]. IDH1 p.R132H (c.395G>A) accounted for more than 90% of the mutation in IDH1/2 mutation and had a significant association with clinical outcomes. IDH1/2 mutations cause gain-of-function resulting in the formation of an oncometabolite, R-2-hydroxyglutarate instead of α-ketoglutarate implying a disruption of oxidative decarboxylation of Kreb’s cycle and other cellular mechanisms [3,4,5]. Immunohistochemistry (IHC) and Sanger sequencing is the most common approach used in molecular diagnostics. Nevertheless, both IHC and Sanger sequencing methods have shortcomings. IHC is prone to miss out on the mutation if the tumour samples are of poor quality, and it has also been reported to have low sensitivity when compared to sequencing-based techniques [6,7]. This study aimed to develop a sensitive, specific and cost-effective assay for genotyping IDH1 p.R132H mutations in glioma patients in order to shorten the time required for confirmatory diagnosis to be made. The tetra primer amplification refractory mutation system polymerase chain reaction (T-ARMS PCR) was used in this study to develop and validate the clinical applicability of the assay. A total of 61 glial specimens were collected and genomic DNA was isolated from all of them. All the samples were subjected to endpoint PCR and Sanger sequencing for mutation detection. T-ARMS PCR was developed and optimized prior to the screening of all the samples, and comparative mutation analysis was carried out. Overall, IDH1 p.R132H mutation was found to be 45.90% (n=28/61) prevalent and was found to be significantly associated with gender, tumour subtypes and grading, and location of the lesions (p=<0.05). With an F1 score of 0.966, we reported T-ARMS PCR with sensitivity, specificity and accuracy of 100% (95% CI: 87.94-100.00%), 93.94% (95% CI: 80.39-98.92%) and 96.72%, respectively. To compare with published studies, a meta-analysis is T-ARMS PCR detected one case with IDH1 p.R132C (c.394C>T), howbeit the case could have a double mutation of p.R132C (c.394C>T) and p.R132H (c.395G>A) or single mutation of p.R132Y (c.394_395CG>TA). However, this study was able to detect IDH1 p.R132G (c.394C>G) mutation via PCR by Sanger sequencing whereas T-ARMS PCR excluded the mutation, suggesting the assay is very specific to IDH1 p.R132HH (c.395G>A) only. Hereby, the performance of the T-ARMS PCR assay sheds a light that can be adapted for preoperative or intraoperative diagnosis.

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Harbeck, Nadia, Raquel von Schumann, Ronald Ernest Kates, Michael Braun, Sherko Kuemmel, Claudia Schumacher, Jochem Potenberg, et al. "Immune Markers and Tumor-Related Processes Predict Neoadjuvant Therapy Response in the WSG-ADAPT HER2-Positive/Hormone Receptor-Positive Trial in Early Breast Cancer." Cancers 13, no. 19 (September 29, 2021): 4884. http://dx.doi.org/10.3390/cancers13194884.

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Prognostic or predictive biomarkers in HER2-positive early breast cancer (EBC) may inform treatment optimization. The ADAPT HER2-positive/hormone receptor-positive phase II trial (NCT01779206) demonstrated pathological complete response (pCR) rates of ~40% following de-escalated treatment with 12 weeks neoadjuvant ado-trastuzumab emtansine (T-DM1) ± endocrine therapy. In this exploratory analysis, we evaluated potential early predictors of response to neoadjuvant therapy. The effects of PIK3CA mutations and immune (CD8 and PD-L1) and apoptotic markers (BCL2 and MCL1) on pCR rates were assessed, along with intrinsic BC subtypes. Immune response and pCR were lower in PIK3CA-mutated tumors compared with wildtype. Increased BCL2 at baseline in all patients and at Cycle 2 in the T-DM1 arms was associated with lower pCR. In the T-DM1 arms only, the HER2-enriched subtype was associated with increased pCR rate (54% vs. 28%). These findings support further prospective pCR-driven de-escalation studies in patients with HER2-positive EBC.

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Li, Mingxun, Xiaomei Sun, Jing Jiang, Yujia Sun, Xianyong Lan, Chuzhao Lei, Chunlei Zhang, and Hong Chen. "Tetra-primer ARMS-PCR is an efficient SNP genotyping method: An example from SIRT2." Anal. Methods 6, no. 6 (2014): 1835–40. http://dx.doi.org/10.1039/c3ay41370e.

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We have successfully genotyped a new identified bovine SIRT2 SNP g.4140A > G by T-ARMS-PCR method and validated the accuracy by PCR-RFLP assay using 1255 animals representing the five main Chinese breeds.

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Nagayama, Aiko, Tetsu Hayashida, Koji Okabayashi, Hiromitsu Jinno, Maiko Takahashi, Tomoko Seki, Akiko Matsumoto, Takeshi Murata, and Yuko Kitagawa. "A network meta-analysis assessing the comparative effectiveness of neoadjuvant therapy for HER2-positive breast cancer." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): e11598-e11598. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e11598.

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e11598 Background: The growing number of anti-HER2 agents suggests the eventual need for defining the optimal choice of neoadjuvant therapy for HER2-positive breast cancer. Multiple-treatments meta-analysis synthesizes information from a network of trials and combines direct and indirect evidence on the relative effectiveness. An indirect estimate of the benefit of A over B can be obtained by comparing trials of A v C with trials of B v C. In this study, we assessed the efficacy and safety of neoadjuvant therapy for HER2-positive breast cancer by conducting the direct and indirect comparisons from multiple RCTs. Methods: The primary outcome of the study was the number of the patients who achieved pathological complete response (pCR) defined as no invasive residual in breast or node. Secondary objectives were the number of patients who completed the treatment as planned and adverse events including diarrhea, neutropenia, cardiac events and skin disorder. Results: We identified 1047 articles by database search and 10 studies met our criteria. A total of 2247 patients in 7 different treatment arms were assessed; chemotherapy (CT) alone, CT with single or dual anti-HER2 agents and dual anti-HER2 agents without CT. Anti-HER2 agents evaluated were trastuzumab (T-mab), lapatinib, pertuzumab (P-mab). There was no significant difference between dual targeting treatment arms (CT + T-mab + lapatinib v CT + T-mab + P-mab, OR; 1.11, [0.42-2.86], p=0.41), however, lapatinib reduced the treatment completion mainly due to adverse events. Patients in dual targeting arms had significantly higher incidence of pCR than in other treatment arms. (CT + T-mab + P-mab v CT + T-mab, OR; 2.29, [1.02-5.02], p=0.02) Surface under the cumulative ranking probability curve (SUCRA) also indicated that CT + T-mab + P-mab had the highest probability of being the best treatment arm for pCR followed by CT + T-mab + lapatinib and CT + T-mab. Conclusions: This study provides evidence that combining two anti-HER2 agents with chemotherapy are the most effective treatment arms. Considering the cost and limited medical resources, CT + T-mab showed a well-balanced profile for efficacy, completion and safety.

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Muñoz-García, Canuto, Obdulia L. Segura-León, Julio C. Gómez-Vargas, Juan González-Maldonado, Juan A. Quintero-Elisea, Juan F. Martínez-Montoya, and Cesar Cortez-Romero. "Investigating mutations in the genes GDF9 and BMP15 in Pelibuey sheep through the amplification-refractory mutation system with tetra-primers." Austral Journal of Veterinary Sciences 55, no. 3 (September 22, 2023): 182–88. http://dx.doi.org/10.4206/ajvs.553.04.

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Single Nucleotide Polymorphisms (SNP) or mutations are variations with a broad distribution in the genome and, as part of genetic studies, SNP allow the identification of allelic variants related to characteristics of economic importance in sheep production. However, the identification of SNP and their genotypes through sequencing is expensive, as it requires specialized materials and equipment. The objective of this study was to identify polymorphisms and their genotypes in the growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes in Pelibuey sheep using the tetra-primer amplification-refractory mutation system through polymerase chain reaction (T-ARMS-PCR). DNA extraction and amplification of BMP15 and GDF9 were conducted from blood samples contained in WhatmanTM FTATM cards from 60 multiparous Pelibuey ewes with reproductive records. The T-ARMS-PCR methodology allowed the identification of wild-type genotypes and mutated homozygous genotypes in polymorphisms G4 and G6 of GDF9, whereas mutations in the BMP15 gene were not found. These results were confirmed by sequencing. In conclusion, the T-ARMS-PCR methodology allowed the identification of mutated and wild-type genotypes in SNP G4 and G6 of GDF9, although no mutations were found in BMP15 in Pelibuey sheep. This technique was found to be reliable, rapid, and easily applied to identify polymorphic genotypes.

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Motta, B. M., P. Dongiovanni, S. Fargion, and L. Valenti. "T-ARMS-PCR for the evaluation of rs12979860 IL28B genotype: an optimized protocol." Journal of Viral Hepatitis 19, no. 3 (February 13, 2012): 228. http://dx.doi.org/10.1111/j.1365-2893.2012.01582.x.

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Marty, M. E., J. Guinebretiere, M. Mathieu, B. Sigal-Zafrani, A. De Roquancourt, M. Spielmann, S. Giacchetti, P. De Cremoux, F. Spyratos, and B. Asselain. "Triple-negative phenotype is a strong predictor of sensitivity to epirubicin-cyclophosphamide (EC) then docetaxel (D) (ECD) primary chemotherapy (PCT) for localized breast cancer." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 21128. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.21128.

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21128 Background: Molecular markers (GEP, p53 mutations,) could overcome usual predictors (size, pathology, Hormone receptors, HER2) in identifying patients (pts) experiencing complete pathological response (pCR) with anthracyclin based chemotherapy (Clin.Cancer Res., 2004, 10 6789). We aimed at validating and refining these finding in pts treated with ECD. Methods: From 05/2004 to 04/2006 170 pts not amenable to Breast Conserving Therapy and/or with high evolutive potential were randomly allocated to EC (75/750mg/sqm)x4 then D (100 mg/sqm)x 4 (with or without celecoxib in HER2-ve or trastuzumab (T) in HER2+ve. The primary endpoint - absence of residual invasive breast carcinoma and of nodal involvement (pCR)- was to be correlated with usual predictors , phenotype, GEP and p53 mutations assessed from core biopsies. pCR ranged from 13 to 14% in the arms without T thus without suggestion of a difference between these arms. pCR in the 30 HER2+ve pts having received ECD + T was 30% (NS). Results in 135 fully evaluable pts not allocated to T and having undergone secondary surgery are analyzed. Results: Main predictors and related pCR are shown in the table below Results of ongoing molecular analysis will be reported. Conclusions: Expression of ER appears to be the major prognosticator for ECD induced pCR. Triple negative breast cancers experience the highest pCR rate (p< 0.0001) (chi2 test with Yates correction). Molecular studies to be presented will show if GEP and/or p53 mutations could allow to improve such prediction. [Table: see text] No significant financial relationships to disclose.

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Poe, Brian L., Doris M. Haverstick, and James P. Landers. "Warfarin Genotyping in a Single PCR Reaction for Microchip Electrophoresis." Clinical Chemistry 58, no. 4 (April 1, 2012): 725–31. http://dx.doi.org/10.1373/clinchem.2011.180356.

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Abstract BACKGROUND Warfarin is the most commonly prescribed oral anticoagulant medication but also is the second leading cause of emergency room visits for adverse drug reactions. Genetic testing for warfarin sensitivity may reduce hospitalization rates, but prospective genotyping is impeded in part by the turnaround time and costs of genotyping. Microfluidics-based assays can reduce reagent consumption and analysis time; however, no current assay has integrated multiplexed allele-specific PCR for warfarin genotyping with electrophoretic microfluidics hardware. Ideally, such an assay would use a single PCR reaction and, without further processing, a single microchip electrophoresis (ME) run to determine the 3 single-nucleotide polymorphisms (SNPs) affecting warfarin sensitivity [i.e., CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9) *2, CYP2C9 *3, and the VKORC1 (vitamin K epoxide reductase complex 1) A/B haplotype]. METHODS We designed and optimized primers for a fully multiplexed assay to examine 3 biallelic SNPs with the tetraprimer amplification refractory mutation system (T-ARMS). The assay was developed with conventional PCR equipment and demonstrated for microfluidic infrared-mediated PCR. Genotypes were determined by ME on the basis of the pattern of PCR products. RESULTS Thirty-five samples of human genomic DNA were analyzed with this multiplex T-ARMS assay, and 100% of the genotype determinations agreed with the results obtained by other validated methods. The sample population included several genotypes conferring warfarin sensitivity, with both homozygous and heterozygous genotypes for each SNP. Total analysis times for the PCR and ME were approximately 75 min (1-sample run) and 90 min (12-sample run). CONCLUSIONS This multiplexed T-ARMS assay coupled with microfluidics hardware constitutes a promising avenue for an inexpensive and rapid platform for warfarin genotyping.

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Більше джерел

Дисертації з теми "T-ARMS-PCR"

Blin, Manon. "Développement d'outils de diagnostic de terrain pour la détection de la schistosomiase : une approche One Health." Electronic Thesis or Diss., Perpignan, 2023. http://www.theses.fr/2023PERP0038.

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Il est maintenant évident que la dégradation des environnements peut favoriser la transmission des maladies infectieuses notamment en rapprochant les humains, des vecteurs ou des animaux. Concernant les Maladies Tropicales Négligées (MTN), l’OMS tente de mobiliser les institutions et la communauté scientifique en identifiant pour chacune des MTN, les lacunes existantes dans les besoins de diagnostic clinique, les critères requis pour leur développement ainsi que les stratégies à adopter pour lutter contre la maladie. Parmi elles, la schistosomiase, seconde maladie parasitaire humaine, souffre d’un manque flagrant d’outils de diagnostic alliant sensibilité et déployabilité afin de détecter les cas de faible intensité parasitaire dans les zones endémiques ; mais également pour permettre la réalisation de diagnostic animal et environnemental visant à adopter une approche intégrative dans la lutte contre la maladie. Les objectifs de cette thèse s’inscrivent dans la stratégie One Health en proposant le développement et l’application d’outils de diagnostics de terrain chez l’Homme, chez l’animal et dans l’environnement. Les efforts continus en matière de recherche, de développement de prévention, de traitement et de sensibilisation sont essentiels pour parvenir à un monde où la schistosomiase et plus généralement les MTN ne seront plus une menace pour la santé humaine
It is now evident that environmental degradation can facilitate the transmission of infectious diseases, particularly by bringing humans into closer proximity with vectors or animals. In the case of Neglected Tropical Diseases (NTDs), the World Health Organization (WHO) is endeavoring to mobilize institutions and the scientific community by identifying, for each NTD, existing gaps in clinical diagnostic needs, the criteria required for their development, and the strategies to be adopted to combat the disease. Among them, schistosomiasis, the second most prevalent human parasitic disease, suffers from a distinct lack of diagnostic tools that combine sensitivity and deployability to detect cases with low parasitic intensity in endemic areas. Additionally, such tools are needed to facilitate animal and environmental diagnosis, enabling an integrated approach to disease control. The objectives of this thesis align with the One Health strategy, proposing the development and application of field-friendly diagnostic tools for humans, animals, and the environment. Ongoing efforts in research, development, prevention, treatment, and awareness are essential to achieve a world where Schistosomiasis and other neglected tropical diseases cease to threaten human health

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