Comparison of TaqMan Real-Time and Tetra-Primer ARMS PCR Techniques for Genotyping of Rs 8066560 Variant in Children and Adolescents with Metabolic Syndrome

Miranzadeh-Mahabadi, Hoda; Miranzadeh-Mahabadi, Hajar; Nikpour, Parvaneh; Emadi‐Baygi, Modjtaba; Kelishadi, Roya

doi:10.17219/acem/29185

Cited by 4 publications

(4 citation statements)

References 22 publications

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“…The tetra-primer ARMS-PCR method applied in the present study is more cost-and time-effective than other commonly used genotyping methods such as PCR-restriction fragment length polymorphism and TaqMan assays (61,62). In addition, the tetra-primer ARMS-PCR method has also been demonstrated to possess a high reliability in genotyping (38,61,62), thus it may be used for detecting polymorphisms.…”

Section: Discussionmentioning

confidence: 82%

“…In addition, the tetra-primer ARMS-PCR method has also been demonstrated to possess a high reliability in genotyping (38,61,62), thus it may be used for detecting polymorphisms. The limitations of the present study were the absence of subgroups analysis due to the small number of patients participating in the study, and the absence of toxicity analysis.…”

Section: Discussionmentioning

confidence: 99%

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Association of single nucleotide polymorphisms in the MVP gene with platinum resistance and survival in patients with epithelial ovarian cancer

Wang

2016

Oncology Letters

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Abstract. The human major vault protein (MVP) has been linked to the development of multidrug resistance in cancer cells, and overexpression of MVP has been observed in ovarian cancer tissues. The aim of the present study was to investigate the association between single nucleotide polymorphisms (SNPs) in the MVP gene and the tumor response to platinum-based chemotherapy and survival of patients affected by epithelial ovarian cancer (EOC), in addition to confirm whether tetra-primer amplification-refractory mutation system (ARMS)-polymerase chain reaction (PCR) is an accurate genotyping method. For this purpose, two polymorphisms in the MVP gene, namely reference SNP (rs)1057451 and rs4788186, were selected from the data obtained by the International haplotype map (HapMap) Project regarding Chinese Han population, and were evaluated by tetra-primer ARMS-PCR. Upon validation by DNA sequencing, the association of these polymorphisms with platinum resistance, progression-free survival (PFS) and overall survival (OS) in patients with EOC was assessed. The results of tetra-primer ARMS-PCR were in agreement with those derived from DNA sequencing. No significant differences were observed between platinum-sensitive and platinum-resistant cohorts in terms of allele and genotype distribution of these two polymorphisms in the MVP gene, which were not associated with PFS or OS. However, a trend toward prolonged PFS was observed in patients carrying the heterozygous AG allele at the rs4788186 locus. These results suggest that rs1057451 and rs4788186 variants in the MVP gene are not associated with favorable therapeutic response to platinum or longer survival in Chinese Han patients affected by EOC. In addition, the data of the present study confirm that tetra-primer ARMS-PCR is a trustworthy and economical genotyping method.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Association of single nucleotide polymorphisms in the MVP gene with platinum resistance and survival in patients with epithelial ovarian cancer

Wang

2016

Oncology Letters

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“…This method is particularly important for evaluating the sensitivity of chemotherapy (Table 3). Additionally, PCR is also widely used in the diagnosis and treatment of other diseases, such as in parasitic diseases [106], metabolic diseases [107][108][109], autoimmune diseases (rheumatoid arthritis and diabetes) [110], pediatric pulmonary diseases [111], spinal muscular dystrophy diseases [112], and so on. In a word, PCR has been used in almost the whole process of disease prevention, diagnosis, treatment, and prognosis.…”

Section: Applications Of Pcr For Cancer and Other Diseasesmentioning

confidence: 99%

PCR Techniques and Their Clinical Applications

Wang¹,

Cai²,

Chen³

et al. 2024

Biochemistry

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Kary B. Mullis developed a revolutionary method name polymerase chain reaction (PCR) in 1983, which can synthesize new strand of DNA complementary to the template strand of DNA and produce billions of copies of a DNA fragment only in few hours. Denaturation, annealing, and extension are the three primary steps involved in the PCR process, which generally requires thermocyclers, DNA template, a pair of primers, Taq polymerase, nucleotides, buffers, etc. With the development of PCR, from traditional PCR, quantitative PCR, to next digital PCR, PCR has become a powerful tool in life sciences and medicine. Applications of PCR techniques for infectious diseases include specific or broad-spectrum pathogen detection, assessment and surveillance of emerging infections, early detection of biological threat agents, and antimicrobial resistance analysis. Applications of PCR techniques for genetic diseases include prenatal diagnosis and screening of neonatal genetic diseases. Applications of PCR techniques for cancer research include tumor-related gene detection. This chapter aimed to discuss about the different types of PCR techniques, including traditional PCR, quantitative PCR, digital PCR, etc., and their applications for rapid detection, mutation screen or diagnosis in infectious diseases, inherited diseases, cancer, and other diseases.

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“…Randawa et al (2017) have developed TARMS-PCR for genotyping SNP rs12303764(G/T) of human Unc-51 like kinase 1t gene and showed 100% concordance with DNA sequencing result which is a gold standard method for genotyping. Another study has evaluated the performance of TARMS-PCR versus TaqMan Real-Time PCR in diagnosing Rs 8066560 polymorphism giving complete concordance of both methods compared (Miranzadeh-Mahabadi et al, 2015). TARMS-PCR also produces a consistent result when it was compared to RFLP-PCR to detect polymorphisms of the CYP2E1 Gene (Suhda et al 2016).…”

Section: Tarms-pcrmentioning

confidence: 99%

Improvement of HER2I655V TARMS-PCR Performance by DNA Quality Analysis

2018

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Reliable TARMS-PCR is a prerequisite in constructing a solid conclusion in genetic diagnostics. The validity of data generated by this molecular technique is hampered by a false positive result. In attempt to develop a TARMS-PCR for HER2I655V genotyping with no interfering of bias we used DNase I to eliminate DNA contaminant resided in PCR reagent. TARMS-PCR without enzyme treatment using recombinant plasmids that contained HER2I655V gene with represented its alleles was used to evaluate the presence of false positive result while DNase I treated-PCR reagent was used in TARMS-PCR to evaluate the effective dose of the enzyme and further to adjust the TARMS-PCR conditions. PCR master mix kit used in this study produced a false positive result on HER2I655V TARMS-PCR as proven by the presence of multiple PCR products in Non-Template Control (NTC) and 0.1 U of the enzyme could eliminate this DNA contaminant effectively, although this pretreatment altered the specificity of HER2I655V TARMS-PCR genotyping on certain genotype. Combination of touchdown TARMS-PCR with another allele-specific primer recovered specificity of detection on this model system. Interestingly, this optimized HER2I655V TARMS-PCR can only be used for genotyping the clinical samples if only further optimization was done using genomic DNA as template

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Comparison of TaqMan Real-Time and Tetra-Primer ARMS PCR Techniques for Genotyping of Rs 8066560 Variant in Children and Adolescents with Metabolic Syndrome

Cited by 4 publications

References 22 publications

Association of single nucleotide polymorphisms in the MVP gene with platinum resistance and survival in patients with epithelial ovarian cancer

Association of single nucleotide polymorphisms in the MVP gene with platinum resistance and survival in patients with epithelial ovarian cancer

PCR Techniques and Their Clinical Applications

Improvement of HER2I655V TARMS-PCR Performance by DNA Quality Analysis

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