Amplification refractory mutation system– polymerase chain reaction (ARMS–PCR) for detection of TGF-β1codon 10 and 25 genetic polymorphisms v1 (protocols.io.bma5k2g6)

protocols.io ◽  
2020 ◽  
Author(s):  
bryar ahmed
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Polymorphisms ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Polymerase Chain

scholarly journals A Tetra-Primer Amplification Refractory Mutation System–Polymerase Chain Reaction (T-ARMS-PCR) for Genotyping of rs8099917 & rs12979860 IL28B Polymorphisms and Its Correlation of Various Variables in Iranian HCV Patients

2020 ◽  
pp. 31-41
Author(s):  
Ali Bahari ◽  
Mohammad Hashemi ◽  
Gholam Reza Bahari ◽  
Tahereh Fakharian ◽  
Sina Gerayli ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Hepatitis C ◽  
Gene Polymorphisms ◽  
Baseline Viral Load ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Polymerase Chain

Background: Selecting patients for new direct acting antiviral treatment of HCV has prompted a conflicting matter worldwide because of its high cost and limited availability. Genotyping of IL28B polymorphisms will aid clinical decision making for identifying priorities of urgent treatment in resource-limited countries. Objectives: The aim of the present study was to design a simple tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS-PCR) for genotyping of the rs8099917 and rs12979860 IL28B gene polymorphisms. Furthermore, we identify the correlation of variables such as gender, serum ALT level, histology of liver and baseline viral load with these polymorphisms. Patients and Methods: We efficiently designed a T-ARMS-PCR for detection of rs12979860 and rs8099917 IL28B gene polymorphisms. Using this method, we genotyped 148 hepatitis C patients. To ensure T-ARMS genotyping quality, we, regenotyped samples with the PCR- sequencing method. Results: Results of genotyping of rs12979860 and rs8099917 by T-ARMS PCR method were 100% concordant with the sequencing results. Among these 148 patients with chronic hepatitis C, the frequency of the rs12979860 CT, TT and CC genotypes was 72.3%, 14.2% and 13.5%, respectively and the frequency of the rs8099917 TT, GT and GG genotypes was 58.1%, 38.5% and 3.4%. Low frequency (2.7%) of association of two unfavourable homozygous genotypes (TT rs12979860 / GG rs809917) as well as 56.7% of association of 3 or 4 favorable alleles could explain good response of Iranians to HCV treatment with interferon-based regimens. About correlation of polymorphisms with different variables, only high viral load showed a statistically significant correlation to unfavorable genotype of TT rs12979860 ( p value = 0/05 ) and there was no correlation of  serum ALT level, gender and  histology of liver to IL28B genotypes. Conclusions: We report that rs8099917 polymorphisms could predict outcomes better than rs12979860 in Iranian HCV patients.

Evaluation of a new efficient procedure for single-nucleotide polymorphism genotyping: tetra-primer amplification refractory mutation system-polymerase chain reaction

2004 ◽  
Vol 42 (1) ◽  
Author(s):  
Naoko Okayama ◽  
Kozue Fujimura ◽  
Junji Nakamura ◽  
Yutaka Suehiro ◽  
Yuichiro Hamanaka ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphism ◽  
Snp Genotyping ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Arms Pcr ◽  
Mutation System ◽  
Polymerase Chain

AbstractTetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) is a new efficient method for single-nucleotide polymorphism (SNP) genotyping. To determine the optimal conditions for ARMS-PCR we attempted to genotype ten SNPs. DNA was extracted from the peripheral blood of 168 unrelated healthy Japanese volunteers. Two problems inhibited uniform efficiency of the amplification of three bands. The first problem was the lower amplification efficiency of the shorter and allele-specific products compared with the largest product. This phenomenon was overcome by increasing the relative concentration of the inner primers. The second problem was non-specific amplification of the shorter products. To reduce the amplification of these nonspecific bands, adjusting any one of the following PCR conditions was effective: i) reducing the ratio of the inner primer concentration relative to that of the outer primers; ii) increasing the annealing temperature for the initial 5–10 cycles; iii) hot start PCR. With these procedures all ten of the SNPs were successfully genotyped. Our present data may be useful in the further application of tetra-primer ARMS-PCR to SNP genotyping.

scholarly journals Amplification Refractory Mutation System – Polymerase Chain Reaction for Rapid Detection of rpoB Gene Mutations in Mycobacterium tuberculosis

2017 ◽  
Vol 5 (1) ◽  
pp. 81-85 ◽  
Author(s):  
Hemanta Kumari Chaudhary ◽  
Mitesh Shrestha ◽  
Prakash Chaudhary ◽  
Bal Hari Poudel
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rpob Gene ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Mdr Tb ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rifampin Resistance

Multidrug-resistant tuberculosis (MDR-TB) has become a serious worldwide threat including in Nepal. MDR-TB refers to the pathological condition whereby Mycobacterium tuberculosis becomes resistant to the first line of drug treatment i.e. rifampin and isoniazid. Resistance to rifampin (RIF) is mainly caused by the mutations in the rpoB gene which codes for the β-subunit of RNA polymerase. In this study, Amplification Refractory Mutation System – Polymerase Chain Reaction (ARMS – PCR) technique has been used to detect mutations in the rpoB gene of Mycobacterium tuberculosis. Total DNA samples of 34 phenotypic MDR-TB were subjected to ARMS – PCR using three different codon specific primers (516, 526 and 531). These three codons occupy large portion of total mutation responsible for rifampin resistance. Out of the total DNA samples, all were bearing mutation in at least one of the three codons mentioned. Of those bearing mutation, the highest number had mutation in codon 531 (97.05 %) followed by codon 516 (17.64 %) and finally in codon 526 (11.76%) respectively. Hence, ARMS – PCR may be used as an alternative diagnostic technique for detection of rifampin resistance in Mycobacterium tuberculosis strains, especially for a developing country like Nepal.Int. J. Appl. Sci. Biotechnol. Vol 5(1): 81-85

scholarly journals CCL5 rs2107538 Polymorphism Increased the Risk of Tuberculosis in a Sample of Iranian Population

2016 ◽  
Vol 117 (2-3) ◽  
pp. 90-97 ◽  
Author(s):  
Hamid Reza Kouhpayeh ◽  
Mohsen Taheri ◽  
Mana Baziboroon ◽  
Mohammad Naderi ◽  
Gholamreza Bahari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Pulmonary Tuberculosis ◽  
Chemokine Receptor ◽  
Iranian Population ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Mutation System ◽  
Chemokine Ligand ◽  
Allele Specific ◽  
Polymerase Chain

Cysteine-cysteine chemokine ligand 5 (CCL5) with immunoregulatory and inflammatory activities has an important role in granuloma formations that activates and stimulates T-cells and macrophages. Cysteine-cysteine chemokine receptor 5 (CCR5) is a chemokine receptor, which is important for migration of immune cells to site of infection. In the present study we investigated the possible association between CCL5 –403G/A (rs2107538), CCL5 –28C/G (rs2280788) and CCR5 Δ32 polymorphisms and pulmonary tuberculosis (PTB) in an Iranian population. This case-control study was performed on 160 patients with pulmonary tuberculosis and 160 unrelated healthy subjects. The CCL5 –403G/A, CCL5 –28C/G and CCR5 Δ32 polymorphisms were genotyped by allele-specific polymerase chain reaction (AS-PCR), tetra amplification refractory mutation system polymerase chain reaction (T-ARMS PCR) and PCR, respectively. Our results showed that GA as well as GA+AA genotypes of CCL5 –403G/A (rs2107538) increased the risk of PTB in comparison with GG genotype (OR=1.70, 95% CI=1.03–2.81, P=0.038 and OR=1.64, 95% CI=1.00–2.68, P=0.049, respectively). No significant association was found between CCL5 –28C/G as well as CCR5 Δ32 polymorphism and PTB risk. In conclusion, our findings proposed that CCL5 –403G>A polymorphism may be a risk factor for susceptibility to PTB in our population. Larger sample sizes with different ethnicities are required to validate our findings.

scholarly journals Molecular Authentication of Dendrobium Species by Multiplex Polymerase Chain Reaction and Amplification Refractory Mutation System Analysis

2012 ◽  
Vol 137 (6) ◽  
pp. 438-444 ◽  
Author(s):  
Chu-Hui Chiang ◽  
Tsong-Ann Yu ◽  
Shu-Fang Lo ◽  
Chao-Lin Kuo ◽  
Wen-Huang Peng ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Polymerase Chain Reaction ◽  
System Analysis ◽  
Pcr Amplification ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
5.8S Rdna ◽  
Traditional Chinese Herbal Medicine ◽  
Mutation System ◽  
Polymerase Chain

The genus Dendrobium is important in traditional Chinese herbal medicine, and the precise identification of Dendrobium species is critical for the treatment and for pharmacological research. In the present study, a ribosomal DNA (rDNA) internal transcribed spacer (ITS) region-based analysis was used to ascertain the phylogenetic relationship among 20 Dendrobium species. The lengths of the ITS regions among the 20 species ranged from 636 to 653 bp, and the identities of the rDNA regions among the different species ranged from 75.7% to 99.1%. The results also showed that the ITS1 and ITS2 regions exhibit more variation than the 5.8S rDNA. A phylogenetic tree derived from the ITS sequence indicated that six medicinal Dendrobium species, of which five are common medicinal plants in the Taiwan market, were closely related and shared a common clade. Multiplex polymerase chain reaction (PCR) amplification was successfully performed to identify the six medicinal Dendrobium species, and amplification refractory mutation system (ARMS) PCR was used to distinguish D. tosaense specifically from the 19 other Dendrobium species. The established PCR-based (multiplex and ARMS) analyses can be used for the authentication of the raw materials of medicinal Dendrobium from other species.

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