Quantification of hepatitis C amino acid substitutions 70 and 91 in the core coding region by real-time amplification refractory mutation system reverse transcription-polymerase chain reaction

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.

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Amplification refractory mutation system polymerase chain reaction versus optimized polymerase chain reaction restriction-fragment length polymorphism for apolipoprotein E genotyping of majorly depressed patients

Molecular Medicine Reports ◽

10.3892/mmr.2015.4251 ◽

2015 ◽

Vol 12 (5) ◽

pp. 6829-6834

Author(s):

HONGMIN YOU ◽

JIN CHEN ◽

JINGJING ZHOU ◽

HUA HUANG ◽

JUNXI PAN ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Restriction Fragment Length Polymorphism ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Amplification Refractory Mutation System ◽

Chain Reaction ◽

Mutation System ◽

Polymerase Chain ◽

Restriction Fragment Length

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

Prague Medical Report ◽

10.14712/23362936.2016.9 ◽

2016 ◽

Vol 117 (2-3) ◽

pp. 90-97 ◽

Cited By ~ 5

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.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.137.6.438 ◽

2012 ◽

Vol 137 (6) ◽

pp. 438-444 ◽

Cited By ~ 12

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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