Tetra-primer amplification refractory mutation system-polymerase chain reaction in SNP genotyping of shrimp Fenneropenaeus chinensis

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.

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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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