scholarly journals Development of a new amplification-refractory mutation system for detection of a single nucleotide polymorphism linked to drug resistance in Ancylostoma caninum

2015 ◽  
Vol 14 (2) ◽  
pp. 5103-5111 ◽  
Author(s):  
L.F. Furtado ◽  
É.M. Rabelo
Keyword(s):  
Drug Resistance ◽  
Single Nucleotide Polymorphism ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ancylostoma Caninum ◽  
Mutation System

Association of BTNL2 gene single nucleotide polymorphism with knee osteoarthritis

2021 ◽  
Vol 25 (2) ◽  
pp. 89-95
Author(s):  
S. S. Sahoo ◽  
O. K. Choudhari ◽  
J. Bhadra ◽  
B. C. Kabi
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Knee Osteoarthritis ◽  
Indian Population ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotypic Distribution ◽  
Mutation System ◽  
Hardy Weinberg Equilibrium

Relevance. Osteoarthritis (OA) is one of the chronic debilitating condition mostly seen in the aged population. The etiology behind the OA is multifactorial and the exact cause of the disease often remains uncertain. Apart from the conventional risk factors, there are the speculations of role of genetics playing a pivotal role in the causation of OA. The available literature showed BTNL2 gene polymorphism association with risk of Osteoarthritis whether the same relation is present in north Indian population needs to be elucidated. Objective. To find the association between single nucleotide polymorphism (SNP) (rs10947262) in BTNL2 gene and the susceptibility in knee Osteoarthritis (OA) subjects from northern Indian population. Materials and Methods. Blood samples of 100 patients of knee osteoarthritis and 100 healthy subjects were collected after institutional ethical clearance and participants consent. The BTNL2 gene fragment was amplified using Amplification Refractory Mutation System (ARMS-PCR) with predesigned primers after DNA extraction. The corresponding product bands were identified on the gel electrophoresis for 200 samples and the results were statistically analyzed. Results and Discussion. The genotypic distribution of the SNP followed Hardy-Weinberg Equilibrium. The genotype frequency analysis of the polymorphism was statistically significant (2=7.788; P=0.005) with Odds Ratio of CT+TT/CC: OR=2.303; P=0.008 revealing association of BTNL2 polymorphism with risk of Knee Osteoarthritis. Conclusion. The SNP (rs10947262) in the BTNL2 gene region is associated with risk of knee osteoarthritis.

Predictive role of single nucleotide polymorphism (rs11614913) in the development of breast cancer in Pakistani population

2020 ◽  
Vol 17 (3) ◽  
pp. 213-227
Author(s):  
Mushtaq Ahmad ◽  
Aftab Ali Shah
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphism ◽  
Target Genes ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Significant Difference ◽  
Mutation System ◽  
Predictive Role

Aim: miRNAs play an important role in breast cancer (BC). Variations in miRNAs influence their maturation, expression and consequently regulation of their target genes. Materials & methods: In this study, single nucleotide polymorphism rs11614913 was genotyped in BC patients (n = 300) and 230 controls by employing tetra primer amplification refractory mutation system PCR and Sanger sequencing (Macrogen Korea). Results: A significant difference was observed in the genotypes through co-dominant ( χ2.#x00A0;= 42.03; p < 0.0001), additive (odds ratio [OR] = 0.6441 [0.4887–0.8490, 95% confidence interval]; p < 0.0019), dominant (OR = 0.3996 [0.2809–0.5686], p < 0.0001) and recessive (OR = 0.2993 [0.1220–0.7347], p < 0.009) statistical models showed decreased risk association of C allele with BC. Conclusion: Females having CT genotype are at higher risk of BC as compared with those having CC genotype.

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 P-0022 Association Between C3435T Single Nucleotide Polymorphism of Multi-Drug Resistance 1 Gene and Risk of Gastric Cancer

2012 ◽  
Vol 23 ◽  
pp. iv37-iv38
Author(s):  
Juliana Oliveira ◽  
Aledson Felipe ◽  
Paula Chang ◽  
Tiago da Silva ◽  
Célia Pimenta ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Drug Resistance ◽  
Single Nucleotide Polymorphism ◽  
Multi Drug Resistance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Simultaneous determination of Mycobacterium leprae drug resistance and single nucleotide polymorphism genotype using nested multiplex PCR with amplicon sequencing

2021 ◽  
Author(s):  
Yasuhisa Iwao ◽  
Shuichi Mori ◽  
Manabu Ato ◽  
Noboru Nakata
Keyword(s):  
Drug Resistance ◽  
Single Nucleotide Polymorphism ◽  
Multiplex Pcr ◽  
Simultaneous Determination ◽  
Mycobacterium Leprae ◽  
Amplicon Sequencing ◽  
Clinical Samples ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Mycobacterium leprae is the predominant cause of leprosy worldwide, and its genotypes can be classified into four single nucleotide polymorphism (SNP) types and 16 subtypes. Determining M. leprae drug resistance and genotype is typically done by PCR and Sanger DNA sequencing, which require substantial effort. Here we describe a rapid method involving multiplex PCR in combination with nested amplification and next generation sequence analysis that allows simultaneous determination of M. leprae drug resistance and SNP genotype directly from clinical specimens. We used this method to analyze clinical samples from two paucibacillary, nine multibacillary, and six type-undetermined leprosy patients. Regions in folP1 , rpoB , gyrA , and gyrB that determine drug resistance and those for 84 SNP-InDels in the M. leprae genome were amplified from clinical samples and their sequences were determined. The results showed that seven samples were subtype 1A, three were 1D, and seven were 3K. Three samples of the subtype 3K had folp1 mutation. The method may allow more rapid genetic analyses of M. leprae in clinical samples.

Correlation of C-reactive protein levels, gene polymorphism and platelets count in Dengue infection

2020 ◽  
pp. 1-16
Author(s):  
Sana Shamshad ◽  
Sara Khan ◽  
Ghazala Kaukab Raja ◽  
Muhammad Sheeraz Ahmad ◽  
Muhammad Javaid Asad ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Dengue Infection ◽  
Serum Levels ◽  
Amplification Refractory Mutation System ◽  
Acid Extraction ◽  
Nucleotide Polymorphism ◽  
C Reactive Protein ◽  
Single Nucleotide ◽  
Protein Levels ◽  
Reactive Protein

Abstract Objective: To determine the correlation of polymorphism in C-reactive protein gene with variation in serum levels in dengue patients. Methods: The cross-sectional study was conducted at Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan, from October 2017 to October 2018, and comprised blood samples from dengue patients which were used to measure the serum levels of C-reactive protein. Deoxyribonucleic acid extraction followed by tetra amplification-refractory mutation system polymerase chain reaction was done to analyse the genotype variation T>G for single nucleotide polymorphism rs199953854 using allele-specific primers. Correlation of serum C-reactive protein levels with the C-reactive protein polymorphism in dengue patients was explored. Data was analysed using SPSS 21. Results: Of the 200 patients, 108(54%) had very high C-reactive protein levels, 48(24%) had levels slightly higher than the upper limit, 14(7%) had low and 30(15%) had normal levels. Also, 162(81%) patients had low platelets count. Amplification of only T alleles was noted. Conclusion: C-reactive protein levels were found to be increased with suppressed platelets count in dengue patients. Single nucleotide polymorphism rs199953854 appeared to have no polymorphism. Key Words: C-reactive protein, Dengue infection, rs199953854, Continuous...

scholarly journals Association of STAT4 rs7582694 with susceptibility to systemic lupus erythematosus in population of Lorestan province, Iran

2018 ◽  
Vol 21 (1) ◽  
pp. 14-18 ◽  
Author(s):  
Gholam Reza Izadkhasti ◽  
Seyed Reza Kazeminezhad ◽  
Mohammad Reza Akhoond
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Single Nucleotide Polymorphism ◽  
Lupus Erythematosus ◽  
Control Group ◽  
Amplification Refractory Mutation System ◽  
Sample Population ◽  
Nucleotide Polymorphism ◽  
Systemic Lupus ◽  
Single Nucleotide ◽  
Increased Risk

Background and aims: Systemic lupus erythematosus (SLE) is a polygenic, inflammatory disease with a complex genetic inheritance that affects almost all the organs and systems of the host body. According to studies, STAT4 is a susceptible gene that can participate in the development of SLE in different populations. The aim of this study was to show the association between rs7582694 single nucleotide polymorphism with increased risk of SLE disease and two serological symptoms of the disease (i.e., anti-dsDNA and ANA) in the population residing in Lorestan province. Methods: The present study was conducted as a case control research. In this study, the prevalence of STAT4 gene G/C (rs7582694) single nucleotide polymorphism (SNP) in the patients with SLE (n=122) and in control group (n=127) was investigated among a sample population from Lorestan province. This SNP was genotyped based on using two methods including PCR-RFLP (polymerase chain reactionrestriction fragment length polymorphism) and tetra-primer ARMS-PCR (amplification-refractory mutation system) methods. Results: According to the obtained results, the frequency of minor allele C from this SNP (related allele with the disease) as compared to the major allele G (normal allele) was significantly higher in SLE patients than the controls. In addition, it showed a significant association (odds ratio [OR] = 1.623, 95% CI = 1.111-2.370, P = 0.012) with susceptibility to SLE. Moreover, a significant correlation (OR = 2.249, 95% CI = 1.031–4.904, P = 0.042) was found between the rs7582694 CC genotype and the risk of SLE in the population of Lorestan. Conclusion: Overall, based on the results it can be concluded that there was a relationship between the STAT4 gene G/C (rs7582694) SNP and the increased risk of SLE. However, no association was observed between the above-mentioned gene and anti-dsDNA or ANA that are some of the symptoms of SLE.

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