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.

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.

scholarly journals Single-Nucleotide Polymorphism of rs11061971 (+219 A>T) in Adiponectin Receptor 2 (AdipoR2) Gene and Its Association with Risk of Type 2 Diabetes Among an Iranian Population ​

2021 ◽  
Author(s):  
Masoud Tahani ◽  
Mohamad Taghi Goodarzi ◽  
Ali Asghar Ahmadi ◽  
Mohammad Hossein Hasani ◽  
Alireza Farrahi ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Single Nucleotide Polymorphism ◽  
Adiponectin Receptor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Adiponectin Receptor 2 ◽  
Genetic Modifications ◽  
Significant Difference

Abstract Genetic modifications in the adiponectin receptor 2 (AdipoR2) gene can affect phenotypes associated with insulin resistance and diabetes. The purpose of this study was to evaluate the possible role of genetic modifications in the AdipoR2 gene, to determine the frequency of genotypes and polymorphism alleles of this gene at rs11061971 (+ 219 A > T), and to investigate its correlation with type 2 diabetes (T2D) and its related metabolic profile. In this case-control study, the single-nucleotide polymorphism (SNP) of interest in 116 T2D patients and 102 controls was evaluated using RFLP PCR and FOK 1 enzyme. Fasting blood sugar, cholesterol, triglyceride, insulin, HDL-C, LDL-C and HbA1c were also measured and their correlation with the studied genetic modifications was assessed. The collected data were analyzed using Chi-square test and Hardy-Weinberg equation. There was a significant association in AT and TT genotypes in rs11061971 (+ 219 A > T) with T2D. However, no significant difference was observed in the frequency of alleles between the case and control groups. In addition, in LDL-C and total cholesterol in the control group, there was a significant difference between AA and TT genotypes as well as with AA and AT genotypes. However, no correlation was found between the other serum studied parameters and the genotype of individuals in the rs1106197171 polymorphism. The role of rs11061971 (+ 219 A > T) polymorphism in T2D incidence seems to be strong. This study showed that AT and TT genotypes versus AA genotype increase the risk of diabetes.

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.

Genetic Association of FTO rs9939609 Polymorphism with Hypertension in Pakistani Population

2021 ◽  
Vol 15 (11) ◽  
pp. 2985-2988
Author(s):  
Sobia Tabassum ◽  
Sadaf Mushtaq ◽  
M. Naveed Anwar ◽  
H. Achakzai ◽  
Naseer Ahmed ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Medical Condition ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphism ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Pakistani Population ◽  
Significant Difference ◽  
Mutation System ◽  
Fto Rs9939609

Background: Hypertension is a medical condition that often occurs parallel to diabetes and obesity. Previously, the role of fat mass and obesity associated (FTO) gene rs9939609 polymorphism (c.46-23525T>A) with obesity has been reported while prevalence and etiological differences exist among different regions and ethnic groups. Aim: To investigate the association of FTO rs9939609 SNP with hypertension in Pakistani population. Study design: Cross-sectional study. Place and duration of study: Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan from 1st January 2019 to 31st December 2020. Methodology: One hundred and ten diagnosed hypertension patients along with 128 healthy volunteers were selected randomly. The single nucleotide polymorphism was analyzed using Amplified Refractory Mutation System-Polymerase Chain Reaction. Results: In hypertension patients, females were found to be relatively more affected and average blood pressure lies in stage 1. However, we found no significant difference in genotypic frequencies of FTO rs9939609; TT (22.6%), AA (39.6%) and AT (37.8%) and TT (17.18%), AA (39.06%), and AT (43.75%) among HT and controls, respectively. The p and OR values for risk type genotype (AA) are 0.4697 and 0.7700 (95% CI=0.3788-1.565), respectively. Subsequently, the high percentage (60.0 %) of risk genotype (AA) was found in obese-body mass index in hypertension patients. Conclusion: FTO rs9939609 single nucleotide polymorphism may not be a genetic risk factor associated with onset of hypertension directly and is linked with obesity in Pakistani patients. Keywords: FTO, Hypertension, Obesity, Pakistani patients, rs9939609

Prediction of prognosis in patients treated with everolimus for extrapancreatic neuroendocrine tumors by a single nucleotide polymorphism in PHLPP2.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 163-163 ◽  
Author(s):  
Seth Albert Bellister ◽  
Yunfei Zhou ◽  
Eric Sceusi ◽  
Lee M. Ellis ◽  
James C. Yao
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Neuroendocrine Tumors ◽  
Single Agent ◽  
Progression Free Survival ◽  
Wild Type ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Subset Analysis ◽  
Significant Difference

163 Background: Rapamycin analogs (rapalogs) have improved outcomes in patients with neuroendocrine tumors (NETs). Few factors affecting response to rapalogs have been characterized. PHLPP2 is a phosphatase that inhibits PI3K-Akt-mTOR signaling. We hypothesized that an inactivating single nucleotide polymorphism (SNP) in PHLPP2 may affect outcomes in NETs treated with the rapalog everolimus. Methods: Blood was collected from 32 patients enrolled in a Phase 2 single arm trial of single agent everolimus in patients with NETs. DNA was extracted and RT-PCR products were sequenced to detect the L1016S SNP in PHLPP2. Outcomes analyses determined the role of the SNP in predicting progression-free survival (PFS), overall survival (OS), and response rates (RR) in patients with NETs treated with everolimus. Response rate (RR) assessed by RECIST criteria was evaluated as a binomial endpoint. A subset analysis was conducted to evaluate the NET site-specific role of the SNP. Results: Overall median PFS was 15.2 months (95% Confidence Interval (CI)=11.5 -18.7). The PHLPP2 SNP did not predict for a significant difference in PFS (Median PFS; wild type vs. SNP 16.8 (95% CI=14-20) vs. 11.3 (95% CI=4-19) mos., respectively, Hazard Ratio (HR)=1.2 (95% CI=0.5-3.1)), p=0.154). In a subset analysis, patients with extra-pancreatic NETs treated with everolimus with wild type PHLPP2 demonstrated increased PFS compared to patients with the SNP (Median PFS = 16.8 (95% CI=7-26) vs. 7.7 (95% CI=6-9) mos., HR=10.8 (95% CI=2-67), p=0.002). OS and RR were unaffected by the presence of the SNP in all analyses. Conclusions: In this preliminary study, the L1016S SNP in PHLPP2 may be prognostic for poorer PFS in patients with extrapancreatic NETs treated with everolimus. This study is hypothesis generating and requires validation in larger retrospective and randomized, placebo controlled studies in patients with NETs treated with everolimus.

scholarly journals Prevalence of ACSL (rs6552828) polymorphism among runners

2019 ◽  
Vol 24 ◽  
pp. 121-128
Author(s):  
Sigal Ben-Zaken ◽  
Yoav Meckel ◽  
Dan Nemet ◽  
Alon Eliakim
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Basis ◽  
Maximal Oxygen Consumption ◽  
Professional Athletes ◽  
Distance Runners ◽  
Nucleotide Polymorphism ◽  
Long Distance ◽  
Single Nucleotide ◽  
The Common

The ACSL A/G polymorphism is associated with endurance trainability. Previous studies have demonstrated that homozygotes of the minor AA allele had a reduced maximal oxygen consumption response to training compared to the common GG allele homozygotes, and that the ACSL A/G single nucleotide polymorphism explained 6.1% of the variance in the VO2max response to endurance training. The contribution of ACSL single nucleotide polymorphism to endurance trainability was shown in nonathletes, however, its potential role in professional athletes is not clear. Moreover, the genetic basis to anaerobic trainability is even less studied. Therefore, the aim of the present study was to examine the prevalence of ACSL single nucleotide polymorphism among professional Israeli long distance runners (n=59), middle distance runners (n=31), sprinters and jumpers (n=48) and non-athletic controls (n=60). The main finding of the present study was that the ACSL1 AA genotype, previously shown to be associated with reduced endurance trainability, was not higher among sprinters and jumpers (15%) compared to middle- (16%) and long-distance runners (15%). This suggests that in contrast to previous studies indicating that the ACSL1 single nucleotide polymorphism may influence endurance trainability among non-athletic individuals, the role of this polymorphism among professional athletes is still not clear.

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