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Showing 8 results for Single Nucleotide Polymorphism
T-138C and A-7G polymorphisms in the MGP gene and the association with coronary arthery disease: Iranian patients
Abiri M, Sadeghian S, Hakki E, Boroumand Ma, Mehdipour P, Izadi M, Keramatipour M,
Volume 67, Issue 2 (5-2009)
Abstract

Normal 0 false false false EN-GB X-NONE AR-SA MicrosoftInternetExplorer4 Background: Coronary Artery Disease (CAD) is a major cause of death worldwide including Iran.  The risk of developing disease in patients without symptoms is assessed in part by factors that are associated with disease. Among these factors family history points to the significance of genetic component in the risk of CAD. The identification of the genetic variants that confer risk for CAD is essential for detecting high-risk individuals, so preventative life style and therapeutic action can be taken before overt disease develops. So far more than 100 genes have been reported with possible role in developing risk for CAD. Matrix- Gla Protein (MGP) is one of these genes that association of its single nucleotide polymorphism (SNP) with CAD has been reported.  Among the polymorphisms, there are two promoter SNPs at position -7 & -138 that their association with CAD has been reported before. Here we investigated the association of these SNPs with CAD in Iranian population.
Methods: 150 cases and 150 controls were selected on the basis of their clinical assessments and angiographic reports. DNA was extracted from blood samples. The genotypes for both SNPs were determined using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method with size fractionation on Polyacrylamide gel.
Results: The comparison of allele & genotype frequencies between patients and controls showed that there is an excess of A allele at position -7 and T allele at position -138 among patients, although these differences were not significant (p<0.2, and p<0.5 respectively).
Conclusions: This study suggests no association of these SNPs with CAD in Iranian population. Confirmation of this finding needs independent repeat of similar studies.
Keywords: Coronary Artery Disease (CAD), Matrix Gla Protein (MGP), Single Nucleotide Polymorphism (SNP).


The -351A>G genetic polymorphism in the estrogen receptor alpha gene and risk of endometriosis: a case-control study
Reihaneh Asadi , Parisa Mohamadynejad , Fatemeh Davari Tanha , Mahdi Safarpour , Ahmad Ebrahimi ,
Volume 72, Issue 12 (3-2015)
Abstract
Background: The major issue to address in endometriosis etiology is to identify the genetic changes in the disease and their occurrence in different populations. Uncovering these genetic changes may be important in developing potential biomarkers for early diagnosis and prognosis of endometriosis. Among all endometriosis susceptibility genes studied before, convincing association has been found with variants in the estrogen receptor alpha (ESR1) gene and this disease however, the contributions of these genetic variants in different populations and ethnic groups are not similar. Accordingly, this study was carried out to replicate the previous findings to assess whether this polymorphism is associated with endometriosis in Iranian women. Methods: A case-control study was designed to determine the possible association between ESR1-351A>G variant and occurrence of endometriosis. The study group consisted of 100 subjects diagnosed with endometriosis as case group and 100 fertile women without endometriosis as controls recruited from subjects referred to the Tehran Women’s General Hospital between January to September 2013. All subjects were genotyped for this marker using amplification refractory mutation system- polymerase chain reaction (ARMS-PCR). Association of risk allele (G) with endometriosis was as-sessed using PLINK software after age adjustment. Results: The results showed that the genotype frequencies were in Hardy-Weinberg Equilibrium (HWE) in both case (F=0.04, P:0.67) and control (F=0.02, P:0.83) groups. In addition, there were no significant differences between case and control groups in terms of genotype frequencies (P=0.17). Moreover, the results indicated that the presence of risk allele (G) did not significantly increase risk of endometriosis (OR: 1.43, 95%CI: 0.96-2.13, P=0.07). Conclusion: The results do not support the previous findings of an association between -351A>G genetic polymorphism in ESR1 gene and endometriosis. Therefore, comprehensive genetic approaches including linkage analyses and family-based tests, together with a number of replication studies with large sample size, are needed to make conclusive claims about the role of this genetic polymorphism in susceptibility to endometriosis.
From genome to gene: A review of genes and genetic variations associated with type 2 diabetes
Mahdi Safarpour , Ahmad Ebrahimi , Maryam Sadat Daneshpour ,
Volume 73, Issue 9 (12-2015)
Abstract

Despite the valuable results achieved in identification of genes and genetic changes associated with type 2 diabetes (T2D), lack of consistency and reproducibility of these results in different populations is one of the challenges lie ahead in introduction of T2D candidate genes. Therefore, the present review article aimed to provide an overview of the most important genes and genetic variations associated with development of T2D based on a systematic search in well-known genetic databases. For this purpose, the National Center for Biotechnology Information, Database of Genotypes and Phenotypes (NCBI dbGaP) and Human Genome Epidemiology Network (HuGENet) database were searched to find the most important genes associated with T2D. In addition, a gray literature search was conducted to collect any available information released by laboratories offering genetic tests such as deCODE genetics and 23andMe. Candidate genes were selected among the results of all databases based on the highest level of similarity. Subsequently, without any time restriction, PubMed, Scopus and Google scholar databases were searched using relevant Medical Subject Headings (MeSH) terms to access related articles. The relevant articles were screened to make a conclusion about the genes and genetic variations associated with T2D. The results revealed that four selected candidate genes, in order of importance, were TCF7L2, CDKAL1, KCNJ11, and FTO. The most significant single nucleotide polymorphism (SNP) associated with T2D in the TCF7L2 gene was rs7903146 however, the results showed a wide range of variation from slight association in the Amish (P= 5.0×10-2) to strong association in European descent populations (P= 2.0×10-51). Then, rs10440833 mapping to the intronic region of the CDKAL1 gene showed significant association with T2D (P= 2.0×10-22). In the KCNJ11 gene, a missense variation (rs5215) in exon one was found to have the highest association with T2D compared with other SNPs discovered in this gene (P= 5.0×10-11). Finally, rs8050136 located in the first intron of the FTO gene had the strongest association with T2D (P= 2.0×10-17). On the basis of these results, it can be concluded that the current study can be introduced as a model for achieving well-documented results among spectrum of information available in genetic databases based on a systematic search strategy. The candidate genes and genetic variations presented in this review article might be applied for early diagnosis, prevention, and treatment of T2D.


Association of FABP2 gene polymorphism (rs1799883) with risk of obesity in the Tehran Lipid and Glucose Study (TLGS) population
Vahid Moslehizadeh , Farzam Ajamian , Ahmad Ebrahimi , Hossein Delshad Siahkali ,
Volume 73, Issue 12 (3-2016)
Abstract

Background: The major issue to address in obesity etiology is to identify the genetic changes in the disease and their occurrence in different populations. Uncovering these genetic changes may be important in developing potential biomarkers for early diagnosis and prognosis of obesity. Among all obesity susceptibility genes studied before, convincing association has been found with variants in the FABP2 gene and this disease; however, the contributions of these genetic variants in different populations and ethnic groups are not similar. Accordingly, this study was carried out to replicate the previous findings to assess whether a missense variation (rs1799883) in this gene is associated with obesity in the Tehran Lipid and Glucose Study (TLGS) population.

Methods: A case–control study was designed to determine the possible association between rs1799883 and occurrence of obesity “in phase IV of the study between the years of 2008 to 2011”. The study group consisted of 217 subjects with body mass index (BMI, kg/m2) greater than 30 as cases and 159 healthy individual as control group (1820). All subjects were recruited among the Tehran Lipid and Glucose Study (TLGS) participants in phase IV of the study between the years of 2008 to 2011. The genomic DNA was extracted from peripheral blood leucocytes using the salting out method and subsequently subjects were genotyped for this marker using The tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Association of risk allele with obesity was assessed using the SPSS software, version 20 (Chicago, IL, USA).

Results: The results showed no significant differences between case and control groups in terms of allele frequency (P=0.61). According to the findings, the presence of T allele as the risk allele was not associated with increased risk of obesity in carriers of this allele compared to individuals carrying the normal allele (OR=1.17; CI%95= 0.62-2.19, P=0.61).

Conclusion: The results did not support the previous findings of an association between genetic polymorphism in the FABP2 gene and risk of obesity. However, a number of replicated studies with other ethnicity are suggested to make a conclusion about the role of this genetic polymorphisms and susceptibility to obesity in Iranian population.


TOX3 Gene polymorphisms and breast cancer; effects and implications of the variations: review article
Amir Tajbakhsh, Fahimeh Afzal Javan , Mostafa Fazeli, Mahdi Rivandi, Mohammad Mahdi Kushyar, Mohammadreza Nassiri, Alireza Pasdar,
Volume 75, Issue 5 (8-2017)
Abstract
Breast carcinoma is the most common cause of cancer mortality among women globally. Primary and secondary prevention through avoiding known risk factors, screening for early detection of tumors with different methods as well as timely treatment, can be effective in reduction of the burden of this devastating disease. This can in turn prevent death and also increase survival in patients with breast cancer. Both environmental and genetic factors are involved in the pathogenesis of breast cancer. Multiple genetic factors can influence the risk and development of breast cancer. Identification of genetic variants including single nucleotide polymorphisms (SNPs), which are associated with the risk of breast cancer development, are mostly done through genetic association studies. It is demonstrated that SNP allele frequencies vary amongst different populations. It has been shown that genetic risk factors like variations in TOX high mobility group box family member 3 (TOX3), which affect the liability for neoplasm, play an important role in the development of breast cancer. Although TOX3 is expressed mainly in the brain, its expression in other tissues especially breast has also been reported. TOX3 maps to chromosome 16q12 and encodes the nuclear high-mobility group (HMG)-box. It has calcium (Ca2+)-dependent transcriptional activities and is a co-factor of cAMP response element (CRE)-binding protein (CREB) and CREB-binding protein (CBP). TOX3, activated with Ca2+, is related with activation of the promoter of some other genes including BCL2 and C3 complement and also CITED1 gene expression. It also induces activation of the c-fos promoter and therefore its expression. Genome-wide association studies (GWAS) in different populations including European, Asian and African-American have demonstrated that a SNP near its 5ʹ end and the promoter of TOX3 gene appears to be significantly associated with breast cancer susceptibility. Furthermore, breast cancer–associated SNPs lead to enhanced FOXA1 bindings and in turn, a reduction in TOX3 gene expression. This review has highlighted the importance of TOX3 function, SNPs and its association with breast cancer risk and also its potential effects on breast cancer treatment; TOX3 plays dual and somehow conflicting roles in cancer initiation and progression which remains to be further investigated.

Study of the association FokI polymorphisms of the XRCC3 gene with the risk of breast cancer in women: brief report
Milad Pezeshki , Jamshid Ansari ,
Volume 76, Issue 10 (1-2019)
Abstract
Background: Breast cancer is one of the most common worldwide malignancies among women. Biological data suggest that damage induced by endogenous and exogenous factors affects the integrity of DNA and associated with susceptibility to breast cancer. Single nucleotide polymorphisms (SNPs) in DNA repair genes can associated with differences in the repair efficiency of DNA damage and may affect breast cancer. The XRCC3 protein participates in DNA double-strand breaks and recombinational repair, in other words the product of XRCC3 gene, plays a key role in homologous recombination repair of DNA double-strand breaks. The polymorphism of FokI plays critical roles in breast cancer development. The aim of the present study was to evaluate associations between the risk of breast cancer and FokI polymorphism in the XRCC3 gene.
Methods: This case-control study was carried out on the women with breast cancer and healthy women located in Markazi province at Arak University Research, Iran, from October 2016 to March 2017. In the present study, the association of FokI polymorphisms and the risk of breast cancer was assessed by Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. In this method, genomic DNA was extracted from blood samples using the kit procedure. Then, PCR was performed and the SNP-containing DNA amplicons were subjected to digestion of enzymes. Following digestion, each sample was immediately analyzed by 3% agarose gel electrophoresis. Statistical analysis was done using SPSS and SNP Analyzer softwares and the final results were determined.
Results: No statistically significant difference was observed between the two groups of patients and controls for three genotypes the site rs1799794 (P=0.435). Genotype AG (P=0.384, OR=0.614, CI=95%, 0.205-1.840) and GG (P=0.867, OR=0.911, CI=95%; 0.308-2.699) had no significant associations with risk of breast cancer.
Conclusion: There was no significant association between FokI polymorphisms of the XRCC3 and risk of susceptibility to breast cancer, which was in accordance to some researchers. FokI polymorphisms of XRCC3 gene cannot be used as a biomarker in clinical predictive studies in relation to risk of breast cancer.

Investigating the correlation between the frequency of single nucleotide polymorphisms in the IFNAR2 gene with the severity of the Covid-19 disease
Mahnaz Safari, Pooneh Rahimi, Akram Sadat Tabatabaee Bafroee,
Volume 81, Issue 8 (11-2023)
Abstract
Background: Understanding the complex processes of the immune system in dealing with the covid-19 infection, which is probably related to polymorphisms in cytokine and chemokine genes, can explain the pro-inflammatory condition of patients. Accordingly, in the present study, the correlation between the frequency of single nucleotide polymorphisms in the pro-inflammatory IFNAR2 gene and the severity of the disease of COVID-19 was investigated.
Methods: This research was reviewed by the ethics committee of the Pasteur Institute of Iran and was approved by this committee with the ethics code IR.PII.REC.1400.042. and continued from December 2021 to November 2022. This study was conducted on 954 patients with COVID-19, who were divided into two groups: those who recovered and those who died. COVID-19 infection in all 954 volunteers has been confirmed through rtReal Time-PCR of oropharyngeal or nasopharyngeal swabs.After taking blood samples from patients and extracting DNA, IFNAR2 gene was amplified using specific primers. Then RFPL method and Cac8I restriction enzyme were used to investigate rs2236757 polymorphisms in IFNAR2 gene. Genotype of people was determined according to the pattern of formed bands. The results were statistically analyzed using SPSS software.
Results: Calculation of genotypic frequency of rs2236757 polymorphism in IFNAR2 gene showed that in general 21% of cases had AA genotype, 47% GA genotype and 32% GG genotype. The allelic frequency of this polymorphism showed that 56% of cases had G allele and 44% had A allele. In investigating the correlation of rs2236757 polymorphism in IFNAR2 gene with the severity of the disease of Covid-19, the OR value for the GG genotype was equal to 1, which indicates the absence of the role of this polymorphism in the severity of the disease. On the other hand, A allele was significantly more in recovered people than in deceased people, and the value of OR<1 also confirmed this issue.
Conclusion: The results showed that rs2236757 in the IFNAR2 gene is related to the reduction of disease severity, which indicates the important role of genes related to inflammatory responses, as well as the role of genetic variants of these genes in the severity of COVID-19.

Investigating the association between K589E polymorphism of EXO1 gene with the susceptibility lung malignancy as a prognostic marker in the Iranian population
Jamshid Ansari, Milad Pezeshki, Azam Ahmadi, Ali Chehrei,
Volume 81, Issue 9 (12-2023)
Abstract
Background: Lung cancer has the highest incidence and mortality rate of all cancers worldwide. In Iran, it is one of the commonly diagnosed malignancies, and its frequency is increasing rapidly. Genetic variants in DNA repair genes are linked to differences in efficiency of repairing DNA damage, which can influence lung cancer susceptibility. EXO1 is a key gene involved in the mismatch repair pathway. The K589E polymorphism in EXO1 may alter the DNA repair activity of the encoded protein and impact lung cancer risk. The aim of this study was to investigate associations between the K589E polymorphism in EXO1 and lung cancer risk in the Iranian population, and evaluate its potential as a prognostic biomarker.
Methods: This case-control study was conducted to investigate EXO1 K589E variant with susceptibility to lung malignancy in the Iranian population. One hundred patients with lung cancer as a patient group and 100 healthy individuals from Khansari Hospital located in Markazi province were studied, from January 2020 to May 2022. DNA extraction from blood samples of participants was done using a kit.  Genotype determination of both patient and control groups was done using PCR-RFLP technique. Finally, statistical results were analyzed using SPSS software and the logistic regression method.
Results: Genotype and allele frequency  analysis showed the AA genotype (P=0.004, OR=5.391, 95% CI: 1.690-17.200) and A allele (P=0.010, OR=2.851, 95% CI: 1.291-6.300) were correlated with susceptibility to lung cancer. On the other hand, people carrying the G variant allele had a lower risk of lung cancer.
Conclusion:  In summary, this study found the AA genotype and A allele of K589E in EXO1 are correlated with risk of lung cancer in Iranians, while the G allele has protective effects. The K589E polymorphism may serve as a prognostic biomarker for lung cancer susceptibility, but more studies with high population size are required.

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