Showing 12 results for Single Nucleotide Polymorphism
Somayyeh Saadatmand, Ahmad Hamta, Abdorrahim Sadeghi, Fathollah Mohaghghegh,
Volume 17, Issue 12 (3-2015)
Abstract
Background: Estrogen hormone regulates cell proliferation in breast tissue physiologically. Evidences show that changes in estrogen signaling pathways, including the receptor alpha (ER&alpha), happen during breast cancer progression. ER&alpha is expressed in most breast tumors and its association with the development of low-grade tumors has been demonstrated. Single nucleotide polymorphisms (SNPs) in genes may differ in susceptibility to cancer and result in different respond to treatment in different populations. The present study aimed investigated the association between single nucleotide polymorphisms (rs2234693: C/T) in gene ESR&alpha in patients with breast cancer.
Materials and Methods: In this case-control study 150 women with breast cancer and 142 healthy women without a family history of breast cancer were enrolled. DNA was extracted from blood samples. After primer design, technique of PCR-RFLP was used and samples were genotyped by acrylamide gel electrophoresis. Statistical analyzes were performed using SPSS version 20 and chi square test and Final findings were specified.
Results: TT and CT genotypes for ra2234693: C/T site compared with the CC had 5.5 and 1.5-fold increased risk respectively. Statistically significant differences were found between cases and controls for fibrocystic disease and age at menarche.
Conclusion: We not found an association between C/T polymorphism and breast cancer. But CC and TT genotypes of this polymorphism in estrogen receptor alpha gene related with breast cancer that are consistent with the findings of some other researchers.
Zahra Soroush, Amin Karimi, Sadegh Valian Boroujeni,
Volume 18, Issue 10 (1-2016)
Abstract
Background: Hemophilia A is an X-linked bleeding disorder caused by heterogenous mutations in factor VIII gene that encodes coagulation factor VIII (F8) protein. Due to the high heterogeneity of mutations, large size (186 kb) and structural complexity of the F8 gene, direct mutation analysis is costly and time consuming. Alternatively, linkage analysis using informative polymorphic markers such as single nucleotide polymorphism (SNP) markers has been introduced as a rapid and cost effective method for hemophilia A carrier detection in families with an affected individual. Several SNP markers associated with the F8 gene region have been studied.
Materials and Methods: In this exprimental study, the characteristics of A/T SNP (rs4898352) as an informative marker located in intron 18 of F8 gene region was investigated in Isfahanin population. rs4898352 marker was genotyped using tetra primer ARMS PCR method followed by agarose gel electrophoresis in 140 unrelated control healthy females in mentioned population. New primers were designed for rs4898352 marker using the oligo 7 software. The allele frequency, degree of heterozygosity and Hardy-Weinberg equilibrium were estimated by use of Genepop program. The polymorphism information content (PIC) value was estimated using the Powermarker software.
Results: The results showed that the allele frequency of rs4898352 polymorphism for A and T alleles was 0.482 and 0.518, respectively. The observed heterozigosity rate was 60%. Analysis of Hardy-Weinberg Equilibrium demonstrated that the Isfahan population was in equilibrium (p>0.05) for rs4898352 marker. Moreover, analysis of PIC value revealed that this marker could be considered as a highly informative marker in the mentioned population.
Conclusion: Together, the data suggested that rs4898352 could be introduced as an informative marker for molecular diagnosis of hemophilia A in Isfahan Population
Mojtaba Salehi, Seyed Reza Mohebbi, Mehrdad Ravanshad, Maryam Karkhane, Pedram Azimzadeh, Behta Keshavarz Pakseresht,
Volume 18, Issue 12 (3-2016)
Abstract
Background: Hepatitis B virus (HBV) is a member of hepadenaviridae family, which is infectious for humans and a few animal species. Successful clearance and elimination of infection from the body or development of HBV infection to chronic disease depend on the host genetic background in immune system genes. Interleukin-12 (IL12) and also Interleukin-12 Receptor B1 (IL 12 RB1) are the key factors in the spontaneous clearance of viral infections, especially HBV. The aim of the present research is to investigate the association between Interleukin-12 receptor B1 gene polymorphism (rs11575934 A/G) and susceptibility to chronic Hepatitis B virus infection.
Materials and Methods: In this case-control study, genomic DNA of 150 chronic HBV infected patients and 150 healthy controls were extracted from peripheral blood cells. Single nucleotide polymorphism (rs11575934 A/G) was genotyped using polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP).
Results: The frequency of GG, AG, AA genotypes was 6.7%, 40.7%, and 52.7% in chronic patients and 12.7%, 41.3%, and 46% in control group, respectively. No statistically significant difference between case and control groups has been observed (p=0.176).
Conclusion: In the present study, no significant correlation between rs11575934 A/G single nucleotide polymorphism of the IL12RB1 gene and susceptibility to chronic hepatitis B virus infection has been observed. According to the study, this polymorphism does not affect the susceptibility to chronic HBV infection.
Ahmad Hamta, Rezvan Ghadbeigi,
Volume 19, Issue 3 (6-2016)
Abstract
Background: ANKK1 (ankyrin repeat and kinase domain containing 1) gene is a member of the serine/threonine kinase family. This family involved in signal transduction pathways. This gene contains Taq1A (rs1800497) single nucleotide polymorphism. The A1 allele carriers of TaqIA polymorphism have shown reduced DRD2 (Dopamine Receptor D2) receptors. This decrease predisposes individuals to seek for addictive substances to compensate this deficiency in dopaminergic system. The present study investigated TaqIA (rs1800497) polymorphism in heroin and methamphetamine addiction.
Materials and Methods: In this case-control study, 91 male methadone-maintained heroin and methamphetamine addicts and 100 male healthy controls were studied. Genomic DNA extraction was carried out from peripheral blood through salting-out method and individuals were genotyped for TaqIA polymorphism by RFLP-PCR technique and TaqI enzyme was used for RFLP.
Results: This survey revealed the significantly higher frequency of the A1 allele of TaqIA polymorphism in patients than control individuals (p<0.001). The frequency of A1 allele in patient and control individuals was %51 and %22.5, respectively. The A1A1 genotype was detected in 25% of patients and 7% of controls (p<0.001, OR=9.7, 95% CI=3.64-25.85).
Conclusion: The results of this study revealed that the A1 allele of TaqIA polymorphism is significantly associated with heroin and methamphetamine addiction.
Mahyar Nourian, Ali Mohammad Asgharian, Hamid Asadzadeh Aghdaei,
Volume 19, Issue 3 (6-2016)
Abstract
Background: Inflammatory bowel disease (IBD) includes two basic categories ulcerative colitis (UC) and Crohn's disease (CD) that the etiology of which remains unclear. Tumor necrosis factor alpha (TNFα) promoter polymorphisms are a good candidate for susceptibility to IBD as there is a significant relationship between them. The main aim of this study was to assess TNFα gene polymorphisms with IBD susceptibility at positions -1031in Iranian patients.
Materials and Methods: In this case-control study, were studied 101 patients with IBD (86 ulcerative colitis, 15 Crohn's disease) and 100 healthy controls were studied. PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) was used for determining of genotyping. In following, allele frequency and genotype distribution of polymorphism T> C in TNFα gene between the case and control groups were typed.
Results: The frequency of genotype TT, TC and CC among patients was 64.4%, 28.7% and 6.9% and in control group was 63%, 29% and 8%, respectively. Also, allele frequency T-1031 of TNFα gene in IBD patients was high, while there is no statistical significant(p>0.05).
Conclusion: There was no significant correlation between TNFα gene polymorphisms and susceptibility to IBD at position -1031. Our results showed that TNFα gene polymorphisms cannot be considered as a potential prognostic marker cause of IBD in Iranian population.
Nasim Ebrahimi, Sadegh Vallian Borujeni,
Volume 19, Issue 6 (9-2016)
Abstract
Background: Niemann-Pick disease (NPD) refers to a group of lysosomal storage diseases that causes abnormal metabolism of lipids. One of the genes that play a role in the pathogenesis of this disease is SMPD1. To date, more than hundred disease- causing mutations have been identified in SMPD1 gene. Due to the large number of mutations in this gene, direct analysis of the mutations is costly and time-consuming. Therefore, indirect linkage analysis using polymorphic markers as an alternative method for molecular diagnosis of the mutations has been recommended. In the present study, allele frequency of rs1542705 genetic marker was analyzed in the Iranian population. The aim was to determine the polymorphic information content (PIC) and the possibility of its application in indirect diagnosing of NPD.
Materials and Methods: After bioinformatics analysis of the SMPD1 gene region, rs1542705 marker was selected for genotyping in Isfahan population. In order to calculate the allele and genotype frequency of the marker, molecular tests were done on 113 DNA samples of unrelated healthy individuals by using ARMS-PCR technique. Finally, the information related to the genotype of the individuals was statistically analyzed using Powermarker and Genepop software.
Results: The analyses showed that the studied population was in accordance with Hardy-Weinberg equilibrium. Allele frequency of rs1542705 marker for T and C alleles was 71.24% and 28.76%, respectively, and the heterozygosity of the marker was 43.36%. Also, polymorphic information content (PIC) was 0.325.
Conclusion: The results of this study showed that rs1542705 marker could be considered as an informative marker for molecular diagnosis of Niemann- Pick disease using linkage analysis in the studied population.
Hamta Ahmad, Ansari Jamshid, Bayati Zahra,
Volume 19, Issue 7 (10-2016)
Abstract
Background: Breast cancer is both the prevailing malignancy and the most common cause of cancer death among women. Many factors may play a role in the susceptibility to the breast cancer and Oxygen Free Radicals may be one of these. There are various known antioxidant systems against oxidative stress, including ParaoxonaseI. The aim of this study was to investigate the association between rs854560 polymorphism in the PON1 gene in patients with breast cancer.
Materials and Methods: We performed genotyping analysis using polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) assay in a case–control study of 83 confirmed breast cancer patients and 100 cancer-free controls in Markazi Province.
Results: In our study of the PON1 gene L55M polymorphism, the LL genotype was found in 2 (2.40%) patients, whereas the LM genotype was found in 69 (83.13%) patients. The MM genotype was present in 12 (14.45%) patients. In the control group, LL, LM and MM genotypes were found in 4 (4%), 81 (81%), and 15 (15%) subjects, respectively. There was no statistically significant difference between patient and control groups in terms of the PON1 gene L55M polymorphism (p= 0.825). Allele distributions were different but this difference did not reach statistical significance (p= 0.920).
Conclusion: We found no association between M55L polymorphism and breast cancer.
Rokhsareh Meamar, Maryam Ostadsharif, Ahmad Chitsaz, Mojgan Asadian Ghahfarokhi, Mehdi Kazemi, Seyed Morteza Javadirad,
Volume 20, Issue 4 (7-2017)
Abstract
Abstract
Background: Vitamin D was recognized with protective effects on nerve cells of Parkinson’s patients. The relationship between several VDR gene polymorphisms and age and risk of the disease was determined. Also, the relationship between VDR gene FOKI genotypes and PD was specified. The main goal of this study is to evaluate the relationship between polymorphic loci of FokI, TaqI, BsmI, ApaI and serum factor related to vitamin D metabolism in Isfahan population.
Materials and Methods: Case- control study of 125 Parkinson’s patients with their matched control individuals has been investigated based on Parkinson's disease brain bank criteria of Great Britain. After receiving consent, serum levels were measured. The genetic material was isolated by Miller protocol and polymorphisms has been analyzed and confirmed by repeated PCR-RFLP.
Results: Comparing the five serum factors between healthy subjects and patients with Parkinson's disease, we have shown a significant reduction in the levels of calcium, ALP and PTH (p<0.01). However, none of the levels of vitamin D and phosphate show any kind of significant relationship between patients and control subjects. Concentration of blood serumic factors including calcium and PTH showed p-values less than 0.01 between Parkinson's patients and control subjects according to different genotypes containing FokI-F allele,ApaI-A allele and BsmI-b allele .
Conclusion: The result of this study showed that each of FokI and ApaI recessive alleles can influence serum calcium and parathyroid hormone between healthy individuals and Parkinson's patients significantly.
Bita Kaviani, Hossein Sazegar, Noosha Zia-Jahromi, Farzane Mohamadi Farsani,
Volume 20, Issue 11 (2-2018)
Abstract
Abstract
Background: The aim of this study is to investigate the role of rs137852599 single-nucleotide polymorphism in the androgen receptor coding gene on drug resistance against treatment with Enzalutamide in individuals diagnosed with prostate cancer.
Materials and Methods: In this case-control study, the ARMS-PCR analysis was conducted on androgen receptor coding gene in 50 patients diagnosed with prostate cancer with drug resistance and on 50 patients diagnosed with prostate cancer without drug resistance. The statistical analyses were performed using the GeNePop server and then the results were investigated by the SISA server.
Results: The allele frequencies of A and C alleles in rs137852599 were 0.78 and 0.22 for drug resistant and 0.94 and 0.06 for non-drug resistance groups. The results indicated that there is a meaningful relationship between drug resistance and rs137852599 single-nucleotide polymorphism
(p = 0.020).
Conclusion: The existence of single-nucleotide polymorphisms may result in drug resistance in individuals diagnosed with prostate cancer. Therefore, investigation of the existence of such polymorphisms can be effective in prescription of suitable drugs for these patients.
Ahmad Hamta, Milad Pezeshki, Jamshid Ansari,
Volume 20, Issue 12 (3-2018)
Abstract
Abstract
Background: Biological and epidemiological data suggest that damage induced by endogenous and exogenous factors affects the integrity and stability of DNA and associated with susceptibility to breast cancer. The XRCC3 protein participates in DNA double-strand breaks and recombination repair. The aim of the present study was to evaluate associations between the risk of breast cancer and Thr241Met polymorphism in the XRCC3 gene.
Materials and Methods: In this study, the effects of Thr241Met polymorphism of the XRCC3 gene and the risk of breast cancer in a population-based case-control study inclusive 80 patients and 80 healthy individuals of women in Markazi province were evaluated. Genomic DNA was extracted from blood samples using the kit procedure. The genotypes of samples were determined by PCR-RFLP technique. Statistical analysis was done using SPSS software (estimation of χ2 and p-value) and the final results were determined.
Results: Statistically significant difference was observed between the two groups of patients and controls for three genotypes of the site rs861539 (p= 0.000). Genotype CT (p= 0.000, OR=2.352, CI= 95%; 2.431 - 39.948) and TT (p = 0.003, OR= 2.352, CI=95%; 0.611 - 9.049) significant associations were showed with risk of breast cancer. Instead, the genotype CC (p= 0.000) showed a protective role against susceptibility to breast cancer.
Conclusion: This study identified that there is significant association between Thr241Met polymorphisms of the XRCC3 and the risk of susceptibility to breast cancer, which is in accordance to some of researchers' studies.
Ahmad Hamta, Sahar Adl,
Volume 24, Issue 1 (3-2021)
Abstract
Background and Aim: Breast cancer is the most common cancer type and the leading cause of cancer-induced deaths in women, worldwide. The Fibroblast Growth Factor Receptor 2 (FGFR2) is a tyrosine kinase receptor that plays an essential role in the growth, invasion, movement, and angiogenesis of tumor cells. Several single nucleotide polymorphisms have been found in the intron 2 of the FGFR2 gene, i.e., associated with a high risk of breast cancer. Genetic variation in this receptor is a new risk factor for breast cancer. The current study aimed to evaluate the association of single-nucleotide polymorphism rs2981582C/T in women with breast cancer.
Methods & Materials: In total, 80 women with breast cancer and 80 healthy women (controls) were selected from Markazi Province, Iran to participate in this research. Polymorphism rs2981582 was analyzed to investigate its association with breast cancer. DNA extraction from blood samples was performed using a kit. The presence of these single-nucleotide polymorphisms was determined by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR - RFLP). Statistical analyses were performed by SPSS using Chi-squared test at P≤0.05.
Ethical Considerations: This study was approved by the Ethics Committee of the Arak University (Code: IR.ARAKMU.REC.1395.28).
Results: Significant differences were observed in the frequency of rs2981582 polymorphism in the FGFR2 gene between the control and patient groups (P=0.000). In the patient group, the TT genotype was significantly associated with the risk of breast cancer (P=0.001; OR=3.566). On the other hand, allele C indicated a protective role against the disease (P=0.000).
Conclusion: The obtained data revealed a significant relationship between rs2981582 C/T polymorphism and the risk of breast cancer; thus, this single-nucleotide polymorphism could be used as a biomarker to predict breast cancer.
Seyedeh Zahra Shifteh, Doctor Ahmad Hamta,
Volume 26, Issue 1 (4-2023)
Abstract
Introduction: Breast cancer is a highly heterogeneous disease. The antigen molecule of four cytotoxic T-lymphocytes is involved in inhibition of T cell response and immune response regulation. Single nucleotide polymorphisms in the CTLA4 gene can affect the expression of the aforementioned molecule. The aim of this study was to investigate the polymorphisms of rs4553808 and rs733618 of CTLA4 gene with the risk of breast cancer.
Methods: In this study to investigation polymorphisms, the DNA of 80 patients with breast cancer and 80 healthy individuals in central province of ARAK were extracted from peripheral blood. Then, PCR-RFLP technique was used. The results were analyzed using SPSS software and SNP Analyzer. This study was approved by the Ethics Committee of the Arak University (Code: Ir.arakmu.rec.1396.25).
Results: Statistical analysis rs4553808 polymorphism showed no significant increase in the risk of patients with GG genotype compared with the control group (OR = 2/013, CI = 95% 1/721-2/353). Also, heterozygotes AG genotype analysis did not show any relationship between the genetic diversity and breast cancer (OR = 1/204, CI = 95% 0/604-2/402). The combination of AG + GG genotypes did not show any significant correlations (OR = 1/130, CI = 95% 0/569-2/242). Statistical analysis for rs733618 polymorphism showed increase in the risk of breast cancer. The results indicate that the TC (OR = 2/992, CI = 95% 1/280-1/998) showed a significant relationship between the genetic diversity and breast cancer. The analysis of the combined CC and TC genotypes was associated with increased risk for breast cancer compared to TT genotypes (OR = 0/334, CI = 95%; 0.143-0.782, P = 0.009). Considering that the distribution of CC and TC genotypes was significant between the two groups of control and the patient, so the frequency of TT genotype with the same amount of P = 0.001 was significant between the two groups of control and the patient.
Conclusions: There was a significant relationship between the genotypes rs733618 polymorphism and breast cancer. However, there was no significant relationship between rs4553808 polymorphism and breast cancer risk.
