scholarly journals Single nucleotide polymorphisms associated with gastric cancer in Iranian patients

2021 ◽  
Vol 7 (2) ◽  
pp. e37-e37
Author(s):  
Arash Alghasi ◽  
Gholamreza Farnoosh ◽  
Ali Saeedi Boroujeni ◽  
Mohammad Bahadoram ◽  
Sima Tahmaseby Gandomkari ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Nucleotide Polymorphisms ◽  
Caspase 9 ◽  
Northern Iran ◽  
Single Nucleotide ◽  
C677t Mthfr ◽  
Increased Risk ◽  
Iranian Patients

Gastric cancer is one of the leading worldwide cancers formed in the lining of the stomach, and is the most prevalent cancer in northern Iran. Recent interventions for the early diagnosis of gastric cancer are based on genetic susceptibility parameters and the interactions between genes and the environment. Accordingly, this narrative review was designed to summarize the genetic markers involved in Iranian patients with gastric cancer, classified by cellular function. There was a significant relationship between single nucleotide polymorphisms (SNPs) in rs1051208 C allele (RAF1), rs531564 (pri-miR-124-1), rs1053023 (STAT3), rs8193 C allele (CD44), rs3130932G allele (OCT4), rs283821943, rs2032586 (ABCB1), codons 72,248 (p53), -137 G/C (IL-18), Pro12Ala (PPARγ), rs1053023 (STAT3), rs4647603 (caspase 3), -712C>T (caspase 9), -1263 A> (caspase 9) and gastric cancer. Increased risk was observed in C677T (MTHFR). Finally, decreased risk of gastric cancer was explored in -938 C>A (bcl2). Asp299Gly (TLR-4), rs1028181-513T/C (IL-19) Pro12Ala (PPARγ) may play a crucial role in susceptibility of Helicobacter pylori and gastric pathogenesis. According to the findings, the genetic polymorphisms in the immune-associated genes were related to the gastric cancer among the Iranian patients. Therefore, further large-scale functional investigations are needed to draw definite conclusions.

scholarly journals DNA Melting Analysis for Detection of Single Nucleotide Polymorphisms

2001 ◽  
Vol 47 (4) ◽  
pp. 635-644 ◽  
Author(s):  
Robert H Lipsky ◽  
Chiara M Mazzanti ◽  
Joseph G Rudolph ◽  
Ke Xu ◽  
Gopal Vyas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dna Melting ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Efficient System ◽  
Gradient Gel Electrophoresis ◽  
Melting Analysis ◽  
Scale Detection

Abstract Background: Several methods for detection of single nucleotide polymorphisms (SNPs; e.g., denaturing gradient gel electrophoresis and denaturing HPLC) are indirectly based on the principle of differential melting of heteroduplex DNA. We present a method for detecting SNPs that is directly based on this principle. Methods: We used a double-stranded DNA-specific fluorescent dye, SYBR Green I (SYBR) in an efficient system (PE 7700 Sequence Detector) in which DNA melting was controlled and monitored in a 96-well plate format. We measured the decrease in fluorescence intensity that accompanied DNA duplex denaturation, evaluating the effects of fragment length, dye concentration, DNA concentration, and sequence context using four naturally occurring polymorphisms (three SNPs and a single-base deletion/insertion). Results: DNA melting analysis (DM) was used successfully for variant detection, and we also discovered two previously unknown SNPs by this approach. Concentrations of DNA amplicons were readily monitored by SYBR fluorescence, and DNA amplicon concentrations were highly reproducible, with a CV of 2.6%. We readily detected differences in the melting temperature between homoduplex and heteroduplex fragments 15–167 bp in length and differing by only a single nucleotide substitution. Conclusions: The efficiency and sensitivity of DMA make it highly suitable for the large-scale detection of sequence variants.

scholarly journals Single Nucleotide Polymorphisms inmiR-122Are Associated with the Risk of Hepatocellular Carcinoma in a Southern Chinese Population

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Chunhua Bei ◽  
Shun Liu ◽  
Xiangyuan Yu ◽  
Moqin Qiu ◽  
Bo Tang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Single Nucleotide Polymorphisms ◽  
Chinese Population ◽  
Target Genes ◽  
Risk Group ◽  
High Risk Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Southern Chinese ◽  
Increased Risk

Single nucleotide polymorphisms (SNPs) in microRNA may affect its expression and regulation of target genes, which may consequently alter individual susceptibility to cancer. In this study we aimed to investigate associations betweenmiR-122polymorphisms and hepatocellular carcinoma (HCC) in a southern Chinese population. Three selected SNPs inmiR-122(rs9966765, rs1135519, and rs17669) were genotyped in 1050 HCC patients and 1079 cancer-free controls using Sequenom MassARRAY platform and the associations of the three SNPs and HCC risk were evaluated. We found that individuals with the rs1135519 CC genotypes had a significant increased risk of HCC than those with TT genotypes (adjusted OR=2.71, 95% CI=1.15-6.36, andP=0.022), while the rs9966765 CC genotypes showed a borderline significant association with increased risk of HCC when compared with the GG genotypes (adjusted OR=2.38, 95% CI=0.99-5.75, andP=0.052). There was also a significant increased risk of HCC when combining risk genotypes of these loci, i.e., rs1135519 CC and rs9966765 CC. Compared with the low-risk group (0 risk genotype), the high risk group (1-2 risk genotypes) had significantly increased risk of HCC (OR=1.61, 95% CI=1.05-2.44, andP=0.028). Further genotype-expression analysis revealed that cases carrying the CC genotype of rs1135519 had lower levels ofmiR-122expression than those with the TT genotype. Our results suggest that SNP of rs1135519 modulatesmiR-122expression and contributes to the genetic susceptibility of HCC, either independently or together with rs9966765 inmiR-122.Further well-designed studies with lager sample sizes are needed to confirm our findings.

scholarly journals Correlation between miRNA target site polymorphisms in the 3′ UTR of AVPR1A and the risk of hypertension in the Chinese Han population

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Liuping Zhang ◽  
Jinwei Liu ◽  
Peng Cheng ◽  
Fangchao Lv
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Mirna Target ◽  
Direct Sequencing ◽  
Chinese Han Population ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Increased Risk

Abstract We aimed to study the relationship between rs11174811 and rs3803107 single nucleotide polymorphisms (SNPs) in miRNA target sites of the 3′ UTR in the arginine vasopressin receptor 1a gene (AVPR1A) and the risk of hypertension in the Chinese Han population. The genotypes at rs11174811 and rs3803107 were analyzed by direct sequencing in 425 Chinese Han patients with hypertension and 425 healthy subjects. AVPR1A expression was investigated by transfecting miR-526b, miR-375, and miR-186 mimics into human umbilical vein endothelial cells (HUVECs) containing AVPR1A rs11174811 CC, CA/AA and AVPR1A rs3803107 GG, GA/AA genotypes. The A alleles of rs11174811 (adjusted OR = 1.424, 95% CI: 1.231–1.599, P<0.001) and rs3803107 (adjusted OR = 1.222, 95% CI: 1.092–1.355; P=0.001) were high risk factors for hypertension. Plasma levels of miR-526b, miR-375, and miR-186 were higher in the study group than in the control group (P<0.001). The expression levels of AVPR1A mRNA in AVPR1A rs11174811 and rs3803107 mutant HUVECs were higher than those in wild-type cells (t = 8.811, 4.068 and P=0.001, 0.015, respectively). The single nucleotide polymorphisms rs11174811 and rs3803107 in the AVPR1A gene are associated with an increased risk of hypertension in the Chinese Han population. This may be related to the effect of these variants on the regulation of AVPR1A expression by miRNAs.

scholarly journals Candidate single nucleotide polymorphisms of irritable bowel syndrome: a systemic review and meta-analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Shiwei Zhu ◽  
Ben Wang ◽  
Qiong Jia ◽  
Liping Duan
Keyword(s):  
Irritable Bowel Syndrome ◽  
Single Nucleotide Polymorphisms ◽  
Meta Analysis ◽  
Systemic Review ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Increased Risk ◽  
Rome Iii ◽  
Irritable Bowel

Abstract Background Genetic factors increase the risk of irritable bowel syndrome (IBS). Analysis of single nucleotide polymorphisms (SNPs) has been used in IBS patients, but the findings are inconsistent. The goal of this review was to synthesize all the published SNPs studies of IBS through meta-analysis to objectively evaluate the relevance of SNPs to IBS risks. Methods IBS - related polymorphisms studies from 2000 to 2018 were searched. Pooled odds ratios with a 95% confidence interval for each SNP were evaluated through five genetic models. Ethnicity, ROME criteria and IBS subtypes were defined for subgroup analyze. Results Ten relevant genes were evaluated. SNPs rs4263839 and rs6478108 of TNFSF15 associated with an increased risk of IBS; IL6 rs1800795 increased the risk for Caucasian IBS patients which diagnosed by Rome III criteria; and IL23R rs11465804 increased the risk for IBS-C patients. IL10 rs1800896 GG genotype associated with a decreased risk of IBS. No evidence supported the association of GNβ3 rs5443, TNFα rs1800629, and IL10 rs1800871 to IBS in this study. Conclusions This meta-analysis presents an in-depth overview for IBS SNPs analysis. It was confirmed that polymorphisms of TNFSF15 associated with increased IBS risk, while IL10 rs1800896 associated with decreased IBS risk. It might offer some insights into polymorphisms of inflammation factors which might affect IBS susceptibility. Moreover, the analysis also emphasizes the importance of diagnostic criteria and phenotype homogeneity in IBS genetic studies.

Identifying novel biomarkers of gastric cancer through integration analysis of single nucleotide polymorphisms and gene expression profile

2015 ◽  
Vol 30 (3) ◽  
pp. 321-326 ◽  
Author(s):  
Tao Wang ◽  
Yan Xu ◽  
Peng Hou
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Transcription Factor ◽  
Single Nucleotide Polymorphisms ◽  
Gene Expression Omnibus ◽  
Trend Test ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Single Nucleotide ◽  
Normal Controls

Purpose Single nucleotide polymorphisms (SNPs) are an important cause of functional variation in proteins leading to tumorigenesis. We aimed to identify candidate biomarkers with polymorphisms in gastric cancer (GC). Methods The SNP microarray profile GSE29996 including 50 GC samples and 50 normal controls, and gene expression data GSE56807 consisting of 5 GC samples and 5 controls were downloaded from the Gene Expression Omnibus database. After preprocessing of raw data, GC-associated SNPs were identified using the Cochran-Armitage trend test, and differentially expressed genes (DEGs) were screened out using the limma package in R. Significant DEGs with risk associated SNP loci were screened using the Fisher combination test. Gene ontology function and pathway enrichment analyses were performed for DEGs with risk associated SNP loci by GenCLip online tool. Transcriptional regulatory analysis was also conducted for transcription factor and target DEGs. Results A total of 79 DEGs with risk associated SNP loci were identified from GC samples compared with normal controls. These DEGs were mainly enriched in anatomical structure development, including embryo development. Additionally, DEGs were significantly involved in the NO1 pathway, including actin, alpha 1, skeletal muscle (ACTA1). In the regulatory network, transcription factor forkhead box L1 (FOXL1) regulated 26 DEGs with risk associated SNP loci, including Iroquois homeobox 1 (IRX1) rs11134044, sex determining region Y (SRY)-box1 (SOX1) rs9549447 and msh homeobox 1 (MSX1) rs41451149. Conclusions IRX1, SOX1 and MSX1 with risk associated SNP loci may serve as candidate biomarkers for diagnosis and prognosis of GC.

scholarly journals Association between a Variant in MicroRNA-646 and the Susceptibility to Hepatocellular Carcinoma in a Large-Scale Population

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Rui Wang ◽  
Jun Zhang ◽  
Weiru Jiang ◽  
Yanyun Ma ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Single Nucleotide Polymorphisms ◽  
Protective Effect ◽  
Large Scale ◽  
Cancer Development ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Scale Population

Background. Single-nucleotide polymorphisms in microRNAs play important roles in oncogenesis and cancer development.Objective. We aim to explore whether miR-646 rs6513497 is associated with the risk of hepatocellular carcinoma.Methods. Total 997 HCC patients and 993 cancer-free controls were enrolled in this study. Genotyping was performed using MassARRAY method.Results. Compared with the T allele of rs6513497, the G allele was associated with a significantly decreased risk of HCC (OR = 0.788, 95% CI = 0.631–0.985,P= 0.037); moreover, a more protective effect of the G allele was shown in males (OR = 0.695, 95% CI = 0.539–0.897,P= 0.005 in HCC and OR = 0.739, 95% CI = 0.562–0.972,P= 0.030 in HBV-related HCC), basically in a dominant manner (HCC: OR = 0.681, 95% CI = 0.162–0.896,P= 0.006; HBV-related HCC: OR = 0.715, 95% CI = 0.532–0.962,P= 0.027).Conclusions. Our findings support the view that the miR-646 SNP rs6513497 may contribute to the susceptibility of HCC.

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