Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Polymorphisms of EpCAM gene and prognosis for non-small-cell lung cancer in Han Chinese.

ABSTRACT: The epithelial cell adhesion molecule (EpCAM) is overexpressed in a wide variety of human cancers and is associated with patient prognosis, including those with lung cancer. However, the association of single nucleotide polymorphisms (SNPs) in the EpCAM gene with the prognosis for non-small-cell lung cancer (NSCLC) patients has never been investigated. We evaluated the association between two SNPs, rs1126497 and rs1421, in the EpCAM gene and clinical outcomes in a Chinese cohort of 506 NSCLC patients. The SNPs were genotyped using the Sequenom iPLEX genotyping system. Multivariate Cox proportional hazards model and Kaplan-Meier curves were used to assess the association of EpCAM gene genotypes with the prognosis of NSCLC. We found that the non-synonymous SNP rs1126497 was significantly associated with survival. Compared with the CC genotype, the CT+TT genotype was a risk factor for both death (hazard ratio, 1.40; 95% confidence interval [CI], 1.02-1.94; P = 0.040) and recurrence (hazard ratio, 1.34; 95% CI, 1.02-1.77; P = 0.039). However, the SNP rs1421 did not show any significant effect on patient prognosis. Instead, the AG+GG genotype in rs1421 was significantly associated with early T stages (T1/T2) when compared with the AA genotype (odds ratio for late stage = 0.65; 95% CI, 0.44-0.96, P = 0.029). Further stratified analysis showed notable modulating effects of clinical characteristics on the associations between variant genotypes of rs1126497 and NSCLC outcomes. In conclusion, our study indicated that the non-synonymous SNP rs1126497 may be a potential prognostic marker for NSCLC patients.

SUBMITTER: Yang Y

PROVIDER: S-EPMC4317886 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

CD226 gene polymorphisms are associated with non-small-cell lung cancer in the Chinese Han population.

Project description:BackgroundThe immunoglobulin-like glycoprotein CD226 (DNAX accessory molecule-1) represents receptor-activating cytotoxic T lymphocyte and natural killer cells taking part in tumor surveillance, the pathogenesis of inflammation, and autoimmune disorders. The aim of the present study is to analyze the association between polymorphisms rs763361 and rs727088 in the CD226 gene and their impact on the pathogenesis of non-small-cell lung cancer (NSCLC).Materials and methodsPolymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) were used to genotype the single nucleotide polymorphisms (SNPs) rs763361 and rs727088 of the CD226 gene in 302 NSCLC patients and 389 ethnicity matched healthy controls.ResultsThe frequencies of the T allele and TT genotype of rs763361 (T allele odds ratio [OR] 1.42, 95% confidence interval [CI] 1.14-1.77; TT genotype OR 2.73, 95% CI 1.70-4.39), as well as the G allele and GG genotype of rs727088 (G allele OR 1.89, 95% CI 1.50-2.39; GG genotype OR 4.62, 95% CI 2.31-9.20) in the NSCLC patients were significantly higher than that of normal controls, indicating that both of these two SNPs as risk factors were associated with NSCLC (P<0.05). Results of stratified analysis revealed that the polymorphism of rs727088 was associated with lymph node invasion and clinical stage cancer (P<0.05). However, there was no association between SNP rs763361 and clinical characteristics.ConclusionOur results demonstrated that CD226 gene polymorphisms (T allele of rs763361 and G allele of rs727088) as risk factors were associated with NSCLC.

| S-EPMC4554428 | biostudies-literature

Genetic polymorphisms in the TERT gene and susceptibility to non-small cell lung cancer in a Chinese Han population.

Project description:Background:Recent studies have revealed that the TERT gene plays crucial roles in cancer initiation and development. Genome-wide analysis studies and case-control studies have demonstrated that polymorphisms in the TERT gene are associated with various cancers. Materials and methods:In the current study, we analyzed the associations of eight single nucleotide polymorphisms (SNPs) in the TERT gene with non-small cell lung cancer (NSCLC) in a Chinese Han population. A total of 467 NSCLC patients and 526 healthy individuals were recruited for SNP genotyping using a TaqMan assay. Results:Our results revealed that the allelic frequencies of rs2853677 and rs2853691 were significantly different between the NSCLC and control groups (P=0.004 and 0.001, respectively). Moreover, the T allele of rs2853677 and the A allele of rs2853691 might be the protective factors against NSCLC (OR=0.766; 95%CI: 0.639-0.918 and OR=0.714; 95%CI: 0.584-0.875, respectively). Additionally, stratified association analysis of the eight SNPs with the different pathological NSCLC stages (I+II and III+IV) and different pathological types (adenocarcinoma and squamous cell carcinoma) revealed that none of the SNPs were significantly different between patients with different pathological stages and pathological types. Conclusion:Our results indicated that rs2853677 and rs2853691 in the TERT gene might be associated with NSCLC in this Chinese Han population.

| S-EPMC6001840 | biostudies-literature

Prognostic assessment of apoptotic gene polymorphisms in non-small cell lung cancer in Chinese.

Project description:Apoptosis plays a key role in inhibiting tumor growth, progression and resistance to anti-tumor therapy. We hypothesized that genetic variants in apoptotic genes may affect the prognosis of lung cancer. To test this hypothesis, we selected 38 potentially functional single nucleotide polymorphisms (SNPs) from 12 genes (BAX, BCL2, BID, CASP3, CASP6, CASP7, CASP8, CASP9, CASP10, FAS, FASLG and MCL1) involved in apoptosis to assess their prognostic significance in lung cancer in a Chinese case cohort with 568 non-small cell lung cancer (NSCLC) patients. Thirty-five SNPs passing quality control underwent association analyses, 11 of which were shown to be significantly associated with NSCLC survival (P < 0.05). After Cox stepwise regression analyses, 3 SNPs were independently associated with the outcome of NSCLC (BID rs8190315: P = 0.003; CASP9 rs4645981: P = 0.007 and FAS rs1800682: P = 0.016). A favorable survival of NSCLC was significantly associated with the genotypes of BID rs8190315 AG/GG (adjusted HR = 0.65, 95% CI: 0.49-0.88), CASP9 rs4645981 AA (HR = 0.22, 95% CI: 0.07-0.69) and FAS rs1800682 GG (adjusted HR = 0.67, 95% CI: 0.46-0.97). Time-dependent receptor operation curve (ROC) analysis revealed that the area under curve (AUC) at year 5 was significantly increased from 0.762 to 0.819 after adding the risk score of these 3 SNPs to the clinical risk score. The remaining 32 SNPs were not significantly associated with NSCLC prognosis after adjustment for these 3 SNPs. These findings indicate that BID rs8190315, CASP9 rs4645981 and FAS rs1800682 polymorphisms in the apoptotic pathway may be involved in the prognosis of NSCLC in the Chinese population.

| S-EPMC3664730 | biostudies-literature

The association of adiponectin gene promoter variations with non-small cell lung cancer in a Han Chinese population.

Project description:Recently, in vitro studies have demonstrated that adiponectin has antiangiogenic and tumor growth-limiting properties. Additionally, serum adiponectin levels have been associated with the risk of several cancers; specifically, serum adiponectin was significantly lower in lung cancer patients with advanced-stage disease. In this study, we examined the association of adiponectin gene promoter variations associated with adiponectin gene expression and plasma levels in non-small cell lung cancer (NSCLC) in a Han Chinese population. A total of 319 patients with NSCLC and 489 healthy individuals were recruited to evaluate the association of four adiponectin gene promoter single-nucleotide polymorphisms (SNPs) (SNP-12140G>A, SNP-11426A>G, SNP-11391G>A and SNP-11377C>G) with NSCLS risk. Additionally, we constructed haplotypes of these four SNPs and evaluated the association of these haplotypes with NSCLS risk. Our results showed that among these four SNPs, only SNP-12140G>A was associated with NSCLC risk (P<0.05). The haplotype analysis showed that no haplotype was associated with NSCLC after performing a Bonferroni correction (P>0.05). Additionally, an association analysis of the four SNPs stratified into pathologic stages I+II and III+IV showed that these SNPs did not exhibit significant differences between pathologic stages I+II and III+IV. Moreover, we did not observe any differences in allele and genotype frequency for these SNPs between adenocarcinoma and squamous cell carcinoma. Our results indicated that the G allele of SNP-12140 may be a risk factor for NSCLC (OR = 1.516; 95% CI: 1.098-2.094) in this Han Chinese population.

| S-EPMC4446305 | biostudies-literature

<i>Methylenetetrahydrofolate reductase</i> tagging polymorphisms are associated with risk of non-small cell lung cancer in eastern Chinese Han population.

Project description:Previous reports implicated 5,10-ethylenetetrahydrofolate reductase (MTHFR) polymorphisms acted as a potential risk factor for several cancers. In order to explore the effect of MTHFR SNPs on non-small cell lung cancer (NSCLC), we selected MTHFR tagging single nucleotide polymorphisms (SNPs) and carried out a case-control study to determine the potential relationship of MTHFR SNPs with NSCLC risk. Our study consisted of 521 NSCLC patients and 1,030 non-cancer controls. MTHFR SNPs were genotyped by SNPscanTM genotyping assay. Using four genetic models (additive, Homozygote, dominant, recessive), the genotype frequencies were compared using the chi-squared (χ2) test. Crude/adjusted odds ratios (ORs) with their 95% confidence intervals (CIs) were used to assess the difference for the genotype distribution. We found that MTHFR rs1801133 G>A polymorphism decreased the risk of overall NSCLC. In a subgroup analysis, MTHFR rs1801133 G>A polymorphism also decreased NSCLC risk in female, < 60 years and never smoking subgroups. However, we identified that MTHFR rs4845882 G>A polymorphism was associated with the development of NSCLC in female subgroup. In addition, MTHFR rs9651118 T>C polymorphism increased the risk of NSCLC in < 60 years, never smoking and BMI < 24 kg/m2 subgroups. In conclusion, the current study highlights MTHFR rs1801133 G>A variants decreases the risk of NSCLC. Nevertheless, MTHFR rs4845882 G>A and rs9651118 T > C polymorphisms may be associated with NSCLC susceptibility. Well-designed large-scale studies are needed to confirm these findings and explore the interactions of gene-gene and gene-environment involved in MTHFR SNPs and NSCLC.

| S-EPMC5746385 | biostudies-literature

Molecular gene signature and prognosis of non-small cell lung cancer.

Project description:The current staging system for non-small cell lung cancer (NSCLC) is inadequate for predicting outcome. Risk score, a linear combination of the values for the expression of each gene multiplied by a weighting value which was estimated from univariate Cox proportional hazard regression, can be useful. The aim of this study is to analyze survival-related genes with TaqMan Low-Density Array (TLDA) and risk score to explore gene-signature in lung cancer. A total of 96 NSCLC specimens were collected and randomly assigned to a training (n = 48) or a testing cohort (n = 48). A panel of 219 survival-associated genes from published studies were used to develop a 6-gene risk score. The risk score was used to classify patients into high or low-risk signature and survival analysis was performed. Cox models were used to evaluate independent prognostic factors. A 6-gene signature including ABCC4, ADRBK2, KLHL23, PDS5A, UHRF1 and ZNF551 was identified. The risk score in both training (HR = 3.14, 95% CI: 1.14-8.67, p = 0.03) and testing cohorts (HR = 5.42, 95% CI: 1.56-18.84, p = 0.01) was the independent prognostic factor. In merged public datasets including GSE50081, GSE30219, GSE31210, GSE19188, GSE37745, GSE3141 and GSE31908, the risk score (HR = 1.50, 95% CI: 1.25-1.80, p < 0.0001) was also the independent prognostic factor. The risk score generated from expression of a small number of genes did perform well in predicting overall survival and may be useful in routine clinical practice.

| S-EPMC5239522 | biostudies-other

<i>PD-1</i> gene promoter polymorphisms correlate with a poor prognosis in non-small cell lung cancer.

Project description:An imbalance to the regulation of the immune system changes the tumor-specific T-cell immunity in the cancer microenvironment and adjusts the tumor progression and metastasis. Inhibiting the interactions of the immune function mediates the antitumor activity in preclinical models. The programmed death 1 (PD-1) gene -606 G/A polymorphism, which may modify promoter activity and is Asian-specific, was investigated by TaqMan quantitative polymerase chain reaction assay in surgically treated non-small cell lung cancer (NSCLC) cases. In the present study, 583 surgically removed NSCLC cases were included for single-nucleotide polymorphism (SNP) analyses. The PD-1 SNP statuses at the promoter region (rs36084323) were 146 AA (25.0%), 293 GA (50.3%) and 144 GG (24.7%). The ratio was extremely similar to the healthy control in a previous study: 24.9% AA, 47.8% GA and 27.3% GG. The ratio of the GG phenotype was not significantly different for gender (25.1% males and 23.9% female), age (25.2% ≤65 years and 24.4% >65 years), smoking status (26.1% smoker and 21.8% non-smoker) and pathological subtypes [25.4% adenocarcinoma (adeno) and 24.2% squamous cell carcinoma (SCC)]. The GG ratio of PD-1 was not significantly different between pathological stage II-IV (25.5%) and stage I cases (24.1%; P=0.6245). The survival time of the patients with the -606 GG phenotype of PD-1 was significantly lower (n=147, 50 succumbed) compared to the patients with -606 GA or -606 AA (n=435, 109 succumbed) (P=0.0183). The GG phenotype patients had a significantly worse prognosis in the SCC population (P=0.009), however, this was not different to the adeno population (P=0.2594). Thus, PD-1 may promote tumor prognosis and provide a candidate for the blockade of its function as a strategy to antagonize the progression process in NSCLC, particularly lung SCC.

| S-EPMC4179826 | biostudies-literature

CYP4F2 and CYP3A5 gene polymorphisms and lung cancer in Chinese Han population.

Project description:This study aimed to explore whether the polymorphisms of CYP4F2 and CYP3A5 are correlated with the risk of lung cancer development. A case-control study was conducted among 510 patients with pathologically confirmed lung cancer as the case group and 504 healthy individuals as the control group. Four single-nucleotide polymorphisms of the CYP4F2 and CYP3A5 genes were genotyped, and their correlations with the risk of lung cancer were examined using Chi-square test and logistic regression analysis. Stratified analysis found that the rs3093105 and rs3093106 loci of CYP4F2 gene were significantly associated with lower risk of lung cancer (P = 0.012, OR 0.64, 95% CI 0.45-0.91). The correlation was related to patients' age and sex and pathological type of lung cancer. Similarly, the rs10242455 loci of CYP3A5 gene showed a statistical significance between the case group and the control group (P = 0.018, OR 0.71, 95% CI 0.53-0.94), which also was associated with reduced risk of squamous cell lung cancer in the dominant and additive models (dominant: OR 0.66, 95% CI 0.46-0.94, P = 0.021; additive: OR 0.71, 95% CI 0.53-0.95, P = 0.023). CYP4F2 and CYP3A5 gene polymorphisms are associated with the reduced risk of non-small cell lung cancer, and its correlation is related to patients' age and sex and pathological type of lung cancer.

| S-EPMC7366610 | biostudies-literature

Polymorphisms of HIF1A gene are associated with prognosis of early stage non-small-cell lung cancer patients after surgery.

Project description:Hypoxia-inducible factor 1α (HIF1α) activates the transcription of genes that are involved in angiogenesis and cell survival. Over-expression of HIF1α caused by intratumoral hypoxia and its genetic alterations are associated with increased mortality in several cancer types including non-small-cell lung cancer (NSCLC). The aim of this study was to investigate the predictive role of single nucleotide polymorphisms (SNPs) in HIF1A gene in NSCLC outcomes. We genotyped two functional SNPs (rs2057482 and rs2301113) in HIF1A gene and assessed their associations with clinicopathological parameters and prognosis of 494 NSCLC patients by Cox proportional hazard model. There was no significant association between the SNPs and clinical outcomes of NSCLC for overall analysis. However, in stratified analysis for NSCLC patients at early stage (I/II), we observed a protective effect conferred by variant genotype of rs2057482 on overall survival (OS) (HR 0.42, 95% CI 0.22-0.80) and recurrence-free survival (RFS) (HR 0.60, 95 % CI 0.36-0.97) in a dominant model. Additionally, multivariate Cox analysis based on dominant model indicated that significant increased death and recurrence risks were observed in patients with early T-stage (T1 and T2) tumors, who carrying variant-containing genotype of rs2301113, as well as in patients without lymph node involvement (N0 stage) for rs2057482. Genetic variations on HIF1A gene are significantly associated with NSCLC outcomes in patients with early stage disease.

| S-EPMC3971443 | biostudies-literature

Association of HIF1-α gene polymorphisms with advanced non-small cell lung cancer prognosis in patients receiving radiation therapy.

Project description:We investigated the association between single nucleotide polymorphisms (SNPs) in the HIF1A gene and the prognosis of advanced non-small cell lung cancer (NSCLC) patients undergoing radiation therapy. Patient overall survival (OS) and progression-free survival (PFS) were analyzed. The rs11549465 TT genotype was associated with poor PFS (P<0.001) and OS (P=0.001). The rs2057482 TT genotype was also associated with poor PFS (P=0.002) and OS (P=0.007). Stratified analyses revealed that these associations occurred in patients with a smoking history, squamous cell carcinoma, and stage IIIA disease, as well as those receiving radiation therapy a radiation dose of ≥70 Gy. We found associations between SNPs and PFS but not OS in patients without a smoking history, other histological types, and stage IIIB disease, as well as those undergoing chemoradiotherapy with a radiation dose of <70 Gy. No associations were observed between rs11549467 or rs110873142 and NSCLC prognosis. These results suggest that HIF1A polymorphisms can be used as independent prognostic biomarkers for NSCLC patients receiving radiation therapy.

| S-EPMC7993740 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data