Cancer-risk module identification and module-based disease risk evaluation: a case study on lung cancer.
Ontology highlight
ABSTRACT:
SUBMITTER: Jia X
PROVIDER: S-EPMC3958511 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
Cancer-risk module identification and module-based disease risk evaluation: a case study on lung cancer.
Jia Xu X Miao Zhengqiang Z Li Wan W Zhang Liangcai L Feng Chenchen C He Yuehan Y Bi Xiaoman X Wang Liqiang L Du Youwen Y Hou Min M Hao Dapeng D Xiao Yun Y Chen Lina L Li Kongning K
PloS one 20140318 3
Gene expression profiles have drawn broad attention in deciphering the pathogenesis of human cancers. Cancer-related gene modules could be identified in co-expression networks and be applied to facilitate cancer research and clinical diagnosis. In this paper, a new method was proposed to identify lung cancer-risk modules and evaluate the module-based disease risks of samples. The results showed that thirty one cancer-risk modules were closely related to the lung cancer genes at the functional le ...[more]
Similar Datasets
Project description:Interstitial lung disease (ILD) seems to be associated with an increased risk of lung cancer (LC) and to have a poorer prognosis than LC without ILD. The frequency of ILD in an LC cohort and its prognosis implication need to be better elucidated. This retrospective, observational, cohort study evaluated the frequency of ILD among LC patients (LC-ILD) diagnosed over a 2-year period. LC-ILD patients' characteristics were compared to those with LC without ILD (LC-noILD). Lastly, we conducted a case-control study within this cohort, matching three LC-noILDs to each LC-ILD patient, to evaluate the ILD impact on LC patients' prognoses. Among 906 LC patients, 49 (5.4%) also had ILD. Comparing LC-ILD to LC-noILD patients, respectively, more were men (85.7% vs. 66.2%; p = 0.02); adenocarcinomas were less frequent (47.1% vs. 58.7%, p = 0.08); median [range] and overall survival was shorter: (9 [range: 0.1-39.4] vs. 17.5 [range: 0.8-50.4] months; p = 0.01). Multivariate analysis (hazard ratio [95% confidence interval]) retained two factors independently associated with LC risk of death: ILD (1.79 [1.22-2.62]; p = 0.003) and standard-of-care management (0.49 [0.33-0.72]; p < 0.001). Approximately 5% of patients with a new LC diagnosis had associated ILD. ILD was a major prognosis factor for LC and should be taken into consideration for LC management. Further studies are needed to determine the best therapeutic strategy for the LC-ILD population.
| S-EPMC7141363 | biostudies-literature
Project description:Introduction:Guidelines recommend that primary care providers complete organ-based routine cancer screening for all transgender patients. Training on critical transgender health topics like cancer screening, as well as residents' confidence in addressing issues their transgender patients may face, remains limited among graduate medical education (GME) programs. Online case-based modules are an effective tool for skills improvement in GME, but their application to transgender health topics has not been assessed. Methods:I developed a brief online module on cancer screening for transgender patients using Google Forms and offered it to first-year internal medicine residents. The module was optional and asynchronous with other didactics presented during an oncology-themed ambulatory learning block. Pre- and postmodule surveys assessed resident confidence in counseling transgender patients about cancer screening and sharing screening resources. Results:Fourteen of 60 interns elected to complete the module, with all participants submitting pre- and postmodule surveys. Respondents reported increased confidence in counseling transgender patients about appropriate cancer screening (mean increase on 5-point Likert scale of 1.29; confidence interval [CI], 0.81-1.76; p < .01) and increased confidence in discussing resources on cancer screening for transgender individuals (mean increase on 5-point Likert scale of 1.36; CI, 0.66-2.06; p < .01). Discussion:While knowledge gaps on transgender health issues like cancer screening remain significant among residents, brief case-based online modules, in conjunction with an expansion of traditional didactics, may help improve confidence among residents in addressing these critical issues with their transgender patients.
| S-EPMC6376892 | biostudies-other
Project description:To investigate the association between long-term exposure to ambient air pollution and lung cancer incidence in Koreans.This was a population-based case-control study covering 908 lung cancer patients and 908 controls selected from a random sample of people within each Korean province and matched according to age, sex, and smoking status. We developed land-use regression models to estimate annual residential exposure to particulate matter (PM??) and nitrogen dioxide (NO?) over a 20-year exposure period. Logistic regression was used to estimate odds ratios (ORs) and their corresponding 95% confidence intervals (CI).Increases in lung cancer incidence (expressed as adjusted OR) were 1.09 (95% CI: 0.96-1.23) with a ten-unit increase in PM?? (?g/m³) and 1.10 (95% CI: 1.00-1.22) with a ten-unit increase in NO? (ppb). Tendencies for stronger associations between air pollution and lung cancer incidence were noted among never smokers, among those with low fruit consumption, and among those with a higher education level. Air pollution was more strongly associated with squamous cell and small cell carcinomas than with adenocarcinoma of the lung.This study provides evidence that PM10 and NO? contribute to lung cancer incidence in Korea.
| S-EPMC5653475 | biostudies-literature
Project description:Laboratory studies suggest that flavonoids are antimutagenic and anticarcinogenic. To investigate the associations between commonly consumed flavonoid compounds and lung cancer, the authors conducted a population-based case-control study of 558 lung cancer cases and a group of 837 controls.Dietary intakes of flavonoids were estimated by combining the intake frequency (collected by a food frequency questionnaire), portion size, and food composition data. Unconditional logistic regression analysis was used to estimate odds ratios (ORs) and 95% confidence limits (95% CLs) with an adjustment for potential confounders, including age, sex, race-ethnicity, years of schooling, smoking status, pack-years of tobacco smoking, and daily energy intake.Lung cancer was associated inversely with the consumption of epicatechin (in 10 mg per day increment: OR, 0.64; 95% CL, 0.46-0.88), catechin (4 mg per day increment: OR, 0.49; 95% CL, 0.35-0.70), quercetin (9 mg per day increment: OR, 0.65; 95% CL, 0.44-0.95), and kaempferol (2 mg per day increment: OR, 0.68; 95% CL, 0.51-0.90) among tobacco smokers. There was little association between lung cancer and the flavonoid compounds mentioned above among nonsmokers. Regardless of smoking status, there was little association with total flavonoids: thearubigins, hesperetin, naringenin, and myricetin. In addition, consumption of vegetables, tea, and wine, all of which are rich sources of flavonoids, was associated inversely with lung cancer among tobacco smokers.Certain flavonoid compounds, including epicatechin, catechin, quercetin, and kaempferol, were associated inversely with lung cancer among tobacco smokers, but not among nonsmokers. Further studies of these associations may be warranted.
| S-EPMC5546301 | biostudies-other
Project description:The authors examined the relation between occupation and lung cancer in the large, population-based Environment And Genetics in Lung cancer Etiology (EAGLE) case-control study. In 2002-2005 in the Lombardy region of northern Italy, 2,100 incident lung cancer cases and 2,120 randomly selected population controls were enrolled. Lifetime occupational histories (industry and job title) were coded by using standard international classifications and were translated into occupations known (list A) or suspected (list B) to be associated with lung cancer. Smoking-adjusted odds ratios and 95% confidence intervals were calculated with logistic regression. For men, an increased risk was found for list A (177 exposed cases and 100 controls; odds ratio = 1.74, 95% confidence interval: 1.27, 2.38) and most occupations therein. No overall excess was found for list B with the exception of filling station attendants and bus and truck drivers (men) and launderers and dry cleaners (women). The authors estimated that 4.9% (95% confidence interval: 2.0, 7.8) of lung cancers in men were attributable to occupation. Among those in other occupations, risk excesses were found for metal workers, barbers and hairdressers, and other motor vehicle drivers. These results indicate that past exposure to occupational carcinogens remains an important determinant of lung cancer occurrence.
| S-EPMC2808498 | biostudies-literature
Project description:Introduction: MicroRNAs (miRNAs) are small, non-coding RNA molecules involved in post-transcriptional gene regulation and have recently been shown to play a role in cancer metastasis. In solid tumors, especially breast cancer, alterations in miRNA expression contribute to cancer pathogenesis, including metastasis. Considering the emerging role of miRNAs in metastasis, the identification of predictive markers is necessary to further understanding of stage-specific breast cancer development. This is a retrospective analysis that aimed to identify molecular biomarkers related to distant breast cancer metastasis development.<br><br>Methods: A retrospective case cohort study was performed in 64 breast cancer patients treated during the period from 1998-2001. The case group (n=29) consisted of patients with a poor prognosis who presented with breast cancer recurrence or metastasis during follow up. The control group (n=35) consisted of a random sample of patients with a good prognosis who did not develop breast cancer recurrence or metastasis. These patient groups were stratified according to TNM clinical stage (CS) I, II and III, and the main clinical features of the patients were homogeneous. miRNA profiling was performed using formalin-fixed, paraffin-embedded tumors. Biomarkers related to metastatic potential were identified independent of clinical stage, and a cutoff point was selected based on the optimal sensitivity and specificity (ROC curve). Finally, a hazard risk analysis of these biomarkers was performed to evaluate their relation to metastatic potential. <br><br>Results: miRNA expression profiling identified several miRNAs that were either specific and shared across all clinical stages (p?0.05). Among these, we identified miRNAs previously associated with cell motility (let-7 family), cell proliferation and invasion (hsa-miR-16 and has-miR-205) and distant metastasis (hsa-miR-21). In addition, hsa-miR-494 and hsa-miR-21 were up-regulated in metastatic cases of CSI and II. Furthermore, the combination of the 3 miRNAs identified for CSII (hsa-miR-494, hsa-miR-183 and hsa-miR-21) was significant and were a more effective risk marker compared to the single miRNAs. <br><br>Conclusions: Women with metastatic breast cancer, especially CSII, presented up-regulated levels of miR-183, miR-494 and miR-21, which were associated with a poor prognosis. These miRNAs therefore represent new risk biomarkers of breast cancer metastasis and may be useful for future targeted therapies.
2013-08-07 | E-MEXP-3947 | biostudies-arrayexpress
Project description:BackgroundPatients living with chronic obstructive pulmonary disease (COPD) are at an increased risk of lung cancer. A common comorbidity of COPD is cardiovascular disease; as such, COPD patients often receive statins. This study sought to understand the association between statin exposure and lung cancer risk in a population-based cohort of COPD patients.MethodsWe identified a population-based cohort of COPD patients based on having filled at least three prescriptions for an anticholinergic or short-acting beta-agonist (SABA). We used an array of methods of defining medication exposure including three conventional methods (ever statin exposure, cumulative duration of use, and cumulative dose) and two novel methods (recency-weighted cumulative duration of use and recency-weighted cumulative dose). To assess residual confounding, a negative control exposure was used to test the validity of our results. All exposure variables were time-dependent.ResultsThe population-based cohort of COPD had 39,879 patients with mean age of 70.6 (SD: 11.2) years and, of which, 53.5% were female. There were 12,469 patients who received at least one statin prescription. Results from the reference case multivariable analysis indicated a reduced risk from statin exposure (HR: 0.85 (95% CI: 0.73-1.00) in COPD patients, but this result not statistically significant. Using the two recency-weighted modelling approaches, statin exposure was associated with a statistically significant reduction in lung cancer risk (recency-weighted cumulative dose, HR: 0.85 (95% CI: 0.77-0.93) and recency-weighted cumulative duration of use, HR: 0.97 (95% CI: 0.96-0.99). Multivariable analysis incorporating the negative control exposure was not statistically significant (HR: 0.89 (95% CI: 0.75-1.10).ConclusionsThe results of this population-based analysis indicate that statin use in COPD patients may reduce the risk of lung cancer. While the effect was not statistically significantly across all exposure definitions, the overall results support the hypothesis that COPD patients might benefit from statin therapy.
| S-EPMC7236956 | biostudies-literature
Project description:OBJECTIVE:The present study aims to explore the role of smoking factors in the risk of lung cancer and screen the feature risk pathways of smoking-induced lung cancer. METHODS:The expression profiles of the patient data from GEO database were standardized, and differentially expressed genes (DEGs) were analyzed by limma algorithm. Samples and genes were analyzed by Unsupervised hierarchical clustering method, while GO and KEGG enrichment analyses were performed on DEGs. The data of the protein-protein interaction (PPI) network were downloaded from the BioGrid and HPRD databases, and the DEGs were mapped into the PPI network to identify the interaction relationship. The enriched significant pathways were used to calculate the anomaly score and RFE method was used to optimize the feature sets. The model was trained using the support vector machine (SVM) and the predicted results were plotted into ROC curves. The AUC value was calculated to evaluate the predictive performance of the SVM model. RESULTS:A total of 1923 DEGs were obtained, of which 826 were down-regulated and 1097 were up-regulated. Unsupervised hierarchical clustering analysis showed that the diagnosis accuracy of lung cancer smokers was 74%, and that of non-lung cancer smokers was 75%. Five optimal feature pathway sets were obtained by screening, the clinical diagnostic ability of which was detected by SVM model with the accuracy improved to 84%. The diagnostic accuracy was 90% after combining clinical information. CONCLUSION:We verified that five signaling pathways combined with clinical information could be used as a feature risk pathway for identifying lung cancer smokers and non-lung cancer smokers and increased the diagnostic accuracy.
| S-EPMC7272018 | biostudies-literature
Project description:OBJECTIVES:To conduct a comprehensive analysis of prospectively measured circulating high sensitivity C reactive protein (hsCRP) concentration and risk of lung cancer overall, by smoking status (never, former, and current smokers), and histological sub-type. DESIGN:Nested case-control study. SETTING:20 population based cohort studies in Asia, Europe, Australia, and the United States. PARTICIPANTS:5299 patients with incident lung cancer, with individually incidence density matched controls. EXPOSURE:Circulating hsCRP concentrations in prediagnostic serum or plasma samples. MAIN OUTCOME MEASURE:Incident lung cancer diagnosis. RESULTS:A positive association between circulating hsCRP concentration and the risk of lung cancer for current (odds ratio associated with a doubling in hsCRP concentration 1.09, 95% confidence interval 1.05 to 1.13) and former smokers (1.09, 1.04 to 1.14) was observed, but not for never smokers (P<0.01 for interaction). This association was strong and consistent across all histological subtypes, except for adenocarcinoma, which was not strongly associated with hsCRP concentration regardless of smoking status (odds ratio for adenocarcinoma overall 0.97, 95% confidence interval 0.94 to 1.01). The association between circulating hsCRP concentration and the risk of lung cancer was strongest in the first two years of follow-up for former and current smokers. Including hsCRP concentration in a risk model, in addition to smoking based variables, did not improve risk discrimination overall, but slightly improved discrimination for cancers diagnosed in the first two years of follow-up. CONCLUSIONS:Former and current smokers with higher circulating hsCRP concentrations had a higher risk of lung cancer overall. Circulating hsCRP concentration was not associated with the risk of lung adenocarcinoma. Circulating hsCRP concentration could be a prediagnostic marker of lung cancer rather than a causal risk factor.
| S-EPMC6315896 | biostudies-other
Project description:OBJECTIVE:Our population-based research aimed to clarify the association between chronic kidney disease (CKD) and mortality risk in patients with lung cancer. DESIGN:Retrospective cohort study SETTING: National health insurance research database in Taiwan PARTICIPANTS: All (n=1?37?077) Taiwanese residents who were diagnosed with lung cancer between 1997 and 2012 were identified. Eligible patients with baseline CKD (n=2269) were matched with controls (1:4, n=9076) without renal disease according to age, sex and the index day of lung cancer diagnosis. METHODS:The cumulative incidence of death was calculated by the Kaplan-Meier method, and the risk determinants were explored by the Cox proportional hazards model. RESULTS:Mortality occurred in 1866 (82.24%) and 7135 (78.61%) patients with and without CKD, respectively (P=0.0001). The cumulative incidences of mortality in patients with and without chronic renal disease were 72.8% vs 61.6% at 1?year, 82.0% vs 76.6% at 2 years and 88.9% vs 87.2% at 5 years, respectively. After adjusting for multiple confounding factors including age and comorbidities, Cox regression analysis revealed that CKD was associated with an increased risk of mortality (adjusted HR 1.38; 95% CI 1.29 to 1.47). Stratified analysis further showed that the association was consistent across patient subgroups. CONCLUSION:Comorbidity associated with CKD is a risk factor for mortality in patients with lung cancer.
| S-EPMC5786081 | biostudies-other