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pmid:31088477
A robust six-gene prognostic signature for prediction of both disease-free and overall survival in non-small cell lung cancer.
Shuguang Zuo · Min Wei · Hailin Zhang · Anxian Chen · Junhua Wu · Jiwu Wei · Jie Dong
Journal of translational medicine · 2019 doi:10.1186/s12967-019-1899-y
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Complete file
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This study aimed to identify and validate a prognostic signature for the prediction of both disease-free survival (DFS) and overall survival (OS) of NSCLC patients by integrating multiple datasets.\nMETHODS: We firstly downloaded three independent datasets under the accessing number of GSE31210, GSE37745 and GSE50081, and then performed an univariate regression analysis to identify the candidate prognostic genes from each dataset, and identified the gene signature by overlapping the candidates. Then, we built a prognostic model to predict DFS and OS using a risk score method. Kaplan-Meier curve with log-rank test was used to determine the prognostic significance. Univariate and multivariate Cox proportional hazard regression models were implemented to evaluate the influences of various variables on DFS and OS. The robustness of the prognostic gene signature was evaluated by re-sampling tests based on the combined GEO dataset (GSE31210, GSE37745 and GSE50081). Furthermore, a The Cancer Genome Atlas (TCGA)-NSCLC cohort was utilized to validate the prediction power of the gene signature. Finally, the correlation of the risk score of the gene signature and the Gene set variation analysis (GSVA) score of cancer hallmark gene sets was investigated.\nRESULTS: We identified and validated a six-gene prognostic signature in this study. This prognostic signature stratified NSCLC patients into the low-risk and high-risk groups. Multivariate regression and stratification analyses demonstrated that the six-gene signature was an independent predictive factor for both DFS and OS when adjusting for other clinical factors. Re-sampling analysis implicated that this six-gene signature for predicting prognosis of NSCLC patients is robust. Moreover, the risk score of the gene signature is correlated with the GSVA score of 7 cancer hallmark gene sets.\nCONCLUSION: This study provided a robust and reliable gene signature that had significant implications in the prediction of both DFS and OS of NSCLC patients, and may provide more effective treatment strategies and personalized therapies.", "claims": [{"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31088477", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31088477"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE31210", "GSE37745", "GSE50081"], "resolved_accessions": ["GSE31210", "GSE37745", "GSE50081"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE31210, GSE37745, GSE50081 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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