DNA methylation biomarkers for head and neck squamous cell carcinoma.

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The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (FAM135B and ZNF610) and 2 hypomethylated-high-expression genes (HOXA9 and DCC) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.", "claims": [{"id": "claim-target-result", "statement": "Using multivariate Cox proportional hazards analysis after validation with Gene Expression Omnibus and The Cancer Genome Atlas data, the study identified FAM135B methylation as a favorable independent prognostic biomarker for overall survival in HNSCC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29927694", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus."}, {"asset": "source:pmid:29927694", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation."}, {"asset": "source:pmid:29927694", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using multivariate Cox proportional hazards analysis after validation with Gene Expression Omnibus and The Cancer Genome Atlas data, the study identified FAM135B methylation as a favorable independent prognostic biomarker for overall survival in HNSCC patients.", "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:29927694"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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