Multigene panel predicting survival of patients with colon cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31839813", "kind": "science-record", "revision": 8, "content_hash": "sha256:4d716bfb594d7983aa0d644407a1c96f283c7ffbe2977da788a4de9bc077aa17", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:01:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Multigene panel predicting survival of patients with colon cancer.", "doi": "10.7150/jca.35902", "pmid": "31839813", "authors": ["Hao-Dong Li", "Chen Liang"], "journal": "Journal of Cancer", "year": 2019, "abstract": "Objective: The purpose of this study was to investigate multigene panel markers to predict long-term survival in patients with colon cancer. Methods and materials: GSE39582 was randomly divided into a training set and a validation set, while TCGA-COAD and GSE17536 were treated as two independent validation cohorts. Survival-associated genes were included in elastic net penalized Cox proportional hazards regression (ENCPH) model. Based on the results of the ENCPH, a multigene panel was constructed. We evaluated predictive performance of the multigene panel by univariate and multivariate survival analysis, and time-dependent ROC analysis. Results: A total of 1025 colon cancer patients were included in the study, and 94 genes were showed to be related with the overall survival of colon cancer patients, of which 7 genes were integrated to construct a multigene panel according to ENCPH model. The multigene panel could stratify colon cancer patients into notably different risk groups in the training set and three verification cohort. Results of multivariable CPH model suggested that the multigene panel was an independent prognostication factor. The multigene-containing nomogram showed reliable prediction ability on the 3- and 5-year survival of colon cancer patients with internally and externally validated C-indexes exceeded 0.7. Conclusion: The multigene panel we introduced showed considerable prognosis performance in colon cancer, and the multigene panel containing nomogram would help clinicians assess long-term survival probability.", "claims": [{"id": "claim-method", "statement": "Student T test was used to compare C-indexes between two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31839813", "locator": "sections[7] \"Comparison of the prognostication performance of our multigene panel with existing multigene markers\" paragraph 2", "quote": "Student T test was used to compare C-indexes between two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the RMA normalized mRNA expression data and the corresponding clinical data (including age, gender, TNM stage, tumor location, overall survival, recurrence free survival) of the associated colon cancer patients from the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31839813", "locator": "sections[3] \"Colon cancer mRNA expression studies\" paragraph 2", "quote": "We obtained the RMA normalized mRNA expression data and the corresponding clinical data (including age, gender, TNM stage, tumor location, overall survival, recurrence free survival) of the associated colon cancer patients from the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:31839813"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE17536"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31839813", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.35902", 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null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39582", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "We obtained the RMA normalized mRNA expression data and the corresponding clinical data (including age, gender, TNM stage, tumor location, overall survival, recurrence free survival) of the associated colon cancer patients from the Gene Expression Omnibus (GEO) 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