The clonal expression genes associated with poor prognosis of liver cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36092878", "kind": "science-record", "revision": 4, "content_hash": "sha256:ca0bb23ac25a5436450b973ec0aebabc55216c0fc9c9c7b07fa68b1fb0da3839", "created_at": "2026-11-01T18:15:19Z", "updated_at": "2026-11-01T22:07:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The clonal expression genes associated with poor prognosis of liver cancer.", "doi": "10.3389/fgene.2022.808273", "pmid": "36092878", "authors": ["Wanfeng Zhang", "Fang Huang", "Xia Tang", "Longke Ran"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "The extensive spatial genomic intratumor heterogeneity (ITH) in liver cancer hindered treatment development and limited biomarker design. Early events that drive tumor malignant transformation in tumor founder cells are clonally present in all tumor cell populations, which provide stable biomarkers for the localization of tumor cells and patients' prognosis. In the present study, we identified the recurrently clonal somatic mutations and copy number alterations (CNAs) (893 clonal somatic mutations and 6,617 clonal CNAs) in 353 liver cancer patients from The Cancer Genome Atlas (TCGA) and evaluated their prognosis potential. We showed that prognosis-related clonal alterations might play essential roles in tumor evolution. We identified 32 prognosis related clonal alterations differentially expressed between paired normal and tumor samples, that their expression was cross-validated by three independent cohorts (50 paired samples in TCGA, 149 paired samples in GSE76297, and 9 paired samples in SUB6779164). These clonal expression alterations were also significantly correlated with clinical phenotypes. Using stepwise regression, we identified five (UCK2, EFNA4, KPAN2, UBE2T, and KIF14) and six (MCM10, UCK2, IQGAP3, EFNA4, UBE2T, and KPNA2) clonal expression alterations for recurrence and survival model construction, respectively. Furthermore, in 10 random repetitions, we showed strong applicability of the multivariate Cox regression models constructed based on the clonal expression genes, which significantly predicted the outcomes of the patients in all the training and validation sets. Taken together, our work may provide a new avenue to overcome spatial ITH and refine biomarker design across cancer types.", "claims": [{"id": "claim-method", "statement": "Then, the prognosis-related clonal expression genes were used to construct a multivariate Cox regression model, and stepwise regression was used to select the clonal expression genes in the most minimalistic model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36092878", "locator": "sections[9] \"Multivariate cox regression model construction\" paragraph 2", "quote": "Then, the prognosis-related clonal expression genes were used to construct a multivariate Cox regression model, and stepwise regression was used to select the clonal expression genes in the most minimalistic model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36092878", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using stepwise regression, we identified five (UCK2, EFNA4, KPAN2, UBE2T, and KIF14) and six (MCM10, UCK2, IQGAP3, EFNA4, UBE2T, and KPNA2) clonal expression alterations for recurrence and survival model construction, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36092878", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using stepwise regression, we identified five (UCK2, EFNA4, KPAN2, UBE2T, and KIF14) and six (MCM10, UCK2, IQGAP3, EFNA4, UBE2T, and KPNA2) clonal expression alterations for recurrence and survival model construction, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using stepwise regression, we identified five (UCK2, EFNA4, KPAN2, UBE2T, and KIF14) and six (MCM10, UCK2, IQGAP3, EFNA4, UBE2T, and KPNA2) clonal expression alterations for recurrence and survival model construction, respectively.", "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:36092878"], "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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