Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34364397", "kind": "science-record", "revision": 4, "content_hash": "sha256:358e3fcece0218e081581a84a400969540bd59575effe7f628e7b0b198e5ed3a", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T21:25:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer.", "doi": "10.1186/s13048-021-00823-y", "pmid": "34364397", "authors": ["Wei Hu", "Mingyue Li", "Qi Zhang", "Chuan Liu", "Xinmei Wang", "Jing Li", "Shusheng Qiu", "Liang Li"], "journal": "Journal of ovarian research", "year": 2021, "abstract": "BACKGROUND: Copy number variation (CNVs) is a key factor in breast cancer development. This study determined prognostic molecular characteristics to predict breast cancer through performing a comprehensive analysis of copy number and gene expression data.\nMETHODS: Breast cancer expression profiles, CNV and complete information from The Cancer Genome Atlas (TCGA) dataset were collected. Gene Expression Omnibus (GEO) chip data sets (GSE20685 and GSE31448) containing breast cancer samples were used as external validation sets. Univariate survival COX analysis, multivariate survival COX analysis, least absolute shrinkage and selection operator (LASSO), Chi square, Kaplan-Meier (KM) survival curve and receiver operating characteristic (ROC) analysis were applied to build a gene signature model and assess its performance.\nRESULTS: A total of 649 CNV related-differentially expressed gene obtained from TCGA-breast cancer dataset were related to several cancer pathways and functions. A prognostic gene sets with 9 genes were developed to stratify patients into high-risk and low-risk groups, and its prognostic performance was verified in two independent patient cohorts (n = 327, 246). The result uncovered that 9-gene signature could independently predict breast cancer prognosis. Lower mutation of PIK3CA and higher mutation of TP53 and CDH1 were found in samples with high-risk score compared with samples with low-risk score. Patients in the high-risk group showed higher immune score, malignant clinical features than those in the low-risk group. The 9-gene signature developed in this study achieved a higher AUC.\nCONCLUSION: The current research established a 5-CNV gene signature to evaluate prognosis of breast cancer patients, which may innovate clinical application of prognostic assessment.", "claims": [{"id": "claim-data-access", "statement": "The analyzed data sets generated during the study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34364397", "locator": "sections[28] \"notes\" paragraph 1", "quote": "The analyzed data sets generated during the 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:34364397"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34364397", "data:geo:GSE20685", "asset:table:pmid:34364397:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20685"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:44:50Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 21035, "completion_tokens": 2098, "cached_tokens": 794}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34364397", "type": "paper", "label": "pmid:34364397"}, {"id": "source:pmid:34364397", "type": "manuscript", "label": "PMID 34364397 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34364397", "type": "paper", "label": "pmid:34364397"}, {"id": "source:pmid:34364397", "type": "manuscript", "label": "PMID 34364397 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34364397", "type": "extraction", "used": ["source:pmid:34364397"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20685", "type": "accession_resolution", "used": ["data:geo:GSE20685"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34364397", "parent_hash": "sha256:c942334f314d69cadfebfe637d123772509c1ba72549dcc9c943719a5a0ff5b7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE31448 licence not read", "asset:data:geo:GSE31448 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}