Systemic Investigation Identifying Salivary miR-196b as a Promising Biomarker for Early Detection of Head-Neck Cancer and Oral Precancer Lesions.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34441345", "kind": "science-record", "revision": 3, "content_hash": "sha256:c5cd1e1ee85f3b5bbafb5a449a3e7aa42a28ee9e8ee84a4744b509cda2f9dc0c", "created_at": "2026-11-01T15:41:49Z", "updated_at": "2026-11-01T21:26:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systemic Investigation Identifying Salivary miR-196b as a Promising Biomarker for Early Detection of Head-Neck Cancer and Oral Precancer Lesions.", "doi": "10.3390/diagnostics11081411", "pmid": "34441345", "authors": ["Ann-Joy Cheng", "Guo-Rung You", "Che-Jui Lee", "Ya-Ching Lu", "Shang-Ju Tang", "Yi-Fang Huang", "Yu-Chen Huang", "Li-Yu Lee", "Kang-Hsing Fan", "Yen-Chao Chen", "Shiang-Fu Huang", "Joseph Tung-Chieh Chang"], "journal": "Diagnostics (Basel, Switzerland)", "year": 2021, "abstract": "BACKGROUND: Liquid biopsy is a rapidly growing field, for it may provide a minimally invasive way to acquire pathological data for personalized medicine. This study developed a systemic strategy to discover an effective salivary biomarker for early detection of patients with head-neck squamous carcinoma (HNSC) and oral precancer lesion (OPC).\nMETHODS: A total of 10 miRNAs were examined in parallel with multiple independent cohorts. These included a training set of salivary samples from HNSC patients, the TCGA-HNSC and GSE31277 cohorts to differentiate miRNAs between tumor and normal tissues, and groups of salivary samples from healthy individuals, patients with HNSC and OPC.\nRESULTS: The combined results from the salivary training set and the TCGA-HNSC cohort showed that four miRNAs (miR-148b, miR-155, miR-196b, and miR-31) consistently increased in HNSC patients. Further integration with the GSE31277 cohort, two miRNAs (miR-31 and miR-196b) maintained at high significances. Further assessment showed that salivary miR-196b was a prominent diagnostic biomarker, as it remarkably discriminated between healthy individuals and patients with HNSC (p < 0.0001, AUC = 0.767, OR = 5.64) or OPC (p < 0.0001, AUC = 0.979, OR = 459).\nCONCLUSION: Salivary miR-196b could be an excellent biomarker for diagnosing OPC and early detection of HNSC. This molecule may be used for early screening high-risk groups of HNSC.", "claims": [{"id": "claim-method", "statement": "The significance of the differential expression level between tumor and normal tissues was examined by the p-value determined using the Student’s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34441345", "locator": "sections[5] \"2.3. Bioinformatic Assessment of the Specific miRNAs in the Diagnostic Potential for HNSC\" paragraph 2", "quote": "The significance of the differential expression level between tumor and normal tissues was examined by the p-value determined using the Student’s t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available on request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34441345", "locator": "sections[19] \"notes\" paragraph 1", "quote": "The data presented in this study are available on request from the corresponding author."}], "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:34441345"], "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:GSE31277"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE31277"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34441345", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/diagnostics11081411", "sha256": "sha256:674d3a717fd34d1adf1dc8ab7948d76732cbc3fec21b00cd84df0510d25d49bb", "bytes": 28758, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/diagnostics11081411", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8392418", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE31277", "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=GSE31277", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31277", "version": null, "note": "The data presented in this study are available on request from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available on request from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1162705", "GSM1162706", "GSM1162707", "GSM1162708", "GSM1162709", "GSM1162710", "GSM1162711", "GSM1162712", "GSM1162713", "GSM1162714", "GSM1162715", "GSM1162716", "GSM480891", "GSM480892", "GSM480893", "GSM480894", "GSM480895", "GSM480896", "GSM480897", "GSM480898", "GSM480899", "GSM480900", "GSM480901", "GSM480902", "GSM480903", "GSM480904", "GSM480905", "GSM480906", "GSM480907", "GSM480908", "GSM480909", "GSM480910", "GSM480911", "GSM480912", "GSM480913", "GSM480914", "GSM480915", "GSM480916", "GSM480917", "GSM480918", "GSM480919", "GSM480920"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "4133;10332;9770", "taxon": "Homo sapiens", "title": "MicroRNA expression profile in Head and Neck Cancer: HOX-cluster embedded microRNA-196 and microRNA-10b dysregulation is implicated in cell proliferation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE31277 not downloaded", "asset:data:geo:GSE31277 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student’s t-test, using OMCD to analyze the TCGA-HNSC dataset and GEO2R to analyze the GSE31277 dataset", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The significance of the differential expression level between tumor and normal tissues was examined by the p-value determined using the Student’s t-test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Student’s t-test, using OMCD to analyze the TCGA-HNSC dataset and GEO2R to analyze the GSE31277 dataset), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE31277"], "resolved_accessions": ["GSE31277"], "statements": ["The data presented in this study are available on request from the corresponding author."], "basis": "The paper names GSE31277 in Gene Expression Omnibus (GEO), NCBI and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34441345", "data:geo:GSE31277"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE31277"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22387, "completion_tokens": 1224, "cached_tokens": 784}}, "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:34441345", "type": "paper", "label": "pmid:34441345"}, {"id": "source:pmid:34441345", "type": "manuscript", "label": "PMID 34441345 full text"}, {"id": "data:geo:GSE31277", "type": "dataset", "label": "GEO GSE31277"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34441345", "type": "paper", "label": "pmid:34441345"}, {"id": "source:pmid:34441345", "type": "manuscript", "label": "PMID 34441345 full text"}, {"id": "data:geo:GSE31277", "type": "dataset", "label": "GEO GSE31277"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34441345", "type": "extraction", "used": ["source:pmid:34441345"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE31277", "type": "accession_resolution", "used": ["data:geo:GSE31277"], "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:34441345", "parent_hash": "sha256:3b95ffd5d157cbe72c56008d03021f732eec22b08eb261c826593de776da287b", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE31277 licence not read", "asset:data:geo:GSE31277 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}