An Eight-CpG-based Methylation Classifier for Preoperative Discriminating Early and Advanced-Late Stage of Colorectal Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33519917", "kind": "science-record", "revision": 7, "content_hash": "sha256:48a7a5e2c8b180be2989b72b761d555ebf22ac099434fda26c3b97d76d9eaf60", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T22:03:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An Eight-CpG-based Methylation Classifier for Preoperative Discriminating Early and Advanced-Late Stage of Colorectal Cancer.", "doi": "10.3389/fgene.2020.614160", "pmid": "33519917", "authors": ["Ji Hu", "Fu-Ying Zhao", "Bin Huang", "Jing Ran", "Mei-Yuan Chen", "Hai-Lin Liu", "You-Song Deng", "Xia Zhao", "Xiao-Fan Han"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "AIM: To develop and validate a CpG-based classifier for preoperative discrimination of early and advanced-late stage colorectal cancer (CRC).\nMETHODS: We identified an epigenetic signature based on methylation status of multiple CpG sites (CpGs) from 372 subjects in The Cancer Genome Atlas (TCGA) CRC cohort, and an external cohort (GSE48684) with 64 subjects by LASSO regression algorithm. A classifier derived from the methylation signature was used to establish a multivariable logistic regression model to predict the advanced-late stage of CRC. A nomogram was further developed by incorporating the classifier and some independent clinical risk factors, and its performance was evaluated by discrimination and calibration analysis. The prognostic value of the classifier was determined by survival analysis. Furthermore, the diagnostic performance of several CpGs in the methylation signature was evaluated.\nRESULTS: The eight-CpG-based methylation signature discriminated early stage from advanced-late stage CRC, with a satisfactory AUC of more than 0.700 in both the training and validation sets. This methylation classifier was identified as an independent predictor for CRC staging. The nomogram showed favorable predictive power for preoperative staging, and the C-index reached 0.817 (95% CI: 0.753-0.881) and 0.817 (95% CI: 0.721-0.913) in another training set and validation set respectively, with good calibration. The patients stratified in the high-risk group by the methylation classifier had significantly worse survival outcome than those in the low-risk group. Combination diagnosis utilizing only four of the eight specific CpGs performed well, even in CRC patients with low CEA level or at early stage.\nCONCLUSIONS: Our classifier is a valuable predictive indicator that can supplement established methods for more accurate preoperative staging and also provides prognostic information for CRC patients. Besides, the combination of multiple CpGs has a high value in the diagnosis of CRC.", "claims": [{"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://xena.ucsc.edu/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48684.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33519917", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://xena.ucsc.edu/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48684."}], "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:33519917"], "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:GSE48684"], "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:group_comparison_mann_whitney", "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:GSE48684"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33519917", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.614160", "sha256": "sha256:4976da5559a378923ea9f6e67cef5cbc8452fdf76cb903ea8377474c280f38e4", "bytes": 34965, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2020.614160", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7838682", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE48684", "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=GSE48684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48684", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://xena.ucsc.edu/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48684.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://xena.ucsc.edu/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48684.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1183439", "GSM1183440", "GSM1183441", "GSM1183442", "GSM1183443", "GSM1183444", "GSM1183445", "GSM1183446", "GSM1183447", "GSM1183448", "GSM1183449", "GSM1183450", "GSM1183451", "GSM1183452", "GSM1183453", "GSM1183454", "GSM1183455", "GSM1183456", "GSM1183457", "GSM1183458", "GSM1183459", "GSM1183460", "GSM1183461", "GSM1183462", "GSM1183463", "GSM1183464", "GSM1183465", "GSM1183466", "GSM1183467", "GSM1183468", "GSM1183469", "GSM1183470", "GSM1183471", "GSM1183472", "GSM1183473", "GSM1183474", "GSM1183475", "GSM1183476", "GSM1183477", "GSM1183478", "GSM1183479", "GSM1183480", "GSM1183481", "GSM1183482", "GSM1183483", "GSM1183484", "GSM1183485", "GSM1183486", "GSM1183487", "GSM1183488", "GSM1183489", "GSM1183490", "GSM1183491", "GSM1183492", "GSM1183493", "GSM1183494", "GSM1183495", "GSM1183496", "GSM1183497", "GSM1183498", "GSM1183499", "GSM1183500", "GSM1183501", "GSM1183502", "GSM1183503", "GSM1183504", "GSM1183505", "GSM1183506", "GSM1183507", "GSM1183508", "GSM1183509", "GSM1183510", "GSM1183511", "GSM1183512", "GSM1183513", "GSM1183514", "GSM1183515", "GSM1183516", "GSM1183517", "GSM1183518", "GSM1183519", "GSM1183520", "GSM1183521", "GSM1183522", "GSM1183523", "GSM1183524", "GSM1183525", "GSM1183526", "GSM1183527", "GSM1183528", "GSM1183529", "GSM1183530", "GSM1183531", "GSM1183532", "GSM1183533", "GSM1183534", "GSM1183535", "GSM1183536", "GSM1183537", "GSM1183538", "GSM1183539", "GSM1183540", "GSM1183541", "GSM1183542", "GSM1183543", "GSM1183544", "GSM1183545", "GSM1183546", "GSM1183547", "GSM1183548", "GSM1183549", "GSM1183550", "GSM1183551", "GSM1183552", "GSM1183553", "GSM1183554", "GSM1183555", "GSM1183556", "GSM1183557", "GSM1183558", "GSM1183559", "GSM1183560", "GSM1183561", "GSM1235135", "GSM1235136", "GSM1235137", "GSM1235138", "GSM1235139", "GSM1235140", "GSM1235141", "GSM1235142", "GSM1235143", "GSM1235144", "GSM1235145", "GSM1235146", "GSM1235147", "GSM1235148", "GSM1235149", "GSM1235150", "GSM1235151", "GSM1235152", "GSM1235153", "GSM1235154", "GSM1235155", "GSM1235156", "GSM1235157", "GSM1235158"], "sample_count": 147, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Global DNA methylation alterations reveal multiple pathways in the initiation and progression of colorectal cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33519917:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:09080ac1c2dc23c413a4e2e43146954281ec7d9e98776f1690078811837ecd4c", "bytes": 886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "Logistic regression analysis of clinical characteristics and methylation classifier.", "structure": {"pmcid": "PMC7838682", "section_index": 12, "section_title": "A Clinical Eepigenetic Nomogram Development and Corresponding Classification Performance", "row_count": 12, "column_count": 7}, "table": {"label": "TABLE 1", "caption": "Logistic regression analysis of clinical characteristics and methylation classifier.", "rows": [["Characteristics", "Univariable analysis", "Multivariable analysis"], ["", "OR", "95% CI", "P-value*", "OR", "95% CI", "P-value**"], ["Age (years)", "", "", "", "", "", ""], ["≤66.5", "1", "", "", "", "", ""], [">66.5", "0.546", "0.377–0.785", "0.001", "0.500", "0.321–0.768", "0.002"], ["CEAlevels (ng/ml)", "", "", "", "", "", ""], ["≤2", "1", "", "", "", "", ""], ["2–20", "7.250", "3.220–20.864", "<0.001", "5.971", "2.498–17.915", "<0.001"], ["≥20", "2.368", "1.368–4.582", "0.004", "1.943", "1.068–3.897", "0.040"], ["Methylation classifier", "", "", "", "", "", ""], ["Low risk group", "1", "", "", "", "", ""], ["High risk group", "4.252", "2.824–6.560", "<0.001", "3.882", "2.510–6.164", "<0.001"]], "row_count": 12, "column_count": 7, "numeric_cells": 34, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE48684 not downloaded", "asset:data:geo:GSE48684 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-2", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "logistic regression"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [], "gaps": ["method.group_comparison_mann_whitney"]}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "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": ["GSE48684"], "resolved_accessions": ["GSE48684"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: https://xena.ucsc.edu/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48684."], "basis": "The paper names GSE48684 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33519917", "data:geo:GSE48684", "asset:table:pmid:33519917:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE48684"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:23:29Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 26415, "completion_tokens": 1062, "cached_tokens": 520}}, "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:33519917", "type": "paper", "label": "pmid:33519917"}, {"id": "source:pmid:33519917", "type": "manuscript", "label": "PMID 33519917 full text"}, {"id": "data:geo:GSE48684", "type": "dataset", "label": "GEO GSE48684"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33519917", "type": "paper", "label": "pmid:33519917"}, {"id": "source:pmid:33519917", "type": "manuscript", "label": "PMID 33519917 full text"}, {"id": "data:geo:GSE48684", "type": "dataset", "label": "GEO GSE48684"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33519917", "type": "extraction", "used": ["source:pmid:33519917"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE48684", "type": "accession_resolution", "used": ["data:geo:GSE48684"], "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:33519917", "parent_hash": "sha256:b3d2316d3150179914e42e71aed7e51efac7d99d70ea089662b4f0e4b277394c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE48684 licence not read", "asset:data:geo:GSE48684 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ht specific CpGs performed well, even in CRC patients with low CEA level or at early stage. CONCLUSIONS"], "order_basis": "paper_text_order:1761", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Mann-Whitney"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}