Colorectal Cancer Prognosis is Not Associated with BRAF and KRAS Mutations-A STROBE Compliant Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30658510", "kind": "science-record", "revision": 7, "content_hash": "sha256:eec32b3681cebf10742a3a49bd2ecd94dbc5655d363fc57cab5fbda801ea73d5", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T21:21:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Colorectal Cancer Prognosis is Not Associated with BRAF and KRAS Mutations-A STROBE Compliant Study.", "doi": "10.3390/jcm8010111", "pmid": "30658510", "authors": ["Joon-Hyop Lee", "Jiyoung Ahn", "Won Seo Park", "Eun Kyung Choe", "Eunyoung Kim", "Rumi Shin", "Seung Chul Heo", "Sohee Jung", "Kwangsoo Kim", "Young Jun Chai", "Heejoon Chae"], "journal": "Journal of clinical medicine", "year": 2019, "abstract": "BACKGROUND: We investigated the associations between v-Raf murine sarcoma viral oncogene homolog B1 (BRAFV600E, henceforth BRAF) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and colorectal cancer (CRC) prognosis, using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GSE39582) datasets.\nMATERIALS AND METHODS: The effects of BRAF and KRAS mutations on overall survival (OS) and disease-free survival (DFS) of CRC were evaluated.\nRESULTS: The mutational status of BRAF and KRAS genes was not associated with overall survival (OS) or DFS of the CRC patients drawn from the TCGA database. The 3-year OS and DFS rates of the BRAF mutation (+) vs. mutation (-) groups were 92.6% vs. 90.4% and 79.7% vs. 68.4%, respectively. The 3-year OS and DFS rates of the KRAS mutation (+) vs. mutation (-) groups were 90.4% vs. 90.5% and 65.3% vs. 73.5%, respectively. In stage II patients, however, the 3-year OS rate was lower in the BRAF mutation (+) group than in the mutation (-) group (85.5% vs. 97.7%, p <0.001). The mutational status of BRAF genes of 497 CRC patients drawn from the GSE39582 database was not associated with OS or DFS. The 3-year OS and DFS rates of BRAF mutation (+) vs. mutation (-) groups were 75.7% vs. 78.9% and 73.6% vs. 71.1%, respectively. However, KRAS mutational status had an effect on 3-year OS rate (71.9% mutation (+) vs. 83% mutation (-), p = 0.05) and DFS rate (66.3% mutation (+) vs. 74.6% mutation (-), p = 0.013).\nCONCLUSIONS: We found no consistent association between the mutational status of BRAF nor KRAS and the OS and DFS of CRC patients from the TCGA and GSE39582 databases. Studies with longer-term records and larger patient numbers may be necessary to expound the influence of BRAF and KRAS mutations on the outcomes of CRC.", "claims": [{"id": "claim-method", "statement": "The potential influence of BRAF and KRAS mutations on each TNM stage on 3-year patient overall survival (OS) and disease-free survival (DFS) was analyzed using the life table method. Kaplan-Meier estimates were calculated for all possible combination of BRAF and KRAS mutation over each TNM stage.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30658510", "locator": "sections[5] \"2.3. Kaplan–Meier Survival Analysis of BRAF and KRAS Mutations\" paragraph 2", "quote": "The potential influence of BRAF and KRAS mutations on each TNM stage on 3-year patient overall survival (OS) and disease-free survival (DFS) was analyzed using the life table method."}, {"asset": "source:pmid:30658510", "locator": "sections[5] \"2.3. Kaplan–Meier Survival Analysis of BRAF and KRAS Mutations\" paragraph 2", "quote": "Kaplan-Meier estimates were calculated for all possible combination of BRAF and KRAS mutation over each TNM stage."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data of 536 patients with genomic variant colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) with corresponding clinical information were obtained from the TCGA GDC portal (https://portal.gdc.cancer.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30658510", "locator": "sections[3] \"2.1. Data Acquisition and Selection\" paragraph 2", "quote": "The data of 536 patients with genomic variant colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) with corresponding clinical information were obtained from the TCGA GDC portal (https://portal.gdc.cancer.gov/)."}], "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:30658510"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30658510", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/jcm8010111", "sha256": "sha256:56d5ee4aba3819a90177da5c6512dd1e6f43df2fe6d9992e0a5349ea1339d433", "bytes": 29136, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/jcm8010111", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6351956", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"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": "The data of 536 patients with genomic variant colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) with corresponding clinical 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Results", "row_count": 18, "column_count": 4}, "table": {"label": "Table 1", "caption": "Baseline characteristics of datasets.", "rows": [["", "", "TCGA", "GSE39582"], ["Total number of patients studied", "", "447", "497"], ["Age at diagnosis (mean ± SD), years old", "", "65.0 ± 12.9", "66.8 ± 13.1"], ["Gender", "", "", ""], ["", "Male", "213 (47.7%)", "271 (54.5%)"], ["", "Female", "234 (52.3%)", "226 (45.5%)"], ["Number of BRAF mutations", "", "59 (13.2%)", "49 (9.9%)"], ["Number of KRAS mutations", "", "384 (85.9%)", "197 (39.6%)"], ["AJCC TNM stage (number of BRAF/KRAS mutations)", "", "", ""], ["", "I", "83 (10/36)", "32 (1/15)"], ["", "II", "172 (31/77)", "242 (21/83)"], ["", "III", "134 (14/50)", "163 (21/70)"], ["", "IV", "58 (4/21)", "60 (6/29)"], ["Survival event", "", "", ""], ["", "Dead", "46 (10.3%)", "40 (8.0%)"], ["", "Alive", "404 (90.4%)", "457 (92.0%)"], ["Median follow-up time, months (range)", "", "23.9 (0–147.9)", "52 (0–201)"], ["Median time to survival event, months (range)", "", "24.4 (4.0–99.9)", "31 (0–183)"]], "row_count": 18, "column_count": 4, "numeric_cells": 29, "header_rows": 1, "locator": "section[6]/table-wrap[1]#jcm-08-00111-t001"}}, {"id": "asset:table:pmid:30658510:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:20e04bd126d101d42b087e578a11042da8b7f681aaef6fb409e880e95f2daef0", "bytes": 897, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#jcm-08-00111-t002", "version": null, "note": "BRAF/KRAS status and prognosis in previous studies.", "structure": {"pmcid": "PMC6351956", "section_index": 10, "section_title": "4. Discussion", "row_count": 9, "column_count": 7}, "table": {"label": "Table 2", "caption": "BRAF/KRAS status and prognosis in previous studies.", "rows": [["Author, Year", "Country", "Time Frame", "Patients", "Stage", "Outcomes", "Poor Prognosis"], ["BRAF", "", "", "", "", "", ""], ["Won et al. 2017", "South Korea", "2010–2013", "1049", "I, II, III", "OS *, DFS **", "Mutant type"], ["Seligmann et al., 2017", "United Kingdom", "2000–2003", "231", "IV", "PFS ***", "Mutant type"], ["Roth et al. 2010", "Switzerland", "(−)", "1404", "II, III", "OS *, DFS **", "Mutant type"], ["KRAS", "", "", "", "", "", ""], ["De Roock et al. 2010", "Belgium", "2001–2008", "229", "IV", "PFS ***", "No difference"], ["Bokemeyer et al. 2011", "Germany", "2006–2007", "315", "IV", "PFS ***", "Mutant type"], ["Schwartzberg et al. 2014", "Spain", "2009–2011", "278", "IV", "PFS ***, OS *", "Mutant type"]], "row_count": 9, "column_count": 7, "numeric_cells": 17, "header_rows": 1, "locator": "section[10]/table-wrap[1]#jcm-08-00111-t002"}}], "gaps": ["asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis using the life table method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "The potential influence of BRAF and KRAS mutations on each TNM stage on 3-year patient overall survival (OS) and disease-free survival (DFS) was analyzed using the life table method. Kaplan-Meier estimates were calculated for all possible combination of BRAF and KRAS mutation over each TNM stage."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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