The types of tumor infiltrating lymphocytes are valuable for the diagnosis and prognosis of breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36386851", "kind": "science-record", "revision": 5, "content_hash": "sha256:77fbafbc73c33e15606434d808bc0ff91308fc108b214a1fd4957ffd8c5de11c", "created_at": "2026-11-01T18:15:49Z", "updated_at": "2026-11-01T22:50:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The types of tumor infiltrating lymphocytes are valuable for the diagnosis and prognosis of breast cancer.", "doi": "10.3389/fgene.2022.1019062", "pmid": "36386851", "authors": ["Ying Sun", "Chunyan Zhang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "This study aimed at constructing a diagnostic immune risk score (dIRS) system and a prognostic immune risk score (pIRS) system for diagnose and prognosis of breast cancer (BC). The gene expression data of BC were downloaded from TCGA dataset (training set), and from GSE65194, GSE29044, GSE42568, and GSE20685 (validation sets). Then, the immune cell type proportions in each dataset were assessed using EPIC tool, and the dIRS system was built based on the SVM-RFE and RF-VIMP algorithms. Subsequently, the pIRS system and the nomogram survival model were established separately using penalized and rms packages. Finally, the differential expressed genes (DEGs) between low and high pIRS groups were screened, and submitted for functional analysis. The dIRS system consisted of B cells, CD8 + T cells, endothelial cells, NK cells, and other cells had high accuracy in distinguishing BC patients from the healthy controls (AUROC >0.7). Subsequently, the pIRS system with the five prognosis-associated immune-infiltrating cell was constructed, and Kaplan-Meier analysis demonstrated that the survival rate of low pIRS group was significantly higher than that of high pIRS group (p < 0.05). Based on age, pathologic stage and the pIRS values, the nomogram survival model was built. The AUROC value, Specificity value, Sensitivity value and C-index of the nomogram survival model were higher than 0.7000, and had a good predictive ability for BC. Finally, a total of 539 DEGs were identified, and significantly enriched in six pathways. The dIRS system and the pIRS system composed of immune cells might be critical for the diagnosis and prognosis of BC patients.", "claims": [{"id": "claim-method", "statement": "Based on the quantitative evaluation proportions of immune cells in the training set (TCGA), Support Vector Machine (SVM)-Recursive Feature Elimination (RFE) and Random Forest Variable Importance (RF-VIMP) algorithms were used to screen the infiltration types of characteristic immune cells.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36386851", "locator": "sections[5] \"Diagnostic analysis\" paragraph 2", "quote": "Based on the quantitative evaluation proportions of immune cells in the training set (TCGA), Support Vector Machine (SVM)-Recursive Feature Elimination (RFE) and Random Forest Variable Importance (RF-VIMP) algorithms were used to screen the infiltration types of characteristic immune cells."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36386851", "locator": "sections[17] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study constructed dIRS and pIRS systems based on estimated immune-cell proportions, with the dIRS system showing AUROC values above 0.7 for distinguishing breast cancer patients from healthy controls and the low-pIRS group showing significantly better survival than the high-pIRS group.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Subsequently, the pIRS system with the five prognosis-associated immune-infiltrating cell was constructed, and Kaplan-Meier analysis demonstrated that the survival rate of low pIRS group was significantly higher than that of high pIRS group (p < 0.05)."}, "evidence": [{"asset": "source:pmid:36386851", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The dIRS system consisted of B cells, CD8 + T cells, endothelial cells, NK cells, and other cells had high accuracy in distinguishing BC patients from the healthy controls (AUROC >0.7)."}, {"asset": "source:pmid:36386851", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Subsequently, the pIRS system with the five prognosis-associated immune-infiltrating cell was constructed, and Kaplan-Meier analysis demonstrated that the survival rate of low pIRS group was significantly higher than that of high pIRS group (p < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study constructed dIRS and pIRS systems based on estimated immune-cell proportions, with the dIRS system showing AUROC values above 0.7 for distinguishing breast cancer patients from healthy controls and the low-pIRS group showing significantly better survival than the high-pIRS group.", "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:36386851"], "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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