{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["14(23)"],"submitter":["Gaiser T"],"pubmed_abstract":["Thymomas are malignant thymic epithelial tumors that are difficult to diagnose due to their rarity and complex diagnostic criteria. They represent a morphologically heterogeneous class of tumors mainly defined by \"organo-typical\" architectural features and cellular composition. The diagnosis of thymoma is burdened with a high level of inter-observer variability and the problem that some type-specific morphological alterations are more on the continuum than clear-cut. Methylation pattern-based classification may help to increase diagnostic precision, particularly in borderline cases. We applied array-based DNA methylation analysis to a set of 113 thymomas with stringent histological annotation. Unsupervised clustering and t-SNE analysis of DNA methylation data clearly segregated thymoma samples mainly according to the current WHO classification into A, AB, B1, B2, B2/B3, B3, and micronodular thymoma with lymphoid stroma. However, methylation analyses separated the histological subgroups AB and B2 into two methylation classes: mono-/bi-phasic AB-thymomas and conventional/\"B1-like\" B2-thymomas. Copy number variation analysis demonstrated methylation class-specific patterns of chromosomal alterations. Our study demonstrates that the current WHO classification is generally well reflected at the methylation level but suggests that B2- and AB-thymomas are (epi)genetically heterogeneous. Methylation-based classifications could help to refine diagnostic criteria for thymoma classification, improve reproducibility, and may affect treatment decisions."],"journal":["Cancers"],"pagination":["5876"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9738683"],"repository":["biostudies-literature"],"pubmed_title":["DNA-Methylation Analysis as a Tool for Thymoma Classification."],"pmcid":["PMC9738683"],"pubmed_authors":["Sahm F","Gaiser T","Hirsch D","Strobel P","von Deimling A","Porth I","Marx A"],"additional_accession":[]},"is_claimable":false,"name":"DNA-Methylation Analysis as a Tool for Thymoma Classification.","description":"Thymomas are malignant thymic epithelial tumors that are difficult to diagnose due to their rarity and complex diagnostic criteria. They represent a morphologically heterogeneous class of tumors mainly defined by \"organo-typical\" architectural features and cellular composition. The diagnosis of thymoma is burdened with a high level of inter-observer variability and the problem that some type-specific morphological alterations are more on the continuum than clear-cut. Methylation pattern-based classification may help to increase diagnostic precision, particularly in borderline cases. We applied array-based DNA methylation analysis to a set of 113 thymomas with stringent histological annotation. Unsupervised clustering and t-SNE analysis of DNA methylation data clearly segregated thymoma samples mainly according to the current WHO classification into A, AB, B1, B2, B2/B3, B3, and micronodular thymoma with lymphoid stroma. However, methylation analyses separated the histological subgroups AB and B2 into two methylation classes: mono-/bi-phasic AB-thymomas and conventional/\"B1-like\" B2-thymomas. Copy number variation analysis demonstrated methylation class-specific patterns of chromosomal alterations. Our study demonstrates that the current WHO classification is generally well reflected at the methylation level but suggests that B2- and AB-thymomas are (epi)genetically heterogeneous. Methylation-based classifications could help to refine diagnostic criteria for thymoma classification, improve reproducibility, and may affect treatment decisions.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Nov","modification":"2025-04-20T03:32:30.969Z","creation":"2025-04-20T03:32:30.969Z"},"accession":"S-EPMC9738683","cross_references":{"pubmed":["36497358"],"doi":["10.3390/cancers14235876"]}}