biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsJulia Salmerongenotyping by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16327Extramedullary (or extraosseous) plasmacytoma (EMP) is a localized plasma cell neoplasm lacking apparent bone marrow involvement and other features of multiple myeloma (MM). The prognosis is usually favorable and progression to MM is infrequent. The genetic landscape of EMP remains largely unknown. Importantly, EMP must be distinguished from extramedullary disease of MM (EMD), which typically exhibits aggressive behavior. We performed a comprehensive molecular analysis of EMP (n=24) in comparison to EMD (n=24) using fluorescence in situ hybridization (FISH), copy number (CN) profiling, and targeted next-generation sequencing.biostudies-arrayexpressNucleic Acid Extraction - Genomic DNA was extracted from FFPE tissue sections after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures. DNA concentration and purity were assessed by spectrophotometry.Hybridization - Biotin-labeled DNA was hybridized to the Affymetrix OncoScan™ FFPE Assay kit/GPL18602 cartridges according to the manufacturer’s recommended protocol.Scaning - Array scanning and feature extraction were performed using Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.Sample Collection - Tissue samples were collected from diagnostic FFPE blocks obtained during routine clinical evaluation. Samples correspond to extramedullary plasmacytomas or extramedullary myeloma lesions. Tissue processing and fixation followed standard pathology proceduresLabeling - Genomic DNA was labeled and processed according to the Affymetrix OncoScan™ FFPE Assay kit/GPL18602 using molecular inversion probes and biotin incorporation.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsJulia SalmeronData Transformation - Raw CEL files were processed using the Affymetrix OncoScan Console software. Copy-number profiles and OSCHP files were generated using the default normalization and analysis pipeline.falseCN analysis of extramedullary plasmacytoma and extramedullary disease of myelomaExtramedullary (or extraosseous) plasmacytoma (EMP) is a localized plasma cell neoplasm lacking apparent bone marrow involvement and other features of multiple myeloma (MM). The prognosis is usually favorable and progression to MM is infrequent. The genetic landscape of EMP remains largely unknown. Importantly, EMP must be distinguished from extramedullary disease of MM (EMD), which typically exhibits aggressive behavior. We performed a comprehensive molecular analysis of EMP (n=24) in comparison to EMD (n=24) using fluorescence in situ hybridization (FISH), copy number (CN) profiling, and targeted next-generation sequencing.2026-05-01T00:00:00Z2026-05-01T01:04:08.523Z2025-12-02T14:01:31.724ZE-MTAB-16327EFO_0002944EFO_0003814EFO_0003813EFO_0002767EFO_0005518EFO_0003816EFO_0003815