Genomewide copy number profiles for Adenosarcoma patients in Taiwan

Müllerian adenosarcomas are malignant gynecologic neoplasms. Advanced disease stage and sarcomatous overgrowth predict aggressive clinical courses. We conducted this study to characterize the genomewide copy number variations (CNV) in adenosarcomas. Paraffin samples from 13 cases were subjected to CNV analysis using OncoScan® FFPE Assay Kit. CNVs were significantly higher in cases with sarcomatous overgrowth. Frequent amplifications of chromosomal segments in 12p12.3 and 12q13.3-23.3 were noted, involving established or potential oncogenes including PIK3C2G (5 cases), MDM2, CPM, YEATS4, CDK4, GLI1, DDIT3 (co-amplified in 4 cases), as well as HMGA2 in 3 cases. MDM2 and CDK4 amplification was verified by fluorescence in situ hybridization. A total of 16 formalin-fixed paraffin-embedded tumor samples from different patients were subjected to genomic DNA extract and SNP array using the novel molecular inversion probe-based OncoScan FFPE Assay Kit (Affymetrix, Santa Clara, California, USA). The raw probe intensity was recorded by using the scanner. Subsequently, intensity value was transformed into copy number by using the official software, Oncoscan Console, provided by Affymetrix Inc. (Santa Clara, CA, USA). The reference model was also provided by the Affymetrix Inc., which included 390 formalin-fixed and paraffin-embedded (FFPE) samples.