Project description:We profiled DNA methylation in fresh-frozen oncocytoma and chRCC tumors and tumor-adjacent adjacent normal tissue to identify a signature of differentially methylated CpG sites that robustly distinguish oncocytoma from chRCC. DNA methylation profiles were generated for renal oncocytomas (n=12), primary kidney chromophobes (chRCC) (n=8) and primary kidney clear cell carcinomas (ccRCC) (n=2). Also profiled were three oncocytic neoplasms of unclear pathological diagnosis, including two masses described as hybrid oncocytic/chromophobe type (n=2), and one mass described as hybrid oncocytic renal neoplasm. Also profiled were histologically normal adjacent kidney parenchyma tissue (NKP) from a subset of these patients, including NKP from oncocytoma (n=7), chRCC (n=5), ccRCC (n=1), hybrid oncocytic/chromophobe type (n=1), and hybrid oncocytic renal neoplasm (n=1) bearing kidneys (combined n=15 NKP).

2020-09-30 | GSE156932 | GEO

Gene expression and SNP profiling discriminates chromophobe renal cell carcinoma and oncocytoma

Project description:Gene expression profiles, high-throughput SNP genotyping, and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. A cytogenetic alteration, loss of chromosome 1p, common to renal oncocytoma and chRCC has been identified, providing the opportunities for identifying novel tumor suppressor genes and we have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma. Oncocytoma and Chromophobe RCC samples - SNP chip analysis

2011-02-02 | E-GEOD-20376 | biostudies-arrayexpress

microRNA profiling in renal cell carcinoma subtypes

Project description:Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma. We performed a miRNA microarray on 10 tumor samples of each papillary renal cell carcinoma (pRCC), chromophobe renal cell carcinoma (chRCC), and oncocytoma.

2012-08-13 | E-GEOD-39790 | biostudies-arrayexpress

Gene Expression Profiling Separates Chromophobe Renal Cell Carcinoma from Oncocytoma

Project description:This study aims to compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes.

2008-07-12 | GSE12090 | GEO

Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma

Project description:[original title] Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma. Background : Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. Methods : Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n=15) and oncocytoma specimens (n=15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. Immunohistochemical validation was performed in an independent set of tumors. Results : A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities. Conclusion : Gene expression profiles and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. We have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.

2010-06-18 | GSE19982 | GEO

Genotyping and copy number analysis of human renal epithelial neoplasms

Project description:Renal tumors with complex morphology require extensive workup for accurate classification. Chromosomal aberrations that define subtypes of renal epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations. Experiment Overall Design: We analyzed 20 paraffin-embedded tissues representing conventional renal cell carcinoma (RCC), papillary RCC, chromophobe RCC, and oncocytoma with Affymetrix GeneChip 10K 2.0 Mapping arrays.

2008-04-10 | E-GEOD-9469 | biostudies-arrayexpress

Transcription profiling of chromophobe renal cell carcinoma and oncocytoma samples

2010-07-08 | E-GEOD-19982 | biostudies-arrayexpress