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Genomic profiling of chromophobe renal cell carcinoma by array-based comparative genomic hybridization

ABSTRACT: In this study, we investigated CNAs of 4 tumor samples from 2 patients, including conventioanl chromophobe renal cell carcinoma(ChRCC), ChRCC with neuroendocrine differentiation and no-tumor region by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

ORGANISM(S): Homo sapiens

PROVIDER: GSE52641 | GEO | 2015/01/21

SECONDARY ACCESSION(S): PRJNA229563

REPOSITORIES: GEO

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Genomic profiling of chromophobe renal cell carcinoma by array-based comparative genomic hybridization

Project description:In this study, we investigated CNAs of 4 tumor samples from 2 patients, including conventioanl chromophobe renal cell carcinoma(ChRCC), ChRCC with neuroendocrine differentiation and no-tumor region by 44k oligonucleotide-based array comparative genomic hybridization (array CGH). 2 cases of ChRCC(NOS) vs ChRCC with neuroendocrine differentiation

2015-01-21 | E-GEOD-52641 | biostudies-arrayexpress

Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

Project description:In this study, we investigated CNAs of 40 tumor samples from 25 patients, including 15 metastatic primary tumor (MPT), paired neck lymph-node metastasis (LNM) and 10 non-metastatic primary tumor (NMPT), by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

2013-09-08 | GSE36942 | GEO

RBPJ::ALK : a novel fusion gene amplified in a metastatic sarcomatoid chromophobe renal cell carcinoma

Project description:Using Fluorescence in situ hybridization (FISH), Comparative genomic hybridization on array (aCGH) and Targeted RNA sequencing (RNASeq), we observed a novel fusion of ALK with RPBJ that was amplified and immunohistochemically overexpressed in both the small sarcomatoid component of a chromophobe renal cell carcinoma (chRCC) and in its lymph node metastasis. The amplified RBPJ::ALK fusion was not detected in the chromophobe component of the primary tumour that harbored chRCC-typical losses of chromosomes 1, 2, 6, 10, 13 and 17. In contrast, the same mutations of PTEN, TP53 and TERT promoter were observed together in the three analyzed samples from chRCC, sarcomatoid component of the chRCC and metastasis.

2024-02-01 | GSE224415 | GEO

Transcription profiling of chromophobe renal cell carcinoma and oncocytoma samples

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. 30 mRNA profiling samples (15 chromophobe RCC, 15 oncocytoma)

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

Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma

2010-06-18 | GSE19982 | 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

Genomic profiling of primary and metastatic clear cell renal cell carcinoma by array-based comparative genomic hybridization.

Project description:In this study, we investigated CNAs of 20 primary clear cell renal cell caricinomas (ccRCCs), 20 corresponding metastases and another subsets of 30 primary ccRCCs by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

2014-10-16 | GSE43477 | GEO

Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

2013-09-08 | E-GEOD-36942 | biostudies-arrayexpress

Intratumoral genomic heterogeneity in submucosal-invasive gastric cancer

Project description:In this study, we investigated CNAs of 59 tumor samples from 27 patients with submucosal-invasive gastric cancers (SMGC) by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

2012-01-20 | GSE26800 | GEO

Chromophobe renal cell carcinoma versus renal oncocytoma: a proteomic approach

Project description:The proteome of clinical tissue samples diagnosed with chromophobe renal cell carcinomas (chRCC) and renal oncocytomas (RO) were evaluated to establish a potential discriminative biomarker panel of proteins for these two tumors subtypes.

2024-01-26 | PXD022018 | Pride

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