GEO DataSets

(Submitter supplied) Detailed genetic profiling of clear cell Renal Cell Carcinoma (ccRCC) has shown that these tumors are characterized by large genetic heterogeneity with some genomic regions commonly affected by structural changes. Loss on chromosomes 3p and 14q, and gain on 5q and 7 are examples of alterations commonly reported in ccRCC. However, there is no consensus regarding the potential prognostic information carried by the identified alterations. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL13829

125 Samples

Download data: TXT

(Submitter supplied) Recent insights into the role of the VHL tumor suppressor gene in hereditary and sporadic clear cell carcinoma of the kidney (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL3720 GPL3921

229 Samples

Download data: CEL

(Submitter supplied) We applied Illumina’s 317K high-density SNP-arrays to profile chromosomal aberrations in clear cell renal cell carcinoma (ccRCC) from 80 patients and analyzed the association of LOH/amplification events with clinicopathological characteristics

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6979 GPL6980

80 Samples

Download data

(Submitter supplied) 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).

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8841

70 Samples

Download data: TXT

(Submitter supplied) We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC) patients to investigate intra-tumour heterogeneity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

62 Samples

Download data: CEL

(Submitter supplied) PBRM1 is a component of the PBAF chromatin remodelling complex and has been observed to be deregulated in a significant proportion of patients with clear-cell Renal Cell Carcinoma (ccRCC). This study employs RNA-Seq to identify differentially expressed genes in cellular models of ccRCC by expressing PBRM1 in PBRM1-deficient Caki2 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) To select signatures of ccRCC, 265 ccRCC samples were obtained from the Van Andel Research Institute. Gene expression profiles of 265 samples were determined using the HG-U133_Plus_2 platform.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

265 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling was performed in ccRCC cells, which either express both HIF1alpha and HIF2alpha (either naturally or by virtue of induced expression of HIF1alpha) or express HIF2alpha alone (either naturally or by virtue of a HIF1alpha shRNA), to identify genes regulated by HIF1alpha in ccRCC cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

20 Samples

Download data: CEL

(Submitter supplied) PBRM1 was found to be mutated in a high percentage of clear cell RCCs. We performed knockdown of PBRM1 via siRNA and compared with scrambled control in three different RCC cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10175

89 Samples

Download data: CEL

(Submitter supplied) We have sampled several tumour regions from a single ccRCC patient after 6 weeks everolimus treatment, including both primary and metastatic site samples to investigate intra-tumour heterogeneity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

9 Samples

Download data: CEL

(Submitter supplied) A great percentage of patients with multiple primary cancers (MPCs) and family history of cancer are suspected to have a hereditary cancer predisposition syndrome. However, only a small proportion of these cases are explained by mutations in high-penetrance genes, suggesting the involvement of undiscovered genes in cancer predisposition. In this study, we report the molecular and clinical characterization of two unrelated patients with MPCs, a positive family history of cancer, no germline pathogenic mutations in BRCA1, BRCA2 and TP53 genes and large genomic rearrangements mapped on chromosome 7q.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL16131 GPL17586

13 Samples

Download data: CEL, CHP, CYCHP

(Submitter supplied) Here we performed 3’ transcriptome single cell sequencing on 7 ccRCC patients’ tumor and matched 5 adjacent normal samples. We identified two different functional subgroups in ccRCC tumor epithelial cells and two different gene transcriptional programs that were associated with survival across a TCGA cohort. We found important transcriptional factor regulons that played roles in ccRCC progression. We identified macrophage and T cell clusters whose higher infiltration in tumor was associated with overall survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV