Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: phs000310.v1.p1
PROVIDER: PRJNA120083 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE17816: Somatic Mutation Screen of Clear Cell RCC I GSE17818: Somatic Mutation Screen of Clear Cell RCC II Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/.
2010-05-16 | E-GEOD-17895 | biostudies-arrayexpress
Project description:<p>The purpose of the original study was to search for somatic mutations in the tyrosine kinome of serous and clear cell endometrial carcinomas (human). The study was conducted in two phases.</p> <p>Phase 1: A mutation discovery screen, in which ~577 exons encoding the catalytic domains of 86 tyrosine kinases were PCR-amplified and bidirectionally Sanger sequenced from 24 serous, 11 clear cell, and 5 mixed histology endometrial tumors. This was followed by alignment of sequence reads to the human reference sequence and subsequent nucleotide variant calling to identify potential somatic (tumor-specific) mutations. Potential somatic mutations were confirmed by re-amplification and sequencing of the relevant tumor DNA as well as matched non-tumor ("normal") DNA from the same case.</p> <p>Phase 2: A mutation prevalence screen, in which the non-catalytic regions two tyrosine kinase genes, TNK2 and DDR1, were PCR-amplified and sequenced from the 40 discovery screen tumors, and all coding exons of TNK2 and DDR1 were PCR-amplified and sequenced from another 10 clear cell, 21 serous, and 41 endometrioid endometrial tumors, in an effort to identify additional somatic mutations in each gene. Exons encoding the exonuclease domain of POLE were also sequenced to document somatic mutations.</p>
| phs000841 | dbGaP
Project description:Mouse Model of Clear Cell Sarcoma
2019-05-14 | E-GEOD-41293 | ExpressionAtlas
Project description:Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.
2014-11-06 | GSE63002 | GEO
Project description:Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.
2014-11-06 | GSE63001 | GEO
Project description:Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.
2014-11-06 | GSE63000 | GEO
Project description:We performed a microRNA (miRNA) microarray on 10 metastatic RCC tumors and compared differential miRNA expresison to 19 primary clear cell renal cell carcinomas (ccRCC). We found there were 65 significantly dysregulated miRNAs; 9 miRNAs were significantly upregulated and 56 miRNAs were significantly downregulated in metastatic RCC when compared to primary clear cell renal cell carcinoma.
2012-08-14 | GSE39440 | GEO
Project description:Approximately 70% of clear cell renal cell carcinoma are characterised by the biallelic inactivation of VHL on chromosome 3p. ELOC-mutated renal cell carcinoma with biallelic ELOC inactivation on chromosome 8q are considered a novel subtype of renal cancer possessing a morphological overlap with ccRCC; however, the frequency and consequences of ELOC alterations in wtVHL and mutVHL is unclear. In this study, we characterise 123 renal tumours with clear cell morphology with known VHL mutation status to assess morphological and molecular consequences of ELOC inactivation. Using Oncoscan and whole exome sequencing we identify 18 ELOC deleted RCC, three of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive, although two ELOC-mutated RCC showed monoallelic VHL alterations. Using High Ambiguity Driven Biomolecular Docking we report a novel ELOC variant containing a duplication event disrupting ELOC-pVHL interaction alongside the frequently seen Y79C alteration. Using HRM mass spectrometry we show RCC with biallelic ELOC alterations have significantly reduced ELOC expression but similar CAIX and VEGFA expression when compared to classical ccRCC with VHL inactivation. These data demonstrate that RCC with ELOC and VHL alterations have comparable downstream effects with similar pathways to ccRCC tumourigenesis indicating that both entities are closely related.
2025-04-22 | GSE201277 | GEO