Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SNP data from 78 pheochromocytomas and paragangliomas

ABSTRACT: SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH. 78 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

ORGANISM(S): Homo sapiens

SUBMITTER: Eric Letouzé

PROVIDER: E-GEOD-38525 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Somatic NF1 inactivation is a frequent event in sporadic pheochromocytoma.

Burnichon Nelly N Buffet Alexandre A Parfait Béatrice B Letouzé Eric E Laurendeau Ingrid I Loriot Céline C Pasmant Eric E Abermil Nasséra N Valeyrie-Allanore Laurence L Bertherat Jérôme J Amar Laurence L Vidaud Dominique D Favier Judith J Gimenez-Roqueplo Anne-Paule AP

Human molecular genetics 20120906 26

Germline mutations in the RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, MAX, TMEM127, NF1 or VHL genes are identified in about 30% of patients with pheochromocytoma or paraganglioma and somatic mutations in RET, VHL or MAX genes are reported in 17% of sporadic tumors. In the present study, using mutation screening of the NF1 gene, mapping of chromosome aberrations by single nucleotide polymorphism (SNP) array, microarray-based expression profiling and immunohistochemistry (IHC), we addressed the implicat ...[more]

PMID: 22962301

Similar Datasets

SNP data from 30 pheochromocytomas and paragangliomas.

Project description:SNP profiles from 30 pheochromocytomas and paragangliomas were analyzed to detect identical-by-descent haplotypes, highlighting a founder mutation of SDHD in two samples. 30 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

2012-03-23 | E-GEOD-32204 | biostudies-arrayexpress

SNP data from 78 pheochromocytomas and paragangliomas

Project description:SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH.

2012-09-11 | GSE38525 | GEO

SNP data from 30 pheochromocytomas and paragangliomas.

Project description:SNP profiles from 30 pheochromocytomas and paragangliomas were analyzed to detect identical-by-descent haplotypes, highlighting a founder mutation of SDHD in two samples.

2012-03-23 | GSE32204 | GEO

Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina HumanMethylation450 arrays

Project description:Genome-scale DNA methylation was analyzed in a cohort of paragangliomas to identify DNA methylation changes. Bisulfite converted DNA from 22 fresh frozen paragangliomas and 2 normal adrenal medulla samples were hybridized to Illumina HumanMethylation450 BeadChips.

2013-05-06 | E-GEOD-43293 | biostudies-arrayexpress

Transcription profiling of pheochromocytomas and paragangliomas (188 tumor samples)

Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 188 tumor samples |Pheochromocytomas and paragangliomas are neuroendocrine tumors occuring in the context of inherited cancer syndromes in approximately 30% of cases, linked to germline mutations in VHL, RET, NF1, SDHA, SDHB, SDHC, SDHD, SDHAF2 or TMEM127 genes. Although progress has been made with regard to tumorigenesis mechanisms in pheochromocytoma/paraganglioma thanks to genome-wide expression studies, the question of a putative molecular distinction between VHL- and SDHx- on one hand, and RET- and NF1-related tumors on the other hand, remained to be addressed as well as the characterization of genetic events in sporadic tumors. With this purpose, 202 pheochromocytomas/paragangliomas, including 75 hereditary tumors, were investigated by expression profiling, array CGH and somatic mutation screening. The systematic characterization of somatic genetic events associated with tumor suppressor gene germline mutations in tumor tissues reveals a majority of loss of heterozygosity (LOH) but also point mutations and copy neutral LOH. Gene-expression signature defined the hereditary tumors according to their genotype. Especially, a complete sub-separation between SDHx- and VHL-related tumors was observed. Moreover, guided by the transcriptome classification and the LOH profile, somatic mutations in VHL or RET genes were identified in 14% of sporadic pheochromocytomas/paragangliomas. A genetic cause was found in 45.5% (92/202) of the large series of pheochromocytomas/paragangliomas analyzed. Regarding mutated genes, specific molecular pathways involved in tumorigenesis mechanisms are showed. Altogether, these new findings suggest that somatic mutation analysis would give important clues for personalized molecular target therapies.

2011-07-07 | E-MTAB-733 | biostudies-arrayexpress

Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina Infinium 27k Human Methylation arrays

Project description:Genome-scale DNA methylation was analyzed in a large cohort of pheochromocytomas and paragangliomas (PCC/PGL). Consensus clustering identified 3 stable clusters significantly associated with expression subgroups, gene mutations, and clinical parameters. Bisulfite-converted DNA from 145 fresh frozen PCC/PGL and 3 normal adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation BeadChips.

2013-05-06 | E-GEOD-39198 | biostudies-arrayexpress

Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina Infinium 27k Human Methylation arrays

2013-05-06 | GSE39198 | GEO

Expression data from benign and malignant pheochromocytomas and paragangliomas

Project description:Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine, usually benign tumors. Currently, for these neoplasms the only reliable criterion of malignancy is the presence of metastases. The aim of the present study was to identify molecular markers that can distinguish malignant from benign PPGL. An mRNA expression array was performed on 40 benign and 11 malignant PPGL. Genes showing a significantly different expression between benign and malignant PPGL with a ratio ? 4 were selected. Differentially expressed genes were confirmed by qRT-PCR and subsequently tested in an independent validation series (4 benign and 4 malignant) by qRT-PCR. Finally, immunohistochemistry was performed for the validated genes on Tissue Micro Arrays, which included 100 PPGL (87 benign and 13 malignant). Ten genes, which were significantly differentially expressed between benign and malignant tumors (False Discovery Rates <0.05), were selected from the mRNA expression array data. Differential expression of Interleukin 13 Receptor Alpha 2 and Contactin 4 was confirmed (p<0.05) and validated by qRT-PCR. However, at the protein level, only Contactin 4 appeared to be significantly overexpressed in malignant tumors (58% in malignant versus 17% in benign; p<0.05). No difference in the immunohistochemical staining for Interleukin 13 Receptor Alpha 2 was observed between benign and malignant PPGL. Contactin 4 expression appears to be associated with malignancy in pheochromocytomas and paragangliomas, and may be predictive of malignant behavior.

2015-03-20 | GSE67066 | GEO

Investigation of post-translational histone modifications in pheochromocytomas and paragangliomas

Project description:Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumours affecting a range of body sites and have the highest degree of heritability of any cancer type. SDHA, SDHB, SDHC, SDHD and SDHAF2 (collectively SDHx) code for subunits of succinate dehydrogenase, an enzyme complex in the tricarboxylic cycle that converts succinate to fumarate. Mutations in all SDHx genes play a role in PPGL pathogenesis and completely abolish succinate dehydrogenase enzymatic activity causing intracellular accumulation of oncometabolites which competitively inhibit 2-oxoglutarate-dependent oxygenases. This is a family of enzymes includes TET DNA demethylases and Jumonji C (JmjC) domain-containing histone demethylates. We and others have found that the inhibition of DNA demethylation leads to profound global DNA hypermethylation which influences expression of genes responsible for important clinical characteristics of these tumours but cannot explain the full spectrum of transcriptomic changes. We profiled histone PMTs to complement DNA methylation data and fully characterise the epigenome of these tumours.

2024-01-26 | PXD025689 | Pride

SNP data from 45 adrenocortical carcinomas

Project description:SNP array data from 45 adrenocortical carcinomas were used to detect recurrent copy number alterations. 7 tumors were analyzed with Illumina Human610-Quad v1.0 BeadChip. 38 tumors were analyzed with Illumina HumanOmniExpress BeadChip.

2014-04-29 | E-GEOD-49276 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data