Search Results - EGA European Genome-Phenome Archive

RNAseq - Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma

We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.

Dataset EGAD00001001050

Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma

We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.

Dataset EGAD00001001046

Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - mobile_elements

Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z

Dataset EGAD00001001048

Whole Exome Sequencing files accompanying Genetic landscape of pediatric Rhabdomyosarcoma

Dataset EGAD00001001059

WES of HCC

WES of HCC by HiSeq 2000,total 71 samples including Hepatocellular carcinoma cell lines and nornal sample(Peripheral Blood or the adjacent tissues of cancer)

Dataset EGAD00001001249

Mesothelioma Whole Genomes

Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project.

Dataset EGAD00001001265

Primary angiosarcoma Whole Genome Sequencing

Whole genome sequencing of primary angiosarcoma

Dataset EGAD00001001266

Anaplastic Meningioma WGS-X10

Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease.

Dataset EGAD00001001267

Whole exome sequencing dataset in follicular lymphoma without evidence of transformation

Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation

Dataset EGAD00001001301

The UCSF Low Grade Glioma Genome Project #2"

Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor

Dataset EGAD00001001305

BLUEPRINT release January 2015, Bisulfite-Seq for Multiple myeloma

Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

Dataset EGAD00001001152

MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells

Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long non-coding RNAs (lncRNAs), on the way MYC is able to influence cellular transcriptome. To this aim we have intersected RNA-sequencing data from two MYC-inducible cell lines and from a cohort of 91 mature B-cell lymphomas carrying, or not carrying, genetic variants resulting in MYC over-expression. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, for MYC-Induced long Non-Coding RNA, showing a strong correlation with MYC expression in MYC-positive lymphomas and also in pancreatic ductal adenocarcinomas. To understand its cellular role we performed RNA interference (RNAi) experiments and found that MINCR knock-down is associated with a reduction in cellular viability, due to an impairment in cell cycle progression. Differential gene expression analysis following RNAi showed a strongly significant enrichment of cell cycle genes among the genes down-regulate following MINCR knock-down. Interestingly these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of MYC transcriptional program. Accordingly, following MINCR knock-down, we observed a reduction in the binding of MYC to the promoters of selected cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.

Dataset EGAD00001001441

Deep sequencing of melanoma for driver mutations

Dataset EGAD00001001445

BLUEPRINT release August 2015, RNA-Seq for Multiple myeloma, on genome GRCh38

RNA-Seq data for 11 Multiple myeloma sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

Dataset EGAD00001001471

Anaplastic Oligodendroglioma AO Exome-seq data

Anaplastic oligodendrogliomas (AOs) are rare primary brain tumors which are generally incurable, with heterogeneous prognosis and few treatment targets identified. Most oligodendrogliomas have chromosome 1p/19q co-deletion and IDH mutation. We analyzed 51 AOs by whole-exome sequencing, identifying previously reported frequent somatic mutations in CIC and FUBP1. We also identified recurrent mutations in TCF12 and in an additional series of 83 AO. Overall 7.5% of AO are mutated for TCF12, which encodes an oligodendrocyte-related transcription factor. 80% of TCF12 mutations identified were in either the bHLH domain, which is important for TCF12 function as a transcription factor, or were frame shift mutations leading to TCF12 truncated for this domain. We show that these mutations compromise TCF12 transcriptional activity and are associated with a more aggressive tumor type. Our analysis provides further insights into the unique and shared pathways driving AO.

Dataset EGAD00001001452

ChIP sequencing in Cancer Cell Lines

The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma.

Dataset EGAD00001001453

Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 100_all_samples

All samples from the "100" project

Dataset EGAD00001001457

CBP has opposing functions during cerebellar development and is a targetable tumor suppressor at late stages of medulloblastoma initiation

Dataset EGAD00001001461

Four lymphoma cell lines (AGO2-PAR-CLIP)

PAR-CLIP was performed on the Argonaute-2 protein (AGO2) in four lymphoma cell lines:NamalwaRajiSU-DHL-4SU-DHL-6

Dataset EGAD00001001468

Chondromyxoid fibroma

Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations.

Dataset EGAD00001001063

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