3794 results for "*oma"

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• SS18-SSX-mediated hijacking of BAF complexes drives synovial sarcoma

  Synovial sarcoma (SS) is defined by a recurrent t(x;18) chromosomal translocation, which produces the hallmark SS18-SSX oncogenic fusion. Incorporation of SS18-SSX into BAF complexes renders BAF complexes aberrant in two distinct manners: the addition of 78aa of SSX onto SS18, and concomitant loss of BAF47 assembly. However, the importance and functional contributions of each of these perturbations on BAF complex targeting and gene expression regulation remain unclear. Here we use an integrative set of genomic approaches in human cancer cell lines and primary tumor samples to define the mechanistic consequences of the SS18-SSX fusion oncoprotein. We find that SS18-SSX hijacks BAF complexes to broad polycomb domains to activate bivalent genes, driving a unique gene expression program distinct from other loss-of-function BAF complex malignancies. Importantly, restoration of BAF47 rescues enhancer activation but is dispensable for proliferative arrest in cell lines. These results demonstrate that gain-of-function SS18-SSX-mediated BAF complex targeting and gene activation is the driving event in SS, and present a mechanism by which distinct functions of BAF complexes can be co-opted to drive oncogenesis.

  Dataset EGAD00001004135

• WES analysis of patients with USP8 wild-type corticotroph adenomas

  The overall goal of the Identification of recurrent mutations in Cushing’s disease project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices. The aims of Project are to implement and establish the feasibility of WES in patients with USP8 wild-type corticotroph adenomas; to develop a framework for the understanding of the molecular mechanism of the pathogenesis of corticotroph adenoma.

  Dataset EGAD00001004136

• Patient-derived neuroblastoma model system OHC-NB1

  The dataset is comprised of seven samples, one blood sample (germline control) of the patient, one neuroblastoma metastasis from the bone marrow and five derived cell models. The models include the primary culture, the first xenogenograft passage, a monolayer culture derived from the first xenograft passage and two samples of the fourth xenograft passage, cells and supernatant. For all these samples, whole-exome sequencing data have been generated. The BAM files contain the alignments against the human genome, assembly GRCh37, and also the unaligned reads.

  Dataset EGAD00001004138

• Whole exome and targeted DNA sequencing data for formalin-fixed paraffin embedded tissue from de novo small cell prostatic carcinoma cases

  This dataset consists of 44 compressed paired fastq files, 15 of which are generated from whole exome sequencing, and 29 of which are generated from DNA sequencing using a targeted gene panel capturing the exonic regions of 73 prostate cancer driver genes. Targeted DNA sequencing was performed on an Illumina MiSeq (v3 600 cycle kit), and exome sequencing was done using an Illumina HiSeq 2500 (v4 250 cycle kit) machine. The fastq files are named in accordance with the sample aliases provided, which reflect the pathology of interest to this study (small cell prostatic carcinoma--SCPC), whether it was sequenced using an exome or targeted gene panel, whether the FFPE sample was sourced from tumor or benign tissue (labeled T or B, respectively), and whether there exists multiple samples belonging to a single patient.

  Dataset EGAD00001004139

• Whole Exome Sequencing of Diffuse Glioma Samples

  This dataset contains FASTQ files obtained through whole exome sequencing of glioma and matched blood samples.

  Dataset EGAD00001004144

• The contribution of POT1 variants to sporadic melanoma development (2018-06-06)

  A case-control series of melanoma cases from Leeds, UK have been sequenced in the Fluidigm platform to identify genetic variants associated with sporadic melanoma development. Samples in which potentially contributing variants have been detected are being sequenced in an orthogonal platform for variant confirmation. . This dataset contains all the data available for this study on 2018-06-06.

  Dataset EGAD00001004151

• Undifferentiated sarcomas develop through distinct evolutionary pathways

  Undifferentiated sarcomas (USARC) of adults are diverse, rare and aggressive soft tissue cancers. Recent efforts have confirmed that USARC exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the genomic basis of this structural complexity by integrating whole genome sequencing, ploidy analysis and methylation profiling of 53 USARC. We identified whole genome doubling as a prevalent and pernicious force in USARC tumourigenesis. Deconvolution of the complex copy number and rearrangement landscapes show distinct signatures associated with chromothripsis, early-haploidy, and successive whole-genome-doubling events, suggesting four divergent models of sarcoma development. We show similar distinct evolutionary tumourigenic pathways in different sarcoma subtypes from the Cancer Genome Atlas. Thirteen percent of tumours exhibited a hypermutator phenotype, opening new avenues for clinical management such as immunotherapy, whilst the period prior to and between genome doubling events may represent clinically relevant interventional points in USARC.

  Dataset EGAD00001004162

• Molecular and phenotypic data for patients enrolled in the IMmotion150 trial

  Tumor transcriptome and whole exome sequencing data (matched tumor/normal for somatic mutation calling) along with key phenotypic information are provided for patients enrolled in the phase 2 IMmotion150 trial, assessing efficacy of atezolizumab monotherapy or combination of atezolizumab and bevacizumab versus standard of care (sunitinib) in 1L renal cell carcinoma. This data set accompanies the respective Nature Medicine publication (PMID: 29867230).

  Dataset EGAD00001004183

• Gene Expression Profiling

  Gene Expression Profiling from 21 cases: 14 CCND1-negative Mantle Cell Lymphoma and 7 CCND1-positive Mantle Cell Lymphoma

  Dataset EGAD00010001582

• Ewing's Sarcoma RNA-Seq

  28 Pretreated Ewing sarcoma tumor blood samples were collected from the Hospital for Sick Children (SickKids) and Mount Sinai Hospital in Toronto, Canada in accordance with each institution’s Research Ethical Board (REB) guidelines. Detailed clinical information (age at presentation, gender, tumor site, stage, etc.) were obtained from the corresponding institutional tumor banks. Transcriptome (RNA-Seq) sequencing was performed using established protocols on Illumina instruments.

  Dataset EGAD00001004188