4984 results for "*oma"

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• Medulloblastoma Cirlce-Seq

  Circle-Seq experiment.

  Dataset EGAD00001009483

• Oesophageal adenocarcinoma scRNAseq from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.

  Dataset EGAD00001009401

• sc-RNA-Seq soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001009002

• RNA-Seq of primary pediatric kidney tumor controls for the soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008709

• RNA-Seq soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008467

• WGS soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008466

• The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

  Transcriptomic sequencing on pre-immunotherapy melanoma patients.

  Dataset EGAD00001007710

• Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

  Dataset EGAD00001007762

• Single cell RNA-Seq of Clear Cell Sarcoma of the Kidney

  Dataset EGAD00001007498

• Immunotesting cohort with RNA-seq data of melanoma samples

  This dataset contains RNA-seq raw data in fastq format from 9 melanoma samples. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006783

• Whole-genome sequencing of a thyroid carcinoma harboring a ETV6-NTRK3 fusion and a NTRK3 G623R mutation (HIPO-021)

  Dataset EGAD00001006243

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001006398

• PromethION (and Illumina) WGS and MinION transcriptome for a patient with diffuse large B-cell lymphoma.

  Dataset EGAD00001006204

• Whole-genome and transcriptome sequencing of a patient with extrapancreatic acinar cell carcinoma

  Dataset EGAD00001006023

• Whole-genome and transcriptome sequencing data of an undifferentiated gastric spindle cell sarcoma

  Dataset EGAD00001006014

• scRNA-seq of glioblastoma cells alone or after co-culture with cerebral organoid cells

  Dataset EGAD00001005315

• Paired-end RNA-seq analysis of the 3D evolution of glioma cell populations. Part 1.

  Dataset includes 160 double-stranded RNAseq libraries collected from 16 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.

  Dataset EGAD00001005222

• Paired-end Whole Exome-seq analysis of the 3D evolution of glioma cell populations. Part 1.

  Dataset contains Exome sequencing data (aligned and base quality score recalibrated BAM files) for 236 tumor samples + matched normal from blood, collected from 21 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.

  Dataset EGAD00001005221

• Transcriptome of Ewing sarcoma tumors - RNA-seq (ICGC)

  Transcriptome of Ewing sarcoma tumors (ICGC project). Fastq files of 57 RNA-seq are available (2x101bp).

  Dataset EGAD00001004493

• Identification of molecular subgroups in multiple myeloma by whole exome sequencing.

  Dataset EGAD00001004408

• Whole Genome Sequencing of HCC

  The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Dataset EGAD00001003994

• Whole exome sequencing data from two patients with isolated myelosarcoma followed by acute myeloid leukemia

  Dataset EGAD00001003831

• RNA-SEQ data from 13 CAF (Cancer Associated Fibroblast) samples sorted from fresh high-grade ovarian carcinoma

  Dataset EGAD00001003460

• Raw sequencing data - Intra-tumor heterogeneity and clonal evolution patterns towards platinum-resistant high-grade serous ovarian cancer

  This dataset includes 69 sampels of whole-exome sequencing data of high-grade serous ovarian carcinoma (HGSOC). We included patients with advanced (International Federation of Gynecology and bstetrics [FIGO] stage IIIeIV) HGSOC for which biopsies were obtained during debulking surgery, the first at initial diagnosis and the second at disease relapse. Where possible, matched normal DNA from each participating patient was obtained from a whole-blood sample. Written informed consent was obtained from all patients and approved by the local ethics committee.

  Dataset EGAD00001001381

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - side_cases_barretts

  Dataset EGAD00001001379

• Whole-Genome Bisulfite Sequencing of a paired initial and recurrent glioma

  Dataset EGAD00001001616

• Carcinoma of the oral tongue (OTSCC) genomic landscape characterisation

  18 Exomes for discovery set and 60 Targeted panel for prevalence set

  Dataset EGAD00001001465

• Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

  Dataset EGAD00001003324

• Targeted resequencing of coding regions of ribosomal protein genes in multiple myeloma samples

  Dataset EGAD00001003302

• Pseudomyxoma peritonei exome sequencing vcf-files

  Dataset EGAD00001003297

• Ewing sarcoma genome sequencing

  Dataset EGAD00001001051

• BAM files from Cholangiocarcinoma exome sequencing

  Dataset EGAD00001001220

• Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients

  Dataset EGAD00001001275

• Integrated molecular analysis of clear cell renal cell carcinoma

  Dataset EGAD00001000597

• Pilocytic Astrocytoma ICGC PedBrain RNA sequencing

  Pilocytic Astrocytoma ICGC PedBrain RNA sequencing

  Dataset EGAD00001000617

• Angiosarcoma follow up study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Dataset EGAD00001000620

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo

  Dataset EGAD00001000704

• DIPG_ICR_WES

  Whole exome sequencing of 6 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG)

  Dataset EGAD00001000706

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

  Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment 'sensitive' to recurrence 'resistant' tumours to identify the genetics of drug resistance.

  Dataset EGAD00001000707

• The UCSF Low Grade Glioma Genome Project #1

  Dataset EGAD00001000714

• Angiosarcoma whole exome

  Extension of angiosarcoma whole genome sequencing study

  Dataset EGAD00001000722

• Matched tumour/normal .bam files generated by QCMG at University of Queensland from HiSeq whole genome sequencing of oesophageal adenocarcinoma cases

  Dataset EGAD00001000845

• HCC.GNE RNA-Seq

  RNA-Sequencing data (raw read sequences) for 23 samples, from 12 patients, for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma"

  Dataset EGAD00001000886

• Mantle Cell Lymphoma Dataset

  Dataset EGAD00001000667

• Whole exome sequencing of peripheral T-cell lymphoma (PTCL)

  Dataset EGAD00001000659

• Novel driver variants in the histone 3.3 genes, H3F3A and H3F3B, define bone and cartilage cancer sub-types

  A selection of human cancers harbours somatic driver mutations in genes encoding histones, most notably childhood brain tumours with K27M substitutions of the histone 3.3 gene, H3F3A. We performed whole genome sequencing of the benign cartilage tumour, chondroblastoma, and targeted sequencing of histone 3.3 genes, H3F3A and H3F3B, in seven further skeletal tumour types. We identified an exceptionally high prevalence of novel histone 3.3 driver mutations at glycine 34 and at lysine 36. Histone 3.3 gene mutations were found in 91% in giant cell tumours of bone (48/53), mainly H3F3A G34W variants, and in 92% of chondroblastoma (73/79), predominantly K36M mutations in H3F3B. H3F3B is paralogous to the cancer gene H3F3A. However, H3F3B driver variants have not previously been reported in human cancer. Our observation demonstrate remarkable tumour-specificity of mutations, with respect to which histone 3.3 gene and residue is mutated, indicating that the advantage these mutations confer is tumour dependent. Moreover, tumour-specific mutation of H3F3A and H3F3B suggests, that although both genes encode identical proteins, they are likely non-redundant and employed differentially during skeletal development.

  Dataset EGAD00001000646

• Exome sequencing of patients with Ewings sarcoma

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing,s sarcoma tumours.

  Dataset EGAD00001000333

• Somatic mutations, clonal architecture and genomic evolution in multiple myeloma

  Multiple myeloma is an incurable plasma cell malignancy whose molecular pathogenesis is incompletely understood. We used whole exome sequencing, copy number profiling and cytogenetic to analyses 84 samples from 67 patients with myeloma. In addition to known myeloma genes, we identify new candidate genes, including truncations of SP140, ROBO1 and FAT3 and clustered missense mutations in EGR1. We find oncogenic mutations in cancer genes not previously implicated in myeloma, including SF3B1, PI3KCA and PTEN. We define diverse processes contributing to the mutational repertoire, including kataegis and somatic hypermutation. Most cases have at least one cluster of subclonal variants, including subclonal driver mutations, implying on-going tumor evolution. Serial samples revealed diverse patterns of clonal evolution, including linear evolution, differential clonal response and branching evolution. Our findings reveal the myeloma genome to be heterogeneous across patients and, within individual patients, to exhibit diversity in clonal admixture and dynamics in response to therapy.

  Dataset EGAD00001000339

• Frequent mutation of the major cartilage collagen gene, COL2A1, in chondrosarcoma

  Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major cartilage collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (27%) and hedgehog signaling (22%).

  Dataset EGAD00001000358

• The genomic architecture of mesothelioma

  The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients.

  Dataset EGAD00001000360