3772 results for "*oma"

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• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Dataset EGAD00001000134

• DATA FILES FOR NBL

  Neuroblastoma whole genome sequencing

  Dataset EGAD00001000135

• Tumor sample of a serious ovarian carcinoma

  Tumor sample of a serious ovarian carcinoma

  Dataset EGAD00001000139

• Osteosarcoma Whole Genome

  Osteosarcoma Whole Genome

  Dataset EGAD00001000147

• Subgroup-specific structural variation across 1,000 medulloblastoma genomes

  Subgroup-specific structural variation across 1,000 medulloblastoma genomes

  Dataset EGAD00001000158

• Whole Genome Sequencing accompanying Genetic landscape of pediatric Rhabdomyosarcoma

  Whole Genome Sequencing accompanying Genetic landscape of pediatric Rhabdomyosarcoma.

  Dataset EGAD00001000164

• Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Dataset EGAD00001000175

• UK10K_RARE_COLOBOMA REL-2012-01-13

  UK10K_RARE_COLOBOMA REL-2012-01-13

  Dataset EGAD00001000179

• UK10K_RARE_COLOBOMA REL-2012-02-22

  UK10K_RARE_COLOBOMA REL-2012-02-22

  Dataset EGAD00001000185

• Neuroblastoma samples

  Neuroblastoma samples

  Dataset EGAD00001000196

• Neuroblastoma samples (Analyses_vcf files)

  Neuroblastoma samples (Analyses_vcf files)

  Dataset EGAD00001000202

• UK10K_RARE_COLOBOMA REL-2012-07-05

  UK10K_RARE_COLOBOMA REL-2012-07-05

  Dataset EGAD00001000206

• A common single nucleotide variant in T is strongly associated with chordoma

  Chordoma is a rare malignant bone tumor that expresses the transcription factor T. We conducted an association study of 40 patients with chordoma and 358 ancestry-matched, unaffected individuals with replication in an independent cohort. Whole-exome and Sanger sequencing of T exons reveals a strong risk association ( allelic odds ratio (OR) = 4.9, P = 3.3x10-11, CI= 2.9-8.1) with the common (minor allelic frequency >5%) non-synonymous SNP rs2305089 in chordoma, which is exceptional in cancer genetics.

  Dataset EGAD00001000226

• Melanoma-TIL Study Exomes

  Melanoma-TIL Study Exomes

  Dataset EGAD00001000243

• Integrative Oncogenomics of multiple myeloma

  Integrative Oncogenomics of multiple myeloma

  Dataset EGAD00001000246

• Integrative Oncogenomics of multiple myeloma

  Integrative Oncogenomics of multiple myeloma

  Dataset EGAD00001000247

• DATA FILES FOR SJRB

  Retinoblastoma whole genome sequencing

  Dataset EGAD00001000261

• Chondrosarcoma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000265

• Osteosarcoma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Osteosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000266

• Chordoma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Chordoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000267

• Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood

  Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood

  Dataset EGAD00001000271

• Meningioma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Meningioma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000273

• Data set for Whole-genome-Sequencing of adult medulloblastoma

  Data set for Whole-genome-Sequencing of adult medulloblastoma

  Dataset EGAD00001000275

• SCAT_Osteosarcoma_Validation

  This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000280

• Whole genome analyses of the childhood cancer neuroblastoma

  Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3-70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients.

  Dataset EGAD00001000282

• Molecular characterization of invasive lobular carcinoma

  Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer accounting for 10-15% of cases. ILC differs from invasive ductal carcinoma (IDC)with respect to epidemiology, histology, and clinical presentation. Moreover, ILC is lesssensitive to chemotherapy, more frequently bilateral, and more prone to form gastrointestinal, peritoneal, and ovarian metastases than IDCs. In contrast to IDC, the prognostic value ofhistological grade (HG) in ILC is controversial. One of the three major components of histological grading (tubule formation) is missing in ILC which hinders the process of gradingin this histological subtype and results in the classification of approximately two thirds of ILC as HG 2.Over the last decade, a number of gene expression signatures have shed light onto breast cancer classification, allowing breast cancer care to become more personalized. Withrespect to the management of estrogen receptor (ER)-positive breast cancer, several gene expression signatures provide prognostic and/or predictive information beyond what is possible with current classical clinico-pathological parameters alone. Nevertheless, most studies using gene expression signature have not considered different histologic subtypesseparately. Recently, a comprehensive research program has elucidated some of the biological underpinnings of invasive lobular carcinoma. Genetic material extracted from 200 ILC tumor samples were studied using gene expression profiling and identified ILCmolecular subtypes. These proliferation-driven gene signatures of ILC appear to have prognostic significance. In particular, the Genomic Grade (GG) gene signature improved upon HG in ILC and added prognostic value to classic clinico-pathologic factors. In addition this study demonstrated that most ILC are molecularly characterized as luminal-A (~75%)followed by luminal-B (~20%) and HER2-positve tumors (~5%). Moreover, we investigated the prognostic value of known gene signatures/ gene modules in the same cohort of ILC. As a second step within the scope of this project, we aim to investigate the interactionsbetween somatic ILC tumor mutations to observed transcriptome findings. To this end, we aim to perform somatic mutation analysis for the ILC tumors for which Affymetrix gene expression profiling is available. To this end, we will use a gene screen assay, which specifically interrogates the mutational status of a few hundreds of cancer genes. We believe that this pioneering effort will be fundamental for a tailored treatment of ILC withimprovement in patients' outcome.

  Dataset EGAD00001000288

• Whole genome sequencing of matched germline-tumour samples in follicular lymphoma

  Whole genome sequencing analysis was performed on 6 patients within matched germline, follicular lymphoma and transformed follicular lymphoma.

  Dataset EGAD00001000292

• UK10K_RARE_COLOBOMA REL-2012-11-27

  UK10K_RARE_COLOBOMA REL-2012-11-27

  Dataset EGAD00001000307

• Melanoma-Til Study RNAseq

  In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.

  Dataset EGAD00001000325

• 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

• Ewings Sarcoma RNA-seq drug sensitivity

  Illumina RNA-Seq will be performed on four Ewing's sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.

  Dataset EGAD00001000337

• 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

• Balanced Ependymoma

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000350

• 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

• Targeted gene fusion sequencing (Fus-seq) in mesothelioma

  This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract.

  Dataset EGAD00001000361

• Balanced Brain Tumour Whole Genome Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000369

• Osteosarcoma whole genome rearrangement screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000368

• Sporadic Parathyroid Carcinoma

  This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.

  Dataset EGAD00001000370

• Uveal melanoma whole genome sequencing, SNP arrays and RNA-seq

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Dataset EGAD00001000372

• Ewings Sarcoma Rearrangement Screen

  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 EGAD00001000389

• Chondrosarcoma Validation Study

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Dataset EGAD00001000392

• A study of the molecular pathogenesis of Splenic Marginal Zone and Diffuse Large B-Cell Lymphoma

  We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.

  Dataset EGAD00001000410

• UK10K_RARE_COLOBOMA REL-2013-04-20

  UK10K_RARE_COLOBOMA REL-2013-04-20

  Dataset EGAD00001000415

• Whole genome sequences of hepatocellular carcinoma (NCCRI)

  Fastq files of 213 samples of hepatocellular carcinoma (NCCRI)

  Dataset EGAD00001000446

• RNAseq of patients with Ewings sarcoma

  Cancer is driven my 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 EGAD00001000444

• Integrated molecular analysis of clear cell renal cell carcinoma

  Dataset EGAD00001000597

• The Transcriptome of PLX4032 resistance

  We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.

  Dataset EGAD00001000599

• Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing

  Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing

  Dataset EGAD00001000616

• Pilocytic Astrocytoma ICGC PedBrain RNA sequencing

  Pilocytic Astrocytoma ICGC PedBrain RNA sequencing

  Dataset EGAD00001000617