4774 results for "*oma"

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• Chordoma Sequencing Project RNAseq

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Dataset EGAD00001000653

• WES from tFL with PMBL GE signature

  Exome sequencing data from transformed Follicular Lymphoma samples that express a PMBL-like gene expression signature

  Dataset EGAD00001008498

• CMF RNA sequencing

  RNA sequencing will be undertaken to reconstruct rearrangements at level of transcription to determine pathogenomic genomic events in chondromyxoid fibroma.

  Dataset EGAD00001000824

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Precursor lesions, clonal architecture and relapse in Wilms nephroblastoma

  Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: * 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) * 40 cases with matched pre-chemotherapy biopsies (240 samples) * 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

  Dataset EGAD00001003217

• Chromatin run-on and transcriptome sequencing of fibrolamellar carcinoma

  Fastq files of chromatin run-on (14 fibrolamellar carcinoma, 3 non-malignant liver; single-end) and transcriptome (23 fibrolamellar carcinoma, 2 non-malignant liver; paired-end) sequencing of fibrolamellar carcinoma

  Dataset EGAD00001005797

• Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

  Background: The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behaviour and can thereby complement the prognostically favorable 1p/19q co-deletion. Results: Genome-wide, 50 base pair single-end, sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analysed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/ 19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors. Conclusions: CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.

  Dataset EGAD00001001000

• CTCF ChIP-sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains CTCF ChIP-sequencing data from seven samples (six tumor samples and one tumor derived cell line). Following library amplification, DNA fragments were sequenced using Illumina HiSeq 2000 paired-end sequencing resulting in 14 FASTQ files.

  Dataset EGAD00001008806

• European Roma whole genomes sequences

  Pair end fastq file of 40 Roma whole genome sequence data. This dataset contains the fastq files obtained using illumina hiseq X generated reads, ~30X coverage. 10 Makedonian Roma - Balkan Roma 10 Spanish Roma - North/Western Roma 10 Hungarian Roma - Vlax and Romungro Roma 5 Lithuanian Roma - North/Western Roma 5 Ukranian Roma - Romungro Roma.

  Dataset EGAD00001006024

• Whole genome sequence of condrosarcoma

  Fastq files of 10 samples of condrosarcoma

  Dataset EGAD00001000873