Search Results - EGA European Genome-Phenome Archive

ICGC PedBrain: Deep-sequencing of childhood brain tumors.

Brain tumors constitute the childhood tumors with the highest mortality rates and survival is often associated with severe long-term sequelae due to intensive multimodal treatment regimens. Thus, the PedBrainTumor network aims at the identification of robust biomarkers for clinical management and novel molecular targets for therapeutic interventions. Using massively parallel whole-genome sequencing, and transcriptome and methylome sequencing for subsets of cases, we aim to decipher the molecular causes of medulloblastoma as well as low-grade astrocytoma, and to identify markers to stratify patients for specialized treatment. As the PedBrain network is affiliated with clinical trials in medulloblastoma and pilocytic astrocytoma, validation cohorts for the translation of key findings into clinical settings are readily available.

Study EGAS00001000215

Fibroblast heterogeneity and immunosuppressive environment in Human breast cancer

Carcinoma-associated fibroblasts (CAF) are key players in the tumor microenvironment. Here, by combining 6 well-known stromal markers, we identify four CAF subsets (CAF-S1 to CAF-S4) in human breast cancer (BC) that exhibit distinct activation patterns and accumulate differently in BC subtypes.

Study EGAS00001002508

Alternative splicing in Shh-MB

We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

Study EGAS00001003220

Paired exome analysis in urothelial carcinoma

In this study we characterized genomic alterations in two to five metachronous tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth), Ultra deep targeted sequencing (~6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor.

Study EGAS00001001686

Spatio-temporal evolution of the primary glioblastoma genome (newly added after 2015)

Since our genomic analysis of 38 GBM patients, we recruited more cases to further study spatial and temporal evolution of glioblastoma with international collaboration of multiple institutes. The cases in this study includes the whole exome and transcriptome of GBM patients newly recruited in Samsung Medical Center.

Study EGAS00001001800

ICGC Oesophageal adenocarcinoma - Barrett's samples

The oesophageal project will focus on adenocarcinoma which is increasing in incidence in the UK and other developed countries and has a very poor outcome. The primary aims of this project are to deeply sequence tumour and normal genomic DNA (including the precursor condition Barrett’s oesophagus when material is available) to provide a comprehensive catalogue of somatic mutations. This will be achieved through a UK-wide network of hospitals involved in a research collaboration called the OCCAMS consortium. The goal of this project is to use high quality clinical material with accurately annotated clinic-pathological, treatment and outcome data.

Study EGAS00001000726

WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

Lymphomas are malignancies originating from the lymphatic system and there is a worldwide significant increase in incidences of this cancer. Lymphomas can be further classified into 2 categories namely Hodgkinâ€™s (HL), and Non-Hodgkinâ€™s lymphoma (NHL). The latter can be divided further into B, T and NK cell NHL. Peripheral T-cell lymphoma (PTCL) and Natural Killer/ T-cell lymphoma (NKTL) arise from mature T lymphocytes and NK cells. The more common subtypes include NKTL, PTCL not-otherwise-specified (PTCL-NOS), systemic anaplastic large cell lymphoma (ALCL), follicular PTCL (F-PTCL), angioimmunoblastic T-cell lymphoma (AITL) and enteropathy-associated T-cell lymphoma (EATL). Whole genome analyses on T-cell and NK-cell lymphoma samples from various countries to gain a better understanding of the pathogenesis and biology of these tumors. The comprehensive profiling and comparison among patients from various countries with different etiopathogenesis will hopefully facilitate the elucidation of key pathways and underlying molecular mechanisms driving these cancers, opening up novel therapeutic strategies in the future.

Study EGAS00001002398

A combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancer

The earlier diagnosis of cancer is one of the keys to reducing future cancer deaths. Here we describe our efforts to develop a non-invasive, blood test for the detection of pancreatic ductal adenocarcinoma. We combined blood tests for KRAS gene mutations with carefully thresholded protein biomarkers to determine whether the combination of these markers was superior to any single marker. The cohort tested included 221 patients with resectable pancreatic ductal adenocarcinoma and 185 control patients without known cancers. KRAS mutations were detected in the plasma of 66 patients (30%) and every mutation found in the plasma was identical to that subsequently found in the patients' primary tumor (100% concordance). The use of KRAS in conjunction with two thresholded protein biomarkers (CA19-9 and prolactin) increased the sensitivity to 67%. Only one of the 185 plasma samples from the control cohort were positive for any of the three markers (99.5% specificity). This combinatorial approach may prove useful for the earlier detection of many cancer types.

Study EGAS00001002444

Molecular determinants of response to PD-L1 blockade across tumor types

Immune checkpoint inhibitors targeting the PD-1/PD-L1 axis lead to durable clinical responses in subsets of cancer patients across multiple indications, including non-small cell lung cancer (NSCLC), urothelial carcinoma (UC) and renal cell carcinoma (RCC). Herein, we complement PD-L1 immunohistochemistry (IHC) and tumor mutation burden (TMB) with RNA-seq in 366 patients to identify unifying and indication-specific molecular profiles that can predict response to checkpoint blockade across these tumor types. Multiple machine learning approaches failed to identify a baseline transcriptional signature highly predictive of response across these indications. Signatures described previously for immune checkpoint inhibitors also failed to validate. At the pathway level, significant heterogeneity was observed between indications, in particular within the PD-L1+ tumors. mUC and NSCLC were molecularly aligned, with cell cycle and DNA damage repair genes associated with response in PD-L1- tumors. At the gene level, the CDK4/6 inhibitor CDKN2A was identified as a significant transcriptional correlate of response, highlighting the association of non-immune pathways to the outcome of checkpoint blockade. This cross-indication analysis revealed molecular heterogeneity between mUC, NSCLC and RCC tumors, suggesting that indication-specific molecular approaches should be prioritized to formulate treatment strategies.

Study EGAS00001004343

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3735 results for "*oma"

in 31.84 milliseconds.

ICGC PedBrain: Deep-sequencing of childhood brain tumors.

Fibroblast heterogeneity and immunosuppressive environment in Human breast cancer

Alternative splicing in Shh-MB

Paired exome analysis in urothelial carcinoma

Spatio-temporal evolution of the primary glioblastoma genome (newly added after 2015)

ICGC Oesophageal adenocarcinoma - Barrett's samples

WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

A combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancer

Molecular determinants of response to PD-L1 blockade across tumor types

Genome and transcriptome sequence data from a infantile fibrosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a CNS sarcoma tumor patient

Genome and transcriptome sequence data from a ocular melanoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a craniopharyngioma tumor patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a pineoblastoma tumor patient

Genome and transcriptome sequence data from a multifocal glioblastoma multiforme tumor patient

Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a diffuse intrinsic pontine glioma tumor patient

Genome and transcriptome sequence data from a ewing sarcoma tumor patient

Genome and transcriptome sequence data from a ependymoma tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a gliomatosis cerebri anaplastic astrocytoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a metastatic alveolar rhabdomyosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a minimally invasive adenocarcinoma tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a metastatic osteosarcoma tumor patient

Genome and transcriptome sequence data from a embryonal rhabdomyosarcoma of the nasopharynx tumor patient

Genome and transcriptome sequence data from a diffuse aarge B-cell lymphoma (relapse) tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a relapsed osteosarcoma tumor patient

Genome and transcriptome sequence data from a synovial sarcoma tumor patient

Genome and transcriptome sequence data from a recurrence nasopharyngeal rhabdomyosarcoma tumor patient

Genome and transcriptome sequence data from a ewing sarcoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient