ABSTRACT: Genome and transcriptome sequence data from an atypical teratoid rhabdoid tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:Genome and transcriptome sequence data from an atypical bronchial carcinoid patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:Genome and transcriptome sequence data from an atypical chronic lymphocytic leukemia patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:Embryonal tumors of the central nervous system (CNS) represent a highly malignant tumor group of medulloblastoma (MB), atypical teratoid/rhabdoid tumor (AT/RT), and primitive neuroectodermal tumor (PNET) that frequently afflict children. In this study, we report transcriptome traits in MB by using gene expression microarray analyses. We also compare MB dataset with AT/RT cases and AT/RT-like cases. 22 MB cases are subjected to transcriptome analysis
Project description:Clinical and molecular risk factors were analyzed in a large cohort of patients with Atypical Teratoid Rhabdoid Tumors (ATRT) recruited to the European Rhabdoid Regsitry (EU-RHAB) and data were validated in a second independent cohort of ATRT patients.
Project description:Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis. golub-00460 Assay Type: Gene Expression Provider: Affymetrix Array Designs: Hu6800 Organism: Homo sapiens (ncbitax) Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA Disease States: synthetic_RNA, organism_part, whole_orMedulloblastoma, renal rhabdoid tumor, Atypical Teratoid/Rhabdoid Tumor, Supratentorial PNET, Supratentorial PNET (pineoblastoma), Normal, Malignant Glioma, Extrarenal Rhabdoid Tumorganism, total_RNA
Project description:The Long-read POG dataset comprises a cohort of 189 patient tumours and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the Personalized Oncogenomics (POG) program and the Marathon of Hope Cancer Centres Network includes accompanying DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. Long-range phasing of variants facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression, including recurrent aDMRs in the cancer genes RET and CDKN2A. Germline promoter methylation in MLH1 can be directly observed in Lynch syndrome. Promoter methylation in BRCA1 and RAD51C is a likely driver behind patterns of homologous recombination deficiency where no driver mutation was found. This dataset demonstrates applications for long-read sequencing in precision medicine, and is available as a resource for developing analytical approaches using this technology.
Project description:Embryonal tumors of the central nervous system (CNS) represent a highly malignant tumor group of medulloblastoma (MB), atypical teratoid/rhabdoid tumor (AT/RT), and primitive neuroectodermal tumor (PNET) that frequently afflict children. In this study, we report transcriptome traits in MB by using gene expression microarray analyses. We also compare MB dataset with AT/RT cases and AT/RT-like cases.
