Data Entry Maintenance

Metadata Commons Identifier

HMC000099

Project Title

Genome-Wide Profiles of Extra-Cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

Project Description

<p>Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.</p><p>Additional information:</p><ul><li><a href="https://www.cancer.gov/ccg/research/genome-sequencing/target/studied-cancers">Therapeutically Applicable Research to Generate Effective Treatments (TARGET)</a></li></ul>

Project Funder(s)

Genome British Columbia, Canadian Institutes of Health Research (CIHR), Canada Foundation for Innovation

Project Institution(s)

University of British Columbia (UBC), Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency

Project Investigator(s)

Martin Hirst, Hye-Jung E. Chun, Marco A. Marra

Data Access Request URL*

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000470.v23.p8

Keywords

cancer, pediatric, childhood, SMARB1, WGS, WGBS, RNA-seq, miRNA-seq, ChIP-seq, epigenetic, neural crest cells

Publication Link

https://pubmed.ncbi.nlm.nih.gov/26977886/

Study Completed

Post to REACH BC Platform

Cohort Name

MRT cohort

Cohort Size

Disease/Condition Studied

rhabdoid cancer, kidney rhabdoid cancer, cancer

Enrollment Time Window

Biobanking Consent Available

Medical History Available

Ethnicity Availability

Time Course

Patient Phenotypes

extra-cranial malignant rhabdoid tumors

Patient Outcomes

Clinical Data Types Available

Pre-therapy tumor and normal DNA from peripheral blood or kidney from rhabdoid tumors, registered on the National Wilms Tumor Study Group 5 or on COG AREN03B2 banked by the COG Biopathology Center with parental informed consent. Studies were performed with the approval of the University of British Columbia - British Columbia Cancer Agency Research Ethics Board.

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Samples and Omics