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Genomic Sequencing of Pediatric Rhabdoid Cancers

UID: 10604

Author(s): Roberts, Charles, Golub, Todd

Description
Study Description from dbGaP: "In this study, we sequenced the exomes of 35 rhabdoid tumors, highly aggressive cancers of early childhood. This study is part of a larger effort to characterize pediatric cancers as part of the Slim Initiative for Genomic Medicine (SIGMA) project."
Subject of Study
Homo sapiens
Subject(s)
Rhabdoid Tumor
OncoTree Cancer Type(s)
Kidney
Rhabdoid Cancer
Access via dbGaP

BAM and SRA files of whole exome sequencing
Accession #: phs000508.v2.p1

Access Restrictions
Application Required
Access Instructions
Full access to this dataset in dbGaP requires authorization through an Authorized Access Portal which can be requested for either 'data download' or 'view only'. Individual level data download requires a project request. With dbGaP DataBrowser approval, users may view the collection compilation of individual-level data from general research use. Upon approval data can be downloaded.

A full list of and information about the SRA runs, BioSamples, and experiments is publicly viewable by going to the 'Molecular Datasets' tab and clicking on 'RunSelector' at the bottom of the page. This will take you to the NCBI SRA Run Selector platform, however view and download of the datasets themselves still requires authorization through dbGaP.
Associated Publications
Msaouel P, Malouf G, Su X, et al. Comprehensive molecular characterization identifies distinct genomic and immune hallmarks of renal medullary carcinoma. Cancer Cell. 2020; 37(5):720-734.e13.
Lee RS, Stewart C, Carter SL, et al. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J Clin Invest. 2012;122(8):2983-2988.
Data Type
Genomic
Equipment Used
Illumina HiSeq 2000

High throughput gene sequencing system

Software Used
SRA Toolkit

The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

Dataset Format(s)
SRA, BAM
Data Tool(s)
WXS
Dataset Size
246 GB
Data Catalog Record Updated
2021-06-24