TARGET: Kidney, Rhabdoid Tumor (RT): A sub-study of National Cancer Institute (NCI) TARGET: Therapeutically Applicable Research to Generate Effective Treatments

UID: 10603

Author(s): Perlman, Elizabeth

Publisher(s): Therapeutically Applicable Research to Generate Effective Treatments (TARGET), United States - National Institutes of Health (NIH) - National Cancer Institute (NCI)

Description: Study Description from dbGaP: "To further explore some more aggressive subtypes in pediatric cancer already under study in OCG, CGCI is partnering with TARGET initiative to support extensive sequencing analysis of three hard to treat childhood cancers: refractory to treatment cases of acute myeloid leukemia and two rare kidney tumors; clear cell sarcoma of the kidney and rhabdoid tumor (RT). Rhabdoid tumors are a rare, very aggressive type of kidney tumor of infancy, and patients typically have a poor prognosis. Up to 40 patient cases of matched tumor and normal samples, as well as some established cell lines, will undergo whole genome sequencing, miRNA-seq and mRNA-seq, DNA methyl-seq and ChIP-seq to generate a comprehensive profile and hopefully facilitate the development of better therapeutic options for this tumor subtype. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website, http://ocg.cancer.gov/programs/target, for additional information on this and other TARGET genomics projects."

70 phenotyped subjects sequenced from Tumor vs. Matched-Normal samples.

Subject of Study

Homo sapiens

Subject(s)

Kidney Neoplasms

Leukemia, Myeloid, Acute

Rhabdoid Tumor

Sarcoma, Clear Cell

OncoTree Cancer Type(s)

Acute Myeloid Leukemia
Clear Cell Sarcoma of Kidney
Rhabdoid Cancer

Access via dbGaP

Accession #: phs000470.v20.p8
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. The data for this study is collected as a substudy. dbGaP Authorized Access requests for this data should be made for study phs000218.v23.p8.

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.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system

Illumina HiSeq 2500
High throughput 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): RNA Seq

ChIP Seq

WGS

miRNA-Seq

Bisulfite-Seq
Dataset Size: 15.4 TB

Other Resources: National Cancer Institute (NCI) TARGET: Therapeutically Applicable Research to Generate Effective Treatments
Publicly available data, still requiring dbGaP authorized access

TARGET Study Weblink
Further information regarding TARGET Studies
Data Catalog Record Updated: 2021-06-24

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