Upper Tract Urothelial Carcinoma PDX (MSK, 2019): MSK-IMPACT sequencing of 34 upper tract urothelial patients and the matching PDX or PDC generated from 17 patient tumors.

UID: 10441

Publisher(s): Memorial Sloan Kettering Cancer Center

Description: This dataset contains summary data visualizations and clinical data from a broad sampling of upper tract unothelial carcinoma tumors. The data was gathered utilizing the MSK-IMPACT targeted sequencing test. The clinical data includes tumor type (based on the opensource OncoTree ontology developed at MSK), mutation count, information about mutated genes, patient demographics, American Joint Committee on Cancer Tumor Stage code, Collaboration Id, Neoplasm Histologic Grade, and Oncotree Code. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Bladder Urothelial Carcinoma
Upper Tract Urothelial Carcinoma

Access via cBioPortal
Access Restrictions: Free to All
Access Instructions: This cBioPortal for Cancer Genomics dataset is publicly available for viewing in tables or, for copy-number segments, via integrated IGV application. The data is also available for download in its entirety as a tarball or as individual TSV (tab separated value) or SEG files. Some features are only available by logging in with a Google or Microsoft account. These features include storing your virtual studies and groups which allows you to access your studies and groups from any computer, and to allow cBioPortal to remember your study view charts preferences for each study (i.e. order of the charts, type of charts and visibility). Login is optional and not required to access any of the other features of cBioPortal. Downloaded SEG files (tab-delimited segmented data text files that list loci and associated numeric values) can be viewed by downloading and installing the Integrative Genomics Viewer desktop application.
Data Type: Genomic
Software Used: Integrative Genomics Viewer (IGV)
High-performance visualization tool for interactive exploration of large, integrated genomic datasets.

OncoTree
Open-source ontology that was developed at Memorial Sloan Kettering Cancer Center (MSK) for standardizing cancer type diagnosis from a clinical perspective by assigning each diagnosis a unique OncoTree code.
Dataset Format(s): TSV, TAR, SEG
Data Tool(s): MSK-IMPACT
Dataset Size: 290 KB

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