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Liver Hepatocellular Adenoma and Carcinomas (MSK, PLOS One 2018): Targeted sequencing of tumor/normal pairs of 9 LIAD and 10 HCC patients via MSK-IMPACT platform.

UID: 10444

Publisher(s): Memorial Sloan Kettering Cancer Center

Description
This dataset contains summary data visualizations and clinical data from a broad sampling of hepatocellular adenomas and carcinomas. 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), Patient ID, Sample ID, Cancer Type Detailed, Mutation Count, Fraction Genome Altered, Collaboration Id, Gene Panel, OncoTree Code, Sample Collection Method, Sample origin, Specimen Preservation Type, and Tissue Site. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
Subject of Study
Homo sapiens
Subject(s)
Adenoma, Liver Cell
Carcinoma, Hepatocellular
DNA Mutational Analysis
Liver Neoplasms
OncoTree Cancer Type(s)
Hepatocellular Carcinoma
Hepatocellular Adenoma
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.
Associated Publications
Zheng J, Sadot E, Vigidal J, et al. Characterization of hepatocellular adenoma and carcinoma using microRNA profiling and targeted gene sequencing. PLoS ONE. 2018; 13(7):e0200776.
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
22 KB
Data Catalog Record Updated
2021-11-09