Thoracic PDX (MSK, Provisional): Targeted sequencing of thoracic PDX lines to characterize genetic alterations in 139 tumor/normal pairs via MSK-IMPACT.

UID: 10445

Publisher(s): Charles Rudin Lab, Memorial Sloan Kettering Cancer Center

Description: This dataset contains summary data visualizations and clinical data from a broad 183 samples of thoracic tumors from 77 patients. The data was generated by the Charles Rudin Lab, 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, disease status, Age at Which Sequencing was Reported (Years), Archer Panel, Gene Panel, Institute Source, M Stage, Metastatic Site, MSI Comment, MSI Score, MSI Type, and N Stage. 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)

Combined Small Cell Lung Carcinoma
Lung Neuroendocrine Tumor
Lung Adenocarcinoma
Large Cell Neuroendocrine Carcinoma
Pleomorphic Carcinoma of the Lung
Lung Squamous Cell Carcinoma
Non-Small Cell Lung Cancer
Poorly Differentiated Non-Small Cell Lung Cancer
Pleural Mesothelioma, Epithelioid Type
Pleural Mesothelioma
Sarcomatoid Carcinoma of the Lung
Small Cell Lung Cancer

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: 290KB

Do you have or know of a dataset that should be added to the catalog? Let us know!